Recovery RNAseq DOX Data

workflowr

• Summary
• Checks
• Past versions

Last updated: 2025-04-15

Checks: 6 1

Knit directory: Recovery_5FU/

This reproducible R Markdown analysis was created with workflowr (version 1.7.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

---

R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

Seed: set.seed(20250217)

The command set.seed(20250217) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: absolute

Using absolute paths to the files within your workflowr project makes it difficult for you and others to run your code on a different machine. Change the absolute path(s) below to the suggested relative path(s) to make your code more reproducible.

absolute	relative
C:/Users/emmap/RDirectory/Recovery_RNAseq/Recovery_5FU/data/ensembl_backup_dox.RDS	data/ensembl_backup_dox.RDS
C:/Users/emmap/RDirectory/Recovery_RNAseq/Recovery_5FU/data/ind_num_dox.RDS	data/ind_num_dox.RDS
C:/Users/emmap/RDirectory/Recovery_RNAseq/Recovery_5FU/data/annot_dox.RDS	data/annot_dox.RDS

Repository version: ff22325

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version ff22325. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:

Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    analysis/figure/
    Ignored:    data/CDKN1A_geneplot_Dox.RDS
    Ignored:    data/Cormotif_prob_gene_list.RDS
    Ignored:    data/Cormotif_prob_gene_list_doxonly.RDS
    Ignored:    data/DMSO_TNN13_plot.RDS
    Ignored:    data/DOX_TNN13_plot.RDS
    Ignored:    data/DOXgeneplots.RDS
    Ignored:    data/MDM2_geneplot_Dox.RDS
    Ignored:    data/SIRT1_geneplot_Dox.RDS
    Ignored:    data/annot_dox.RDS
    Ignored:    data/counts_DE_df_dox.RDS
    Ignored:    data/ensembl_backup_dox.RDS
    Ignored:    data/filt_gene_list_dox.RDS
    Ignored:    data/gene_postprob_motif.RDS
    Ignored:    data/heartgenes.csv
    Ignored:    data/heartgenes_dox.csv
    Ignored:    data/ind_num_dox.RDS
    Ignored:    data/initial_cormotif.RDS
    Ignored:    data/initial_cormotif_dox.RDS
    Ignored:    data/plot_leg_d.RDS
    Ignored:    data/plot_leg_d_horizontal.RDS
    Ignored:    data/plot_leg_d_vertical.RDS
    Ignored:    data/tableED_GOBP.RDS
    Ignored:    data/tableESR_GOBP_postprob.RDS
    Ignored:    data/tableLD_GOBP.RDS
    Ignored:    data/tableLR_GOBP_postprob.RDS
    Ignored:    data/tableNR_GOBP.RDS
    Ignored:    data/tableNR_GOBP_postprob.RDS
    Ignored:    data/top.table_V.D144r_dox.RDS
    Ignored:    data/top.table_V.D24_dox.RDS
    Ignored:    data/top.table_V.D24r_dox.RDS

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

---

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/Recovery_DOX.Rmd) and HTML (docs/Recovery_DOX.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
Rmd	ff22325	emmapfort	2025-04-15	workflowr::wflow_publish(files = c("analysis/Recovery_DOX.Rmd"))
Rmd	82840fa	emmapfort	2025-04-15	Updating website
html	84d5599	emmapfort	2025-04-14	Build site.
Rmd	3db2eb6	emmapfort	2025-04-14	DOX only page

---

I want to separate out my dataset for this to only include the DOX and DMSO vehicle samples

fC_Matrix_Full_cpm_filter <- readRDS("data/fC_Matrix_Full_cpm_filter.RDS")

fC_Matrix_Full_cpm_filter_dox <- as.data.frame(fC_Matrix_Full_cpm_filter) %>% dplyr::select(-(contains("FLUO")))
#this dataset is the original log2cpm transformed and rowMeans filtered dataset which I need for heatmaps

counts_DE_df <- readRDS("data/counts_DE_df.RDS")
#this dataframe is pre-filtered and only contains genes (rows) that were present after log2cpm transformation and filtering by rowMeans > 0

DOX_counts_DE_df <- counts_DE_df %>% dplyr::select(-(contains("FLUO")))
dim(DOX_counts_DE_df)

[1] 14170    42

#this should have 42 variables if we remove the 21 variables from 5FU

col_tx_large <- rep(c("#499FBD" , "#63666D"), 21)
col_tx_large_2 <- c(rep("#499FBD" , 3), rep("#63666D", 3), 21)


ind_col <- c("#003F5C", "#45AE91",  "#58508D", "#BC4099", "#8B3E9B", "#FF6361", "#FF2362")

tx_col <- c("#499FBD","#63666D")

time_col <- c("#fbb4b9", "#f768a1", "#ae017e")

##Add columns with more information to each gene I pull out##
ind_names <- c(rep("Ind1", 6), rep("Ind2", 6), rep("Ind3", 6), rep("Ind4", 6), rep("Ind5", 6), rep("Ind6", 6), rep("Ind6REP", 6))
time_names <- c(rep("24", 2), rep("24rec", 2), rep("144rec", 2))
time_names2 <- c("24", "24rec", "144rec")
time_names <- c(rep(time_names, 7))
time_names2 <- c(rep(time_names2, 7))
tx_names <- c("DOX", "DMSO")
tx_names <- c(rep(tx_names, 21))
tx_names2 <- c(rep("DOX", 3), rep("DMSO", 3))
tx_names2 <- c(rep(tx_names2, 21))
txtime_names <- c("DOX_24", "DMSO_24", "DOX_24rec", "DMSO_24rec", "DOX_144rec", "DMSO_144rec")
txtime_names <- c(rep(txtime_names, 7))
txtime_names2 <- c("DOX_24", "DOX_24rec", "DOX_144rec", "DMSO_24", "DMSO_24rec", "DMSO_144rec")
txtime_names2 <- c(rep(txtime_names2, 7))


genematrix_dox <- fC_Matrix_Full_cpm_filter_dox %>% rownames_to_column(var = "entrezgene_id")

###CDKN1A - 1026###
CDKN1A_d <- genematrix_dox %>% filter(entrezgene_id=="1026")
CDKN1A_new_d <- as.data.frame(CDKN1A_d) %>% dplyr::select("entrezgene_id", "DOX_24_Ind1", "DOX_24rec_Ind1", "DOX_144rec_Ind1", "DMSO_24_Ind1", "DMSO_24rec_Ind1", "DMSO_144rec_Ind1","DOX_24_Ind2", "DOX_24rec_Ind2", "DOX_144rec_Ind2", "DMSO_24_Ind2", "DMSO_24rec_Ind2", "DMSO_144rec_Ind2", "DOX_24_Ind3", "DOX_24rec_Ind3", "DOX_144rec_Ind3",  "DMSO_24_Ind3", "DMSO_24rec_Ind3", "DMSO_144rec_Ind3", "DOX_24_Ind4", "DOX_24rec_Ind4", "DOX_144rec_Ind4", "DMSO_24_Ind4", "DMSO_24rec_Ind4", "DMSO_144rec_Ind4", "DOX_24_Ind5", "DOX_24rec_Ind5", "DOX_144rec_Ind5", "DMSO_24_Ind5", "DMSO_24rec_Ind5", "DMSO_144rec_Ind5", "DOX_24_Ind6", "DOX_24rec_Ind6", "DOX_144rec_Ind6", "DMSO_24_Ind6", "DMSO_24rec_Ind6", "DMSO_144rec_Ind6", "DOX_24_Ind6REP", "DOX_24rec_Ind6REP", "DOX_144rec_Ind6REP", "DMSO_24_Ind6REP", "DMSO_24rec_Ind6REP", "DMSO_144rec_Ind6REP")
CDKN1A_melt_d <- melt(CDKN1A_d, variable.name = "sample")

Using entrezgene_id as id variables

CDKN1A_melt_new_d <- melt(CDKN1A_new_d, variable.name = "sample")

Using entrezgene_id as id variables

CDKN1A_melt_df_d <- data.frame(tx = factor(tx_names, levels = unique(tx_names)),
                               ind = factor(ind_names, levels = unique(ind_names)),
                               txtime = factor(txtime_names, levels = unique(txtime_names)),
                               time = factor(time_names, levels = unique(time_names)))
CDKN1A_melt_df2_d <- data.frame(tx = factor(tx_names2, levels = unique(tx_names2)),
                               ind = factor(ind_names, levels = unique(ind_names)),
                               txtime = factor(txtime_names2, levels = unique(txtime_names2)),
                               time = factor(time_names2, levels = unique(time_names2)))
CDKN1A_melt_df_all_d <- cbind(CDKN1A_melt_d, CDKN1A_melt_df_d)
CDKN1A_melt_df_all2_d <- cbind(CDKN1A_melt_new_d, CDKN1A_melt_df2_d)


####CDKN1A####
CDKN1A_melt_df_all2_d %>% ggplot(aes(x = txtime, y = value))+
  geom_boxplot(aes(fill = tx))+
  geom_point(aes(color = ind)) +
  labs(title = "CDKN1A")+
  theme_bw(base_size = 16)+
  scale_fill_manual(values = c(tx_col))+
  scale_color_manual(values = c(ind_col))+
  xlab("Conditions")+
  ylab("log2cpm")+
  theme(plot.title = element_text(face = "italic"))

Past versions of "Pull out Genes of Interest-1.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

#saveRDS(CDKN1A_geneplot_Dox, "data/CDKN1A_geneplot_Dox.RDS")

###MDM2 - 4193###
MDM2_d <- genematrix_dox %>% filter(entrezgene_id=="4193")
MDM2_new_d <- as.data.frame(MDM2_d) %>% dplyr::select("entrezgene_id", "DOX_24_Ind1", "DOX_24rec_Ind1", "DOX_144rec_Ind1", "DMSO_24_Ind1", "DMSO_24rec_Ind1", "DMSO_144rec_Ind1","DOX_24_Ind2", "DOX_24rec_Ind2", "DOX_144rec_Ind2", "DMSO_24_Ind2", "DMSO_24rec_Ind2", "DMSO_144rec_Ind2", "DOX_24_Ind3", "DOX_24rec_Ind3", "DOX_144rec_Ind3",  "DMSO_24_Ind3", "DMSO_24rec_Ind3", "DMSO_144rec_Ind3", "DOX_24_Ind4", "DOX_24rec_Ind4", "DOX_144rec_Ind4", "DMSO_24_Ind4", "DMSO_24rec_Ind4", "DMSO_144rec_Ind4", "DOX_24_Ind5", "DOX_24rec_Ind5", "DOX_144rec_Ind5", "DMSO_24_Ind5", "DMSO_24rec_Ind5", "DMSO_144rec_Ind5", "DOX_24_Ind6", "DOX_24rec_Ind6", "DOX_144rec_Ind6", "DMSO_24_Ind6", "DMSO_24rec_Ind6", "DMSO_144rec_Ind6", "DOX_24_Ind6REP", "DOX_24rec_Ind6REP", "DOX_144rec_Ind6REP", "DMSO_24_Ind6REP", "DMSO_24rec_Ind6REP", "DMSO_144rec_Ind6REP")
MDM2_melt_d <- melt(MDM2_d, variable.name = "sample")

Using entrezgene_id as id variables

MDM2_melt_new_d <- melt(MDM2_new_d, variable.name = "sample")

Using entrezgene_id as id variables

MDM2_melt_df_d <- data.frame(tx = factor(tx_names, levels = unique(tx_names)),
                               ind = factor(ind_names, levels = unique(ind_names)),
                               txtime = factor(txtime_names, levels = unique(txtime_names)),
                               time = factor(time_names, levels = unique(time_names)))
MDM2_melt_df2_d <- data.frame(tx = factor(tx_names2, levels = unique(tx_names2)),
                               ind = factor(ind_names, levels = unique(ind_names)),
                               txtime = factor(txtime_names2, levels = unique(txtime_names2)),
                               time = factor(time_names2, levels = unique(time_names2)))
MDM2_melt_df_all_d <- cbind(MDM2_melt_d, MDM2_melt_df_d)
MDM2_melt_df_all2_d <- cbind(MDM2_melt_new_d, MDM2_melt_df2_d)

####MDM2####
MDM2_melt_df_all2_d %>% ggplot(aes(x = txtime, y = value))+
  geom_boxplot(aes(fill = tx))+
  geom_point(aes(color = ind)) +
  labs(title = "MDM2")+
  theme_bw(base_size = 16)+
  scale_fill_manual(values = c(tx_col))+
  scale_color_manual(values = c(ind_col))+
  xlab("Conditions")+
  ylab("log2cpm")+
  theme(plot.title = element_text(face = "italic"))

Past versions of "Pull out Genes of Interest-2.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

#saveRDS(MDM2_geneplot_Dox, "data/MDM2_geneplot_Dox.RDS")


###SIRT1 - 23411###
SIRT1_d <- genematrix_dox %>% filter(entrezgene_id=="23411")
SIRT1_new_d <- as.data.frame(SIRT1_d) %>% dplyr::select("entrezgene_id", "DOX_24_Ind1", "DOX_24rec_Ind1", "DOX_144rec_Ind1", "DMSO_24_Ind1", "DMSO_24rec_Ind1", "DMSO_144rec_Ind1","DOX_24_Ind2", "DOX_24rec_Ind2", "DOX_144rec_Ind2", "DMSO_24_Ind2", "DMSO_24rec_Ind2", "DMSO_144rec_Ind2", "DOX_24_Ind3", "DOX_24rec_Ind3", "DOX_144rec_Ind3",  "DMSO_24_Ind3", "DMSO_24rec_Ind3", "DMSO_144rec_Ind3", "DOX_24_Ind4", "DOX_24rec_Ind4", "DOX_144rec_Ind4", "DMSO_24_Ind4", "DMSO_24rec_Ind4", "DMSO_144rec_Ind4", "DOX_24_Ind5", "DOX_24rec_Ind5", "DOX_144rec_Ind5", "DMSO_24_Ind5", "DMSO_24rec_Ind5", "DMSO_144rec_Ind5", "DOX_24_Ind6", "DOX_24rec_Ind6", "DOX_144rec_Ind6", "DMSO_24_Ind6", "DMSO_24rec_Ind6", "DMSO_144rec_Ind6", "DOX_24_Ind6REP", "DOX_24rec_Ind6REP", "DOX_144rec_Ind6REP", "DMSO_24_Ind6REP", "DMSO_24rec_Ind6REP", "DMSO_144rec_Ind6REP")
SIRT1_melt_d <- melt(SIRT1_d, variable.name = "sample")

Using entrezgene_id as id variables

SIRT1_melt_new_d <- melt(SIRT1_new_d, variable.name = "sample")

Using entrezgene_id as id variables

SIRT1_melt_df_d <- data.frame(tx = factor(tx_names, levels = unique(tx_names)),
                               ind = factor(ind_names, levels = unique(ind_names)),
                               txtime = factor(txtime_names, levels = unique(txtime_names)),
                               time = factor(time_names, levels = unique(time_names)))
SIRT1_melt_df2_d <- data.frame(tx = factor(tx_names2, levels = unique(tx_names2)),
                               ind = factor(ind_names, levels = unique(ind_names)),
                               txtime = factor(txtime_names2, levels = unique(txtime_names2)),
                               time = factor(time_names2, levels = unique(time_names2)))
SIRT1_melt_df_all_d <- cbind(SIRT1_melt_d, SIRT1_melt_df_d)
SIRT1_melt_df_all2_d <- cbind(SIRT1_melt_new_d, SIRT1_melt_df2_d)

####SIRT1####
SIRT1_vertplot <- SIRT1_melt_df_all2_d %>% ggplot(aes(x = txtime, y = value))+
  geom_boxplot(aes(fill = tx))+
  geom_point(aes(color = ind)) +
  labs(title = "SIRT1")+
  theme_bw(base_size = 16)+
  scale_fill_manual(values = c(tx_col))+
  scale_color_manual(values = c(ind_col))+
  xlab("Conditions")+
  ylab("log2cpm")+
  theme(plot.title = element_text(face = "italic"))

# get_legend_func <- function(plot) {
#   legends <- cowplot::get_plot_component(plot, "guide-box", return_all = TRUE)
#   nonzero <- vapply(plot_legend_d, \(x) !inherits(x, "zeroGrob"), TRUE)
#   idx <- which(nonzero)
# #this will return the first nonzero legend since it's not in the standard spot

# if (length(idx) >0) {
#   return(legends[[idx[1]]])  
# } else {
#   return(legends[[1]])
# }
# }

# plot_leg_d_hor <- get_legend_func(plot = SIRT1_vertplot + guides(color = guide_legend(nrow=1))+
#     theme(legend.position = "bottom")
# )


plot_leg_d_ver <- cowplot::get_legend(SIRT1_vertplot)

Warning in get_plot_component(plot, "guide-box"): Multiple components found;
returning the first one. To return all, use `return_all = TRUE`.

# ggdraw(plot_leg_d_hor)
ggdraw(plot_leg_d_ver)

Past versions of "Pull out Genes of Interest-3.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

#saveRDS(plot_leg_d_hor, "data/plot_leg_d_horizontal.RDS")
#saveRDS(plot_leg_d_ver, "data/plot_leg_d_vertical.RDS")

#saveRDS(SIRT1_geneplot_Dox, "data/SIRT1_geneplot_Dox.RDS")
#I saved these with no legend

#plot all of these genes together in one set

CDKN1A_geneplot_Dox <- readRDS("data/CDKN1A_geneplot_Dox.RDS")
MDM2_geneplot_Dox <- readRDS("data/MDM2_geneplot_Dox.RDS")
SIRT1_geneplot_Dox <- readRDS("data/SIRT1_geneplot_Dox.RDS")
plot_legend_d_ver <- readRDS("data/plot_leg_d_vertical.RDS")
plot_legend_d_hor <- readRDS("data/plot_leg_d_horizontal.RDS")

DOXgeneplots <- plot_grid(CDKN1A_geneplot_Dox,
                          MDM2_geneplot_Dox, 
                          SIRT1_geneplot_Dox, nrow = 1, ncol = 3)
DOXgeneplots

Past versions of "Pull out Genes of Interest-4.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

#saveRDS(DOXgeneplots, "data/DOXgeneplots.RDS")

genes_dox <- as.data.frame(fC_Matrix_Full_cpm_filter_dox)
genes_dox_df <- rownames_to_column(fC_Matrix_Full_cpm_filter_dox, var = "entrezgene_id")
###now let's pull some classic cardiac genes expressed in iPSC-CMs###
genecardiccheck_dox <- c("MYH7", "TNNT2","MYH6","ACTN2","BMP3","TNNI3","RYR2","CACNA1C","KCNQ1", "HCN1", "ADRB1", "ADRB2")

#ensembl_dox <- useMart("ensembl", dataset="hsapiens_gene_ensembl")
#saveRDS(ensembl_dox, "data/ensembl_backup_dox.RDS")
ensembl_dox <- readRDS("C:/Users/emmap/RDirectory/Recovery_RNAseq/Recovery_5FU/data/ensembl_backup_dox.RDS")
my_chr_dox <- c(1:22, 'M', 'X', 'Y')  ## creates a filter for each database

my_attributes_dox <- c('entrezgene_id', 'ensembl_gene_id', 'hgnc_symbol')

heartgenes_dox <- getBM(attributes=my_attributes_dox,filters ='hgnc_symbol',
                values = genecardiccheck_dox, mart = ensembl_dox)
write.csv(heartgenes_dox, "data/heartgenes_dox.csv")
heartgenes_dox <-read.csv("data/heartgenes_dox.csv")

fungraph_dox <- as.data.frame(fC_Matrix_Full_cpm_filter_dox[rownames(fC_Matrix_Full_cpm_filter_dox) %in% heartgenes_dox$entrezgene_id,])


fungraph_dox %>% 
  rownames_to_column("entrezgene_id") %>% 
  pivot_longer(-entrezgene_id, names_to = "samples",values_to = "counts") %>% 
  mutate(gene = case_match(entrezgene_id,"88"~"ACTN2","153"~"ADRB1",
  "154"~"ADRB2","651"~"BMP3","775"~"CACNA1C", "100874369"~"CACNA1C","348980"~"HCN1",
                           "3784"~"KCNQ1", "4624"~"MYH6","4625"~"MYH7","6262"~"RYR2",
                           "7137"~"TNNI3","7139"~"TNNT2",.default = entrezgene_id)) %>% 
  ggplot(., aes(x=reorder(gene,counts,decreasing=TRUE), y=counts))+
  geom_boxplot()+
  ggtitle(expression("Expression of typical cardiac tissue genes"))+
  xlab("")+
  ylim(c(0,20))+
  ylab(expression("log"[2]~"cpm"))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(2), hjust = 0.5),
        axis.title = element_text(size = 15, color = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size =10, color = "black", angle = 0),
        strip.text.y = element_text(color = "white"))

#Now I want to plot these with DOX vs Veh to see if there are any changes

#I'll choose a subset of these genes - TNN13, TNNT2, NPPB, MYH7, ACTN2

fungraph_dox_only <- fungraph_dox %>% dplyr::select("DOX_24_Ind1", "DOX_24rec_Ind1", "DOX_144rec_Ind1", "DOX_24_Ind2", "DOX_24rec_Ind2", "DOX_144rec_Ind2", "DOX_24_Ind3", "DOX_24rec_Ind3", "DOX_144rec_Ind3", "DOX_24_Ind4", "DOX_24rec_Ind4", "DOX_144rec_Ind4", "DOX_24_Ind5", "DOX_24rec_Ind5", "DOX_144rec_Ind5", "DOX_24_Ind6", "DOX_24rec_Ind6", "DOX_144rec_Ind6", "DOX_24_Ind6REP", "DOX_24rec_Ind6REP", "DOX_144rec_Ind6REP")

fungraph_dmso_only <- fungraph_dox %>% dplyr::select("DMSO_24_Ind1", "DMSO_24rec_Ind1", "DMSO_144rec_Ind1", "DMSO_24_Ind2", "DMSO_24rec_Ind2", "DMSO_144rec_Ind2", "DMSO_24_Ind3", "DMSO_24rec_Ind3", "DMSO_144rec_Ind3", "DMSO_24_Ind4", "DMSO_24rec_Ind4", "DMSO_144rec_Ind4", "DMSO_24_Ind5", "DMSO_24rec_Ind5", "DMSO_144rec_Ind5", "DMSO_24_Ind6", "DMSO_24rec_Ind6", "DMSO_144rec_Ind6", "DMSO_24_Ind6REP", "DMSO_24rec_Ind6REP", "DMSO_144rec_Ind6REP")

fungraph_dox_only %>% 
  rownames_to_column("entrezgene_id") %>% 
  pivot_longer(-entrezgene_id, names_to = "samples",values_to = "counts") %>% 
  mutate(gene = case_match(entrezgene_id,"88"~"ACTN2","153"~"ADRB1",
  "154"~"ADRB2","651"~"BMP3","775"~"CACNA1C", "100874369"~"CACNA1C","348980"~"HCN1",
                           "3784"~"KCNQ1", "4624"~"MYH6","4625"~"MYH7","6262"~"RYR2",
                           "7137"~"TNNI3","7139"~"TNNT2",.default = entrezgene_id)) %>% 
  ggplot(., aes(x=reorder(gene,counts,decreasing=TRUE), y=counts))+
  geom_boxplot()+
  ggtitle(expression("Expression Cardiac Genes DOX Only"))+
  xlab("")+
  ylim(c(0,20))+
  ylab(expression("log"[2]~"cpm"))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(2), hjust = 0.5),
        axis.title = element_text(size = 15, color = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size =10, color = "black", angle = 0),
        strip.text.y = element_text(color = "white"))

fungraph_dmso_only %>% 
  rownames_to_column("entrezgene_id") %>% 
  pivot_longer(-entrezgene_id, names_to = "samples",values_to = "counts") %>% 
  mutate(gene = case_match(entrezgene_id,"88"~"ACTN2","153"~"ADRB1",
  "154"~"ADRB2","651"~"BMP3","775"~"CACNA1C", "100874369"~"CACNA1C","348980"~"HCN1",
                           "3784"~"KCNQ1", "4624"~"MYH6","4625"~"MYH7","6262"~"RYR2",
                           "7137"~"TNNI3","7139"~"TNNT2",.default = entrezgene_id)) %>% 
  ggplot(., aes(x=reorder(gene,counts,decreasing=TRUE), y=counts))+
  geom_boxplot()+
  ggtitle(expression("Expression Cardiac Genes Vehicle Only"))+
  xlab("")+
  ylim(c(0,20))+
  ylab(expression("log"[2]~"cpm"))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(2), hjust = 0.5),
        axis.title = element_text(size = 15, color = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size =10, color = "black", angle = 0),
        strip.text.y = element_text(color = "white"))

#I want to just plot TNNI3 now

fungraph_dox_only_TNNI3 <- fungraph_dox_only %>% 
  rownames_to_column("entrezgene_id") %>% 
  pivot_longer(-entrezgene_id, names_to = "samples",values_to = "counts") %>% 
  filter(entrezgene_id == "7137") %>% 
  mutate(gene = case_match(entrezgene_id,"7137"~"TNNI3",.default = entrezgene_id)) %>% 
  ggplot(., aes(x=reorder(gene,counts,decreasing=TRUE), y=counts))+
  geom_boxplot()+
  ggtitle(expression("TNNI3 DOX"))+
  xlab("")+
  ylim(c(0,10))+
  ylab(expression("log"[2]~"cpm"))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(2), hjust = 0.5),
        axis.title = element_text(size = 15, color = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size =10, color = "black", angle = 0),
        strip.text.y = element_text(color = "white"))

#saveRDS(fungraph_dox_only_TNNI3, "data/DOX_TNN13_plot.RDS")

fungraph_dmso_only_TNNI3 <- fungraph_dmso_only %>% 
  rownames_to_column("entrezgene_id") %>% 
  pivot_longer(-entrezgene_id, names_to = "samples",values_to = "counts") %>% 
  filter(entrezgene_id == "7137") %>% 
  mutate(gene = case_match(entrezgene_id,"7137"~"TNNI3",.default = entrezgene_id)) %>% 
  ggplot(., aes(x=reorder(gene,counts,decreasing=TRUE), y=counts))+
  geom_boxplot()+
  ggtitle(expression("TNNI3 VEH"))+
  xlab("")+
  ylim(c(0,10))+
  ylab(expression("log"[2]~"cpm"))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(2), hjust = 0.5),
        axis.title = element_text(size = 15, color = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size =10, color = "black", angle = 0),
        strip.text.y = element_text(color = "white"))

#saveRDS(fungraph_dmso_only_TNNI3, "data/DMSO_TNN13_plot.RDS")

fungraph_dox_only_TNNI3

fungraph_dmso_only_TNNI3

plot_grid(fungraph_dox_only_TNNI3,
                          fungraph_dmso_only_TNNI3, 
                          nrow = 1, ncol = 2)

####SPEARMAN FILTERED####
fC_Matrix_Full_cpm_filter_spearmancor_dox <-
  cor(
    fC_Matrix_Full_cpm_filter_dox,
    y = NULL,
    use = "everything",
    method = "spearman"
  )


Individual <- as.factor(c(rep("Ind1", 6), rep("Ind2", 6), rep("Ind3", 6), rep("Ind4", 6), rep("Ind5", 6), rep("Ind6", 6), rep("Ind6REP", 6)))

#Factor 2 - Treatment
tx_factor <- c("DOX", "DMSO")
Tx <- as.factor(c(rep(tx_factor, 21)))
#view(Treatment)

#Factor 3 - Timepoint
time_factor <- c(rep("24", 2), rep("24rec", 2), rep("144rec", 2))
Time <- as.factor(c(rep(time_factor, 7)))

####annotation for colors####
annot_col_hm = list(Tx = c(DOX = "blue", DMSO = "black"),
                             Ind = c(Ind1 = "#66E2A5", Ind2 = "#FC8D62", Ind3 = "#1F78B4", Ind4 = "#EFEDA3", Ind5 = "#A6D854", Ind6 = "#FFD92A", Ind6REP = "#8B3E9B"),
                             Time = c("24" = "#096F38", "24rec" = "#0050B5", "144rec" = "#B725AD"))

####annotation for values####
annot_list_hm <- data.frame(Individual = as.factor(c(rep("Ind1", 6), rep("Ind2", 6), rep("Ind3", 6), rep("Ind4", 6), rep("Ind5", 6), rep("Ind6", 6), rep("Ind6REP", 6))),
                                               Tx = as.factor(c(rep(tx_factor, 21))), 
                                               Time = as.factor(c(rep(time_factor, 7))))

  
##add in the annotations from above into the dataframe
row.names(annot_list_hm) <- colnames(fC_Matrix_Full_cpm_filter_spearmancor_dox)

####ANNOTATED HEATMAPS####

pheatmap(fC_Matrix_Full_cpm_filter_spearmancor_dox, border_color = "black", legend = TRUE, angle_col = 90, display_numbers = FALSE, number_color = "black", fontsize = 10, fontsize_number = 5, annotation_col = annot_list_hm, annotation_colors = annot_col_hm)

Past versions of "Spearman Heatmap-1.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

Now that I’ve put together my data, let’s begin DE!

group_1d <- rep(c("DOX_24",
                  "DMSO_24",
                  "DOX_24rec", 
                  "DMSO_24rec",
                  "DOX_144rec",
                  "DMSO_144rec"), 6)

group_2d <- rep(c("DOX_24",
                  "DMSO_24",
                  "DOX_24rec",
                  "DMSO_24rec",
                  "DOX_144rec",
                  "DMSO_144rec"), 7)

dge_d <- DGEList.data.frame(counts = DOX_counts_DE_df, group = group_2d, genes = row.names(DOX_counts_DE_df))


#calculate the normalization factors with method TMM
dged_calc <- calcNormFactors(dge_d, method = "TMM")


#Pull out factors
snames_d <- data.frame("samples" = colnames(dged_calc)) %>% separate_wider_delim(., cols = samples, names = c("Treatment", "Time", "Individual"), delim = "_", cols_remove = FALSE)

snames_time_d <- snames_d$Time
snames_tx_d <- snames_d$Treatment
snames_ind_d <- snames_d$Individual

#Create my model matrix
mm_r_d <- model.matrix(~0 + group_2d)

p_d <- voom(dged_calc$counts, mm_r_d, plot = TRUE)

Past versions of "Differential Expression Analysis-1.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

corfit_d <- duplicateCorrelation(p_d, mm_r_d, block = snames_ind_d)

v_d <- voom(dged_calc$counts, mm_r_d, block = snames_ind_d, correlation = corfit_d$consensus)

fit_d <- lmFit(v_d, mm_r_d, block = snames_ind_d, correlation = corfit_d$consensus)

#make sure to check which order the columns are in - otherwise they won't match right (it was moved into alphabetical and number order)
colnames(mm_r_d) <- c("DMSO_144rec","DMSO_24","DMSO_24rec","DOX_144rec","DOX_24","DOX_24rec")

cm_r_d <- makeContrasts(
        V.D24 = DOX_24 - DMSO_24,
        V.D24r = DOX_24rec - DMSO_24rec,
        V.D144r = DOX_144rec - DMSO_144rec,
        levels = mm_r_d
)

vfit_r_d <- lmFit(p_d, mm_r_d)
vfit_r_d <- contrasts.fit(vfit_r_d, contrasts = cm_r_d)

efit2_d <- eBayes(vfit_r_d)

results_d = decideTests(efit2_d)
summary(results_d)
       V.D24 V.D24r V.D144r
Down    9709   6869      31
NotSig  3276   6379   13680
Up      1185    922     459
# #       V.D24 V.D24r V.D144r
# Down    9709   6869      31
# NotSig  3276   6379   13680
# Up      1185    922     459

####plot your voom####
voom_plot_d <- voom(dged_calc, mm_r_d, plot = TRUE)

Past versions of "Differential Expression Analysis-2.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

top.table_V.D24_dox <- topTable(fit = efit2_d, coef = "V.D24", number = nrow(dged_calc), adjust.method = "BH", p.value = 1, sort.by = "none")
head(top.table_V.D24_dox)

#saveRDS(top.table_V.D24_dox, "data/top.table_V.D24_dox.RDS")

top.table_V.D24r_dox <- topTable(fit = efit2_d, coef = "V.D24r", number = nrow(dged_calc), adjust.method = "BH", p.value = 1, sort.by = "none")
head(top.table_V.D24r_dox)

#saveRDS(top.table_V.D24r_dox, "data/top.table_V.D24r_dox.RDS")

top.table_V.D144r_dox <- topTable(fit = efit2_d, coef = "V.D144r", number = nrow(dged_calc), adjust.method = "BH", p.value = 1, sort.by = "none")
head(top.table_V.D144r_dox)

#saveRDS(top.table_V.D144r_dox, "data/top.table_V.D144r_dox.RDS")


#plot the top 5 most DE genes for each condition
#i sorted the toptable by the top 5 most DE genes for each + found the corresponding gene name
#####24hr Tx####
topDEG_dox24 <- top.table_V.D24_dox %>% 
  dplyr::slice_min(., n=5, order_by=P.Value) %>% 
  rownames_to_column(var = "GeneID")

Gene_Name <- c("FAM163A","SLC26A8","THBS-AS1","FOXD3-AS1","GRIK3")

topDEG_dox24 %>% mutate(GeneID = factor(GeneID, levels = c("148753", "116369", "101929523", "100996301", "2899"))) %>% 
  cbind(Gene_Name)
  

#top 5 DE genes based on p-value and adj p value 
ggplot(topDEG_dox24, aes(x=Gene_Name, y=logFC))+
  geom_boxplot(aes(colour = adj.P.Val))+
  ggtitle(expression("Top 5 DE Genes DOX 24"))+
  xlab("")+
  ylim(c(-10, 10))+
  ylab(expression("logFC"))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5)),
        axis.title = element_text(size = 15, color = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size =10, color = "black", angle = 0),
        strip.text.y = element_text(color = "white"))

Past versions of "Make a TopTable-1.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

####24hr Recovery####
topDEG_dox24R <- top.table_V.D24r_dox %>% 
  dplyr::slice_min(., n=5, order_by=P.Value) %>% 
  rownames_to_column(var = "GeneID")

Gene_Name1 <- c("KCNK10", "CSTA", "LCE1B", "OTP", "KRTAP19-1")

topDEG_dox24R %>% mutate(GeneID = factor(GeneID, levels = c("54207", "1475", "353132", "23440", "337882"))) %>% 
  cbind(Gene_Name1)
  

ggplot(topDEG_dox24R, aes(x=Gene_Name1, y=logFC))+
  geom_boxplot(aes(colour = adj.P.Val))+
  ggtitle(expression("Top 5 DE Genes DOX 24 Recovery"))+
  xlab("")+
  ylim(c(-10,10))+
  ylab(expression("logFC"))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5)),
        axis.title = element_text(size = 15, color = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size =10, color = "black", angle = 0),
        strip.text.y = element_text(color = "white"))

Past versions of "Make a TopTable-2.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

####144R####
topDEG_dox144R <- top.table_V.D144r_dox %>% 
  dplyr::slice_min(., n=5, order_by=P.Value) %>% 
  rownames_to_column(var = "GeneID")

Gene_Name2 <- c("LINC03025", "SLC4A10", "VIT", "PSMA8", "MYO3B")

topDEG_dox144R %>% mutate(GeneID = factor(GeneID, levels = c("440896", "57282", "5212", "143471", "140469"))) %>% 
  cbind(Gene_Name2)
  

ggplot(topDEG_dox144R, aes(x=Gene_Name2, y=logFC))+
  geom_boxplot(aes(colour = adj.P.Val))+
  ggtitle(expression("Top 5 DE Genes DOX 144 Recovery"))+
  xlab("")+
  ylim(c(-10,10))+
  ylab(expression("logFC"))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5)),
        axis.title = element_text(size = 15, color = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size =10, color = "black", angle = 0),
        strip.text.y = element_text(color = "white"))

Past versions of "Make a TopTable-3.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

generate_volcano_plot <- function(toptable, title) {
  
  #make significance labels
  toptable$Significance <- "Not Significant"
  toptable$Significance[toptable$logFC > 0 & toptable$adj.P.Val < 0.05] <- "Upregulated"
  toptable$Significance[toptable$logFC < 0 & toptable$adj.P.Val < 0.05] <- "Downregulated"
  
  #add number of genes for each significance label
  upgenes <- toptable %>% filter(Significance == "Upregulated") %>% nrow()
  downgenes <- toptable %>% filter(Significance == "Downregulated") %>% nrow()
  nsgenes <- toptable %>% filter(Significance == "Not Significant") %>% nrow()

  #make legend labels for no of genes
  legend_lab <- c(
    str_c('Upregulated: ', upgenes),
    str_c('Not Significant: ', nsgenes),
    str_c('Downregulated: ', downgenes)
  )

  #generate volcano plot w/ legend
  ggplot(toptable, aes(x = logFC, y = -log10(P.Value), color = Significance)) +
    geom_point(alpha = 0.4, size = 2) + 
    scale_color_manual(values = c("Upregulated" = "blue", "Downregulated" = "red", "Not Significant" = "gray"), labels = legend_lab) +
    xlim(-5, 5) +
    labs(title = title, x = expression(x = "log"[2]*"FC"), y = expression(y = "-log"[10]*"P-value")) +
    theme(legend.position = "none", 
          plot.title = element_text(size = rel(1.5), hjust = 0.5),
          axis.title = element_text(size = rel(1.25))) +
    theme_bw()
}

#now that I've made a function, I can make volcano plots for each of my comparisons (6 total)

volcano_plots <- list(
  "V.D24" = generate_volcano_plot(top.table_V.D24_dox, "Volcano Plot DOX 24hr (adj P-val<0.05)"),
  "V.D24r" = generate_volcano_plot(top.table_V.D24r_dox, "Volcano Plot DOX 24hr Recovery (adj P-val<0.05)"),
  "V.D144r" = generate_volcano_plot(top.table_V.D144r_dox, "Volcano Plot DOX 144hr Recovery (adj P-val<0.05)")
)

# Display each volcano plot
for (plot_name in names(volcano_plots)) {
  print(volcano_plots[[plot_name]])
}

Warning: Removed 90 rows containing missing values or values outside the scale range
(`geom_point()`).

Past versions of "Volcano Plots from Pairwise Gene Analysis-1.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

Warning: Removed 11 rows containing missing values or values outside the scale range
(`geom_point()`).

Past versions of "Volcano Plots from Pairwise Gene Analysis-2.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

Past versions of "Volcano Plots from Pairwise Gene Analysis-3.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

#I want to add the number of DEG onto this for each
#make each volcano plot into an object so I can see how many rows it has

# Alternative function from Renee to combine them all into one image
# volcanosig <- function(df, psig.lvl,topg) {
#     df <- df %>% 
#     mutate(threshold = ifelse(adj.P.Val > psig.lvl, "A", ifelse(adj.P.Val <= psig.lvl & logFC<=0,"B","C")))
#     
#   ggplot(df, aes(x=logFC, y=-log10(adj.P.Val))) + 
#     geom_point(aes(color=threshold))+
#     xlab(expression("Log"[2]*" FC"))+
#     ylim(0,30)+
#     ylab(expression("-log"[10]*"P Value"))+
#     scale_color_manual(values = c("black", "red","blue"))+
#     theme_cowplot()+
#     theme(legend.position = "none",
#           plot.title = element_text(size = rel(0.8), hjust = 0.5),
#           axis.title = element_text(size = rel(0.8))) 
# }
# 
# vol1 <- volcanosig(top.table_V.D24_dox, 0.01,0)+ ggtitle("Doxorubicin \n 24 hour")
# vol2 <- volcanosig(top.table_V.D24r_dox, 0.01,0)+ ggtitle("Doxorubicin \n 24 hour Recovery")
# vol3 <- volcanosig(top.table_V.D144r_dox, 0.01,0)+ ggtitle("Doxorubicin\n 144 hour Recovery")+ylab("")
# 
# 
# Volcanoplots <- plot_grid(vol1,vol2,vol3, nrow = 1, ncol = 3)
# Volcanoplots

#now like the hypoxia paper, I'd like to put together comparisons between samples and conditions to check if they are more similar than others

PCA_data_d <- fC_Matrix_Full_cpm_filter_dox %>% 
  prcomp(.) %>% 
  t()

PCA_data_test_d <- (prcomp(t(fC_Matrix_Full_cpm_filter_dox), scale. = TRUE))


#ind_num_dox <- c("1", "1", "1", "1", "1", "1", "2", "2", "2", "2", "2", "2", "3", "3", "3", "3", "3", "3", "4", "4", "4", "4", "4", "4","5", "5", "5", "5", "5", "5", "6", "6", "6", "6", "6", "6", "6R", "6R", "6R", "6R", "6R", "6R")

#saveRDS(ind_num_dox, "data/ind_num_dox.RDS")

ind_num_dox <- readRDS("C:/Users/emmap/RDirectory/Recovery_RNAseq/Recovery_5FU/data/ind_num_dox.RDS")

####now make an annotation for my PCA####
annot_d <- data.frame("samples" = colnames(fC_Matrix_Full_cpm_filter_dox)) %>% separate_wider_delim(., cols = samples, names = c("Tx", "Time", "Ind"), delim = "_", cols_remove = FALSE) %>% unite(., col = "Tx_Time", Tx, Time, sep = "_", remove = FALSE) %>% cbind(., ind_num_dox)

#saveRDS(annot_d, "C:/Users/emmap/RDirectory/Recovery_RNAseq/Recovery_5FU/data/annot_dox.RDS")


#combine the prcomp matrix and annotation
annot_PCA_matrix_d <- PCA_data_test_d$x %>% cbind(., annot_d)


#now I can make a graph where I have filled values for individual! I have seven colors for seven individuals
# I have three fill values for three timepoints

#using annotation matrix above as well as annotated PCA matrix #(annot_PCA_matrix)

#extra info for colors in the graph (fill parameter)
fill_col_ind <- c("#66C2A5", "#FC8D62", "#1F78B4", "#E78AC3", "#A6D854", "#FFD92A", "#8B3E9B")

fill_col_ind_dark <- c("#003F5C", "#45AE91",  "#58508D", "#BC4099", "#8B3E9B", "#FF6361", "#FF2362")

fill_col_tx_dox <- c("#63666D", "#499FBD")

fill_col_txtime_d <- c("#45AE91",  "#58508D", "#BC4099", "#FF2362", "#A6D854", "#FC8D62")

#I want the color parameter to be treatment, the shape as time, and individual as number

####PC1/PC2####
annot_PCA_matrix_d %>% ggplot(., aes(x=PC1, y=PC2, size=10)) +
  geom_point(aes(color = Tx, shape = Time)) +
  scale_color_manual(values = c(fill_col_tx_dox))+
  scale_shape_manual(values = c(15, 19, 17))+
  geom_text_repel(aes(label = ind_num_dox))+
  theme_bw(base_size = 10)+
  ggtitle(expression("PCA of filtered log"[2]*"cpm"))+
  guides(size="none")

Warning: ggrepel: 27 unlabeled data points (too many overlaps). Consider
increasing max.overlaps

Past versions of "DOX only PCA plots no RUVs-1.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

####PC1/PC2 autoplot####
prcomp_res_d <- prcomp(t(fC_Matrix_Full_cpm_filter_dox), scale. = FALSE, center = TRUE)
annot_prcomp_res_d <- prcomp_res_d$x %>% cbind(., annot_d)

ggplot2::autoplot(prcomp_res_d, data = annot_d, colour = "Tx_Time", size =4)+
  theme_bw()+
  scale_color_manual(values = c(fill_col_txtime_d))+
  ggrepel::geom_text_repel(label= ind_num_dox)+
  ggtitle("PCA of DOX filtered log2cpm")

Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider
increasing max.overlaps

Past versions of "DOX only PCA plots no RUVs-2.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

####PC2/PC3####
annot_PCA_matrix_d %>% ggplot(., aes(x=PC2, y=PC3, size=10)) +
  geom_point(aes(color = Tx, shape = Time)) +
  scale_color_manual(values = c(fill_col_tx_dox))+
  scale_shape_manual(values = c(15, 19, 17))+
  geom_text_repel(aes(label = ind_num_dox))+
  theme_bw(base_size = 10)+
  ggtitle(expression("PCA of filtered log"[2]*"cpm"))+
  guides(size="none")

Warning: ggrepel: 7 unlabeled data points (too many overlaps). Consider
increasing max.overlaps

Past versions of "DOX only PCA plots no RUVs-3.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

####PC3/PC4####
annot_PCA_matrix_d %>% ggplot(., aes(x=PC3, y=PC4, size=10)) +
  geom_point(aes(color = Tx, shape = Time)) +
  scale_color_manual(values = c(fill_col_tx_dox))+
  scale_shape_manual(values = c(15, 19, 17))+
  geom_text_repel(aes(label = ind_num_dox))+
  theme_bw(base_size = 10)+
  ggtitle(expression("PCA of filtered log"[2]*"cpm"))+
  guides(size="none")

Past versions of "DOX only PCA plots no RUVs-4.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

fC_Matrix_Full <- readRDS("data/fC_Matrix_Full.RDS")

fC_Matrix_Full_dox <- as.data.frame(fC_Matrix_Full) %>% dplyr::select(-(contains("FLUO")))

Counts_Full_df_dox <- data.frame(fC_Matrix_Full_dox)

#filter this dataframe by the filtered gene list I have
filt_gene_list_dox <- row.names(fC_Matrix_Full_cpm_filter_dox)
#saveRDS(filt_gene_list_dox, "data/filt_gene_list_dox.RDS")

counts_DE_df_dox <- Counts_Full_df_dox[! (rownames(Counts_Full_df_dox) %in% filt_gene_list_dox), ]

#saveRDS(counts_DE_df_dox, "data/counts_DE_df_dox.RDS")

RUV_filt_counts_dox <- fC_Matrix_Full_dox %>% 
  as.data.frame() %>% 
  dplyr::filter(., row.names(.)%in% filt_gene_list_dox)

#add in the annotation files
ind_num_dox <- readRDS("C:/Users/emmap/RDirectory/Recovery_RNAseq/Recovery_5FU/data/ind_num_dox.RDS")
annot_d <- readRDS("C:/Users/emmap/RDirectory/Recovery_RNAseq/Recovery_5FU/data/annot_dox.RDS")


#  counts need to be integer values and in a numeric matrix
# note: the log transformation needs to be accounted for in the isLog argument in RUVs function.
counts_d <- as.matrix(RUV_filt_counts_dox)
dim(counts_d)

[1] 14225    42

#14225 genes
# Create a DataFrame for the phenoData
phenoData_d <- DataFrame(annot_d)

# Now create the RangedSummarizedExperiment necessary for RUVs input
# looks like it did need both the phenodata and the counts.
set_dox <- SummarizedExperiment(assays =  counts_d, metadata = phenoData_d)

# Generate a background matrix
# The column "Cond" holds the comparisons that you actually want to make. DOX_24, DMSO_24,5FU_24, DOX_3,etc.
scIdx_d <-RUVSeq::makeGroups(phenoData_d$Tx_Time)
scIdx_d

     [,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,]    6   12   18   24   30   36   42
[2,]    2    8   14   20   26   32   38
[3,]    4   10   16   22   28   34   40
[4,]    5   11   17   23   29   35   41
[5,]    1    7   13   19   25   31   37
[6,]    3    9   15   21   27   33   39

#now I've made all of the data I need for this - they are located in each section for k values

#DO NOT USE THESE COUNTS FOR LINEAR MODELING

#colors for all of the plots
fill_col_ind <- c("#66C2A5", "#FC8D62", "#1F78B4", "#E78AC3", "#A6D854", "#FFD92A", "#8B3E9B")

fill_col_ind_dark <- c("#003F5C", "#45AE91",  "#58508D", "#BC4099", "#8B3E9B", "#FF6361", "#FF2362")

fill_col_tx_dox <- c("#63666D", "#499FBD")

fill_col_txtime_dox <- c("#45AE91",  "#58508D", "#BC4099", "#FF2362", "#A6D854", "#FC8D62")

# before ruv
prcomp_res_d <- prcomp(t(counts_d), scale. = FALSE, center = TRUE)
ggplot2::autoplot(prcomp_res_d, data = annot_d, colour = "Tx_Time", size =4)+
  theme_bw()+
  scale_color_manual(values = c(fill_col_txtime_dox))+
  ggrepel::geom_text_repel(label= ind_num_dox)+
  ggtitle("No RUV")

Past versions of "RUVs Correction Start DOX Only Set-1.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

####new PCA plots no correction####
#PCA plots for each value of k attached in each section
prcomp_res_d <- prcomp(t(counts_d), scale. = FALSE, center = TRUE)
annot_prcomp_res_d <- prcomp_res_d$x %>% cbind(., annot_d)

group_2d <- rep(c("DOX_24",
                  "DMSO_24",
                  "DOX_24rec",
                  "DMSO_24rec",
                  "DOX_144rec",
                  "DMSO_144rec"), 7)


dge1_d <- DGEList.data.frame(counts = fC_Matrix_Full_dox, group = group_2d, genes = row.names(fC_Matrix_Full_dox))

#calculate the normalization factors with method TMM
dge1_calc_d <- calcNormFactors(dge1_d, method = "TMM")

#Pull out factors
snames1_d <- data.frame("samples" = colnames(dge1_calc_d)) %>% separate_wider_delim(., cols = samples, names = c("Treatment", "Time", "Individual"), delim = "_", cols_remove = FALSE)

snames1_ind_d <- snames1_d$Individual

#Apply RUVs function from RUVSeq
#"k" will be iteratively adjusted over time depending on your PCA.
set_d <- RUVSeq::RUVs(x = counts_d, k =1, scIdx = scIdx_d, isLog = FALSE)

#get the ruv weights to put into the linear model. n weights = k.
#k=1
RUV_df_d <- set_d$W %>% as.data.frame()
RUV_df_d$Names <- rownames(RUV_df_d)


#Check that the names match
#k=1
RUV_df_rm_d <- RUV_df_d[RUV_df_d$Names %in% annot_d$samples, ] 
RUV_1_d <-  RUV_df_rm_d$W_1

# after ruv k=1

#PCA checks
#k=1
prcomp_res_1_d <- prcomp(t(set_d$normalizedCounts), scale. = FALSE, center = TRUE)
annot_prcomp_res_1_d <- prcomp_res_1_d$x %>% cbind(., annot_d)

ggplot2::autoplot(prcomp_res_1_d, data = annot_d, colour = "Tx_Time", size =4)+
  theme_bw()+
  scale_color_manual(values = c(fill_col_txtime_dox))+
  ggrepel::geom_text_repel(label= ind_num_dox)+
  ggtitle("RUVs Correction k=1")

Warning: ggrepel: 5 unlabeled data points (too many overlaps). Consider
increasing max.overlaps

Past versions of "RUVs k1 DOX only set-1.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

#k=1
annot_d$samples == RUV_df_rm_d$Names

 [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[16] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[31] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE

annot_d$RUV_1_d <- RUV_df_rm_d$W_1

#Create my model matrix
#k=1
mm_r1_d <- model.matrix(~0 + group_2d + RUV_1_d, data = annot_d)

p1_d <- voom(dge1_calc_d$counts, mm_r1_d, plot = TRUE)

Past versions of "RUVs k1 DOX only set-2.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

corfit1_d <- duplicateCorrelation(p1_d, mm_r1_d, block = snames1_ind_d)

v1_d <- voom(dge1_calc_d$counts, mm_r1_d, block = snames1_ind_d, correlation = corfit1_d$consensus)

fit1_d <- lmFit(v1_d, mm_r1_d, block = snames1_ind_d, correlation = corfit1_d$consensus)

#k=1
mm_r1_names_d <- str_replace(string = colnames(mm_r1_d), pattern = "group_2d", replacement = "")
design_d <- model.matrix(~ group_2d + RUV_1_d , annot_d)
colnames(mm_r1_d) <- mm_r1_names_d

#k=1
cm_r1_d <- makeContrasts(
        V.D24 = DOX_24 - DMSO_24,
        V.D24r = DOX_24rec - DMSO_24rec,
        V.D144r = DOX_144rec - DMSO_144rec,
        RUV_1_24 = RUV_1_d - DMSO_24,
        RUV_1_24r= RUV_1_d - DMSO_24rec,
        RUV_1_144r = RUV_1_d - DMSO_144rec,
        levels = mm_r1_d
)

#k=1
vfit_r1_d <- lmFit(p1_d, mm_r1_d)
vfit_r1_d <- contrasts.fit(vfit_r1_d, contrasts = cm_r1_d)

#k=1
efit1_d <- eBayes(vfit_r1_d)

#k=1
results1_d = decideTests(efit1_d)
summary(results1_d)

       V.D24 V.D24r V.D144r RUV_1_24 RUV_1_24r RUV_1_144r
Down    5222   2650     486    13532     13539      13491
NotSig 14886  16841   26921     1645      1641       1721
Up      8287   8904     988    13218     13215      13183

#         V.D24 V.D24r V.D144r RUV_1_24 RUV_1_24r RUV_1_144r
# Down    5222   2650     486    13532     13539      13491
# NotSig 14886  16841   26921     1645      1641       1721
# Up      8287   8904     988    13218     13215      13183

#k=1
toptable_Dupcor_DOX_d <- topTable(efit1_d, coef = "V.D24", number = nrow(dge1_calc_d$counts), p.value = 1)
toptable_Dupcor_DOXrec_d <- topTable(efit1_d, coef = "V.D24r", number = nrow(dge1_calc_d$counts), p.value = 1)
toptable_Dupcor_DOX144_d <- topTable(efit1_d, coef = "V.D144r", number = nrow(dge1_calc_d$counts), p.value = 1)
#k=1 plots
toptable_Dupcor_DOX_d$logFC %>% hist(, main= "RUVs k=1 DOX 24hr Toptable")

Past versions of "RUVs k1 DOX only set-3.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

toptable_Dupcor_DOXrec_d$logFC %>% hist(, main = "RUVs k=1 DOX 24Rec Toptable")

Past versions of "RUVs k1 DOX only set-4.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

toptable_Dupcor_DOX144_d$logFC %>% hist(, main = "RUVs k=1 DOX 144Rec Toptable")

Past versions of "RUVs k1 DOX only set-5.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

#function is on the previous
annot_data_d <- annot_d %>% dplyr::select("Tx_Time", "Time", "Tx", "Ind", "samples")

Cormotif_d <- counts_DE_df_dox %>% cpm(., log = TRUE)
Cormotif_df_d <- as.data.frame(Cormotif_d)

groupid_d <- rep(c(1, 2, 3, 4, 5, 6), 7)

compid_d <- data.frame(c1 = c(1, 3, 5), c2 = c(2, 4, 6))

set.seed(12345)
# initial_cormotif_dox <- cormotiffit(exprs = Cormotif_d,
#                                  groupid = groupid_d,
#                                  compid = compid_d,
#                                  K=1:8  , max.iter = 500, runtype = "logCPM")

#only need to run this once! 
#save this to an object so I can retrieve it as needed

#saveRDS(initial_cormotif_dox, "data/initial_cormotif_dox.RDS")

initial_cormotif_dox <- readRDS("data/initial_cormotif_dox.RDS")

plotIC(initial_cormotif_dox)

Past versions of "Plot AIC and BIC-1.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

plotMotif(initial_cormotif_dox)

Past versions of "Plot Motifs DOX Only-1.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

myColors <-  rev(c("#FFFFFF", "#E6E6E6" ,"#CCCCCC", "#B3B3B3", "#999999", "#808080", "#666666","#4C4C4C", "#333333", "#191919","#000000"))

plot.new()
legend('bottomleft',fill=myColors, legend =rev(c("0", "0.1", "0.2", "0.3", "0.4",  "0.5", "0.6", "0.7", "0.8","0.9", "1")), box.col="white",title = "Probability\nlegend", horiz=FALSE,title.cex=.8)

Past versions of "Plot Motifs DOX Only-2.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

topgenelist_d <- generank(initial_cormotif_dox$bestmotif$p.post)
rownames(topgenelist_d) <- rownames(Cormotif_df_d)


motif_prob_d <- initial_cormotif_dox$bestmotif$clustlike
rownames(motif_prob_d) <- rownames(topgenelist_d)
#saveRDS(motif_prob_d, "data/Cormotif_prob_gene_list_doxonly.RDS")

#Define the gene probability groups - I have 3
clust1_d <- motif_prob_d %>% 
  as.data.frame() %>% 
  filter(V1>0.5) %>% 
  rownames

length(clust1_d)

[1] 11482

#11482
#is this clust1 a non-response?

clust2_d <- motif_prob_d %>% 
  as.data.frame() %>% 
  filter(V2>0.5) %>% 
  rownames

length(clust2_d)

[1] 0

#0
#is clust2 a dox early response?

clust3_d <- motif_prob_d %>% 
  as.data.frame() %>% 
  filter(V3>0.5) %>% 
  rownames

length(clust3_d)

[1] 538

#538
#this one is not showing any genes

clust4_d <- motif_prob_d %>% 
  as.data.frame() %>% 
  filter(V4>0.5) %>% 
  rownames

length(clust4_d)

[1] 1576

#1576
#is clust4 a DOX late response?

clusterdata_d <- data.frame(
  Category = c("No Response", "Late Response", "Early Sustained Response"), 
  Value = c(11482, 538, 1576)
)

piecolors <- c("No Response" = "#007896", 
               "Late Response" = "#58508D", 
               "Early Sustained Response" = "#BC5090")

#make a piechart of these distributions
clusterdata_d %>% ggplot(aes(x = "", y = Value, fill = Category))+
  geom_bar(width = 1, stat = "identity")+
  coord_polar("y", start = 0)+
  geom_text(aes(label = Value),
            position = position_stack(vjust = 0.5),
            size = 4, color = "black")+
  labs(title = "Distribution of Gene Clusters Identified By Cormotif", x = NULL, y = NULL)+
  theme_void()+
  scale_fill_manual(values = piecolors)

Past versions of "Cormotif Cluster Probabilities-1.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

#now let's look at each of these motifs by study with the posterior probability
#changing the cutoffs based on the look of each motif - if it's very dark = > 0.5
#if white < 0.5 
#if grey try a less stringent cutoff > 0.1

#gene_postprob_motif <- initial_cormotif_dox$bestmotif$p.post
#rownames(gene_postprob_motif) <- rownames(Cormotif_df_d)

#saveRDS(gene_postprob_motif, "data/gene_postprob_motif.RDS")

gene_postprob_motif <- readRDS("data/gene_postprob_motif.RDS")

gene_postprob_motif_df <- as.data.frame(gene_postprob_motif)

#motif 1 no response
prob_motif_1 <- rownames(gene_postprob_motif_df[(gene_postprob_motif_df[,1] < 0.5 
                                              & gene_postprob_motif_df[,2] < 0.5 
                                              & gene_postprob_motif_df[,3] < 0.5),])
length(prob_motif_1)

[1] 10903

#10903 genes post prob

#motif 2 acute response
prob_motif_2 <- rownames(gene_postprob_motif_df[(gene_postprob_motif_df[,1] > 0.1 
                                              & gene_postprob_motif_df[,2] < 0.5 
                                              & gene_postprob_motif_df[,3] < 0.5),])
length(prob_motif_2)

[1] 2586

#2586 genes post prob

#motif 3 late response
prob_motif_3 <- rownames(gene_postprob_motif_df[(gene_postprob_motif_df[,1] > 0.1 
                                              & gene_postprob_motif_df[,2] > 0.5 
                                              & gene_postprob_motif_df[,3] > 0.5),])
length(prob_motif_3)

[1] 451

#451 genes post prob

#motif 4 early sustained response
prob_motif_4 <- rownames(gene_postprob_motif_df[(gene_postprob_motif_df[,1] > 0.5 
                                              & gene_postprob_motif_df[,2] > 0.1 
                                              & gene_postprob_motif_df[,3] < 0.5),])
length(prob_motif_4)

[1] 2600

#2600 genes post prob

#this totals 16540

clusterdata_postprob <- data.frame(
  Category = c("No Response", "Acute Response", "Late Response", "Early Sustained Response"), 
  Value = c(10903, 2586, 451, 2600)
)

piecolors_2 <- c("No Response" = "#007896",
               "Acute Response" = "#58508D",
               "Late Response" = "#ABCC59", 
               "Early Sustained Response" = "#BC5090")

#make a piechart of these distributions
clusterdata_postprob %>% ggplot(aes(x = "", y = Value, fill = Category))+
  geom_bar(width = 1, stat = "identity")+
  coord_polar("y", start = 0)+
  geom_text(aes(label = Value),
            position = position_stack(vjust = 0.5),
            size = 4, color = "black")+
  labs(title = "Distribution of Gene Clusters Identified By Cormotif", x = NULL, y = NULL)+
  theme_void()+
  scale_fill_manual(values = piecolors_2)

Past versions of "Assess Gene Distribution Post Prob Cormotif-1.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

Now we will use Gene Ontology analysis to discover biological relevance to the genes that are assigned to this cluster This set is for the No Response motif (motif 1) with clustlike

motif_NR_d <- clust1_d

NRmotif_genes_d <- gost(query = motif_NR_d,
                      organism = "hsapiens",
                      ordered_query = FALSE,
                      measure_underrepresentation = FALSE,
                      evcodes = FALSE,
                      user_threshold = 0.05,
                      correction_method = c("fdr"),
                      sources = c("GO:BP", "KEGG"))

cormotifNFclust_d <- gostplot(NRmotif_genes_d, capped = FALSE, interactive = TRUE)
cormotifNFclust_d

tableNR_d <- NRmotif_genes_d$result %>% 
  dplyr::select(c(source, term_id, term_name, intersection_size, term_size, p_value))

tableNR_d %>% 
  mutate_at(.vars = 6, .funs = scales::label_scientific(digits=4)) %>% 
  kableExtra::kable(.,) %>% 
  kableExtra::kable_paper("striped", full_width = FALSE) %>% 
  kableExtra::kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "hover")) %>% 
  kableExtra::scroll_box(width = "100%", height = "400px")

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0050907	detection of chemical stimulus involved in sensory perception	394	443	2.099e-211
GO:BP	GO:0035195	miRNA-mediated post-transcriptional gene silencing	477	612	4.095e-206
GO:BP	GO:0007606	sensory perception of chemical stimulus	418	497	2.501e-204
GO:BP	GO:0050911	detection of chemical stimulus involved in sensory perception of smell	362	397	2.924e-203
GO:BP	GO:0035194	regulatory ncRNA-mediated post-transcriptional gene silencing	478	624	4.629e-201
GO:BP	GO:0016441	post-transcriptional gene silencing	479	630	4.448e-199
GO:BP	GO:0009593	detection of chemical stimulus	404	480	7.960e-198
GO:BP	GO:0050906	detection of stimulus involved in sensory perception	419	515	5.041e-194
GO:BP	GO:0007608	sensory perception of smell	369	423	1.005e-191
GO:BP	GO:0031047	regulatory ncRNA-mediated gene silencing	485	686	1.000e-178
GO:BP	GO:0051606	detection of stimulus	460	643	1.638e-172
GO:BP	GO:0007186	G protein-coupled receptor signaling pathway	702	1275	1.993e-169
GO:BP	GO:0007600	sensory perception	561	955	1.695e-150
GO:BP	GO:0050877	nervous system process	654	1489	1.255e-95
GO:BP	GO:0010608	post-transcriptional regulation of gene expression	516	1087	6.436e-89
GO:BP	GO:0003008	system process	814	2266	2.014e-68
GO:BP	GO:0010629	negative regulation of gene expression	637	1640	1.677e-66
GO:BP	GO:0042221	response to chemical	1122	3867	5.099e-40
GO:BP	GO:0065007	biological regulation	2992	12671	6.636e-36
GO:BP	GO:0042742	defense response to bacterium	170	326	6.062e-34
GO:BP	GO:0006959	humoral immune response	142	254	1.701e-32
GO:BP	GO:0050789	regulation of biological process	2896	12278	1.784e-32
GO:BP	GO:0006952	defense response	588	1809	2.171e-32
GO:BP	GO:0032501	multicellular organismal process	1842	7234	8.240e-32
GO:BP	GO:0050794	regulation of cellular process	2800	11876	1.068e-29
GO:BP	GO:0009617	response to bacterium	284	721	5.585e-29
GO:BP	GO:0010558	negative regulation of macromolecule biosynthetic process	808	2772	1.486e-27
GO:BP	GO:0098542	defense response to other organism	418	1228	8.345e-27
GO:BP	GO:0009890	negative regulation of biosynthetic process	816	2838	8.551e-26
GO:BP	GO:0031424	keratinization	62	82	5.996e-24
GO:BP	GO:0019730	antimicrobial humoral response	83	131	9.733e-24
GO:BP	GO:0043207	response to external biotic stimulus	491	1558	3.572e-23
GO:BP	GO:0051707	response to other organism	489	1555	7.492e-23
GO:BP	GO:0009607	response to biotic stimulus	498	1593	1.062e-22
GO:BP	GO:0140546	defense response to symbiont	376	1125	2.767e-22
GO:BP	GO:0009605	response to external stimulus	672	2367	4.718e-19
GO:BP	GO:0007165	signal transduction	1490	5979	9.766e-19
GO:BP	GO:0001906	cell killing	107	219	2.841e-18
GO:BP	GO:0141060	disruption of anatomical structure in another organism	62	98	1.639e-17
GO:BP	GO:0006954	inflammatory response	286	847	2.720e-17
GO:BP	GO:0061844	antimicrobial humoral immune response mediated by antimicrobial peptide	55	83	7.921e-17
GO:BP	GO:0044419	biological process involved in interspecies interaction between organisms	506	1724	8.800e-17
GO:BP	GO:0006955	immune response	574	2008	1.288e-16
GO:BP	GO:0031640	killing of cells of another organism	58	91	1.309e-16
GO:BP	GO:0141061	disruption of cell in another organism	58	91	1.309e-16
GO:BP	GO:0010605	negative regulation of macromolecule metabolic process	852	3197	1.946e-16
GO:BP	GO:0045087	innate immune response	317	977	1.946e-16
GO:BP	GO:0007154	cell communication	1578	6496	2.330e-15
GO:BP	GO:0023052	signaling	1571	6471	3.737e-15
GO:BP	GO:0045109	intermediate filament organization	48	73	1.917e-14
GO:BP	GO:0050830	defense response to Gram-positive bacterium	66	120	2.533e-14
GO:BP	GO:0009892	negative regulation of metabolic process	887	3418	6.520e-14
GO:BP	GO:0002252	immune effector process	236	703	7.908e-14
GO:BP	GO:0050896	response to stimulus	2093	8993	2.383e-13
GO:BP	GO:0050909	sensory perception of taste	44	67	3.535e-13
GO:BP	GO:0030216	keratinocyte differentiation	83	176	5.400e-13
GO:BP	GO:0097530	granulocyte migration	76	156	8.440e-13
GO:BP	GO:0050829	defense response to Gram-negative bacterium	53	91	8.440e-13
GO:BP	GO:0002697	regulation of immune effector process	144	381	1.380e-12
GO:BP	GO:1990266	neutrophil migration	66	129	2.468e-12
GO:BP	GO:0030593	neutrophil chemotaxis	57	106	9.133e-12
GO:BP	GO:0007586	digestion	67	136	1.612e-11
GO:BP	GO:0050913	sensory perception of bitter taste	31	42	3.164e-11
GO:BP	GO:0071621	granulocyte chemotaxis	64	129	3.650e-11
GO:BP	GO:0050912	detection of chemical stimulus involved in sensory perception of taste	31	43	8.803e-11
GO:BP	GO:0009913	epidermal cell differentiation	101	250	1.169e-10
GO:BP	GO:0002237	response to molecule of bacterial origin	131	355	1.496e-10
GO:BP	GO:0001580	detection of chemical stimulus involved in sensory perception of bitter taste	28	37	1.530e-10
GO:BP	GO:0002323	natural killer cell activation involved in immune response	27	35	1.731e-10
GO:BP	GO:0030595	leukocyte chemotaxis	96	237	3.354e-10
GO:BP	GO:0002376	immune system process	720	2796	3.674e-10
GO:BP	GO:0050900	leukocyte migration	140	396	9.295e-10
GO:BP	GO:0019731	antibacterial humoral response	40	68	9.295e-10
GO:BP	GO:0032496	response to lipopolysaccharide	123	337	1.549e-09
GO:BP	GO:0045104	intermediate filament cytoskeleton organization	49	94	1.915e-09
GO:BP	GO:0097529	myeloid leukocyte migration	94	237	2.134e-09
GO:BP	GO:0071219	cellular response to molecule of bacterial origin	90	224	2.467e-09
GO:BP	GO:0051716	cellular response to stimulus	1702	7320	2.514e-09
GO:BP	GO:0046651	lymphocyte proliferation	114	308	2.958e-09
GO:BP	GO:0045103	intermediate filament-based process	49	95	2.964e-09
GO:BP	GO:0070098	chemokine-mediated signaling pathway	47	90	4.220e-09
GO:BP	GO:0007283	spermatogenesis	201	637	5.143e-09
GO:BP	GO:0019221	cytokine-mediated signaling pathway	166	503	5.685e-09
GO:BP	GO:0070661	leukocyte proliferation	125	351	6.046e-09
GO:BP	GO:0032943	mononuclear cell proliferation	115	315	6.046e-09
GO:BP	GO:0071222	cellular response to lipopolysaccharide	86	214	6.046e-09
GO:BP	GO:0002526	acute inflammatory response	53	109	7.814e-09
GO:BP	GO:0048232	male gamete generation	204	654	1.064e-08
GO:BP	GO:0007218	neuropeptide signaling pathway	53	110	1.179e-08
GO:BP	GO:0002682	regulation of immune system process	416	1526	1.256e-08
GO:BP	GO:0008544	epidermis development	135	394	2.033e-08
GO:BP	GO:0007338	single fertilization	71	169	2.540e-08
GO:BP	GO:0042100	B cell proliferation	51	106	2.685e-08
GO:BP	GO:0060326	cell chemotaxis	114	319	2.989e-08
GO:BP	GO:0052695	cellular glucuronidation	18	21	3.186e-08
GO:BP	GO:0033141	positive regulation of peptidyl-serine phosphorylation of STAT protein	18	21	3.186e-08
GO:BP	GO:0002699	positive regulation of immune effector process	95	253	4.432e-08
GO:BP	GO:0070663	regulation of leukocyte proliferation	98	265	6.144e-08
GO:BP	GO:0002684	positive regulation of immune system process	302	1066	7.008e-08
GO:BP	GO:0045321	leukocyte activation	274	951	7.263e-08
GO:BP	GO:0002548	monocyte chemotaxis	37	68	8.828e-08
GO:BP	GO:0001775	cell activation	309	1098	9.336e-08
GO:BP	GO:0002703	regulation of leukocyte mediated immunity	91	243	1.128e-07
GO:BP	GO:0022414	reproductive process	417	1556	1.138e-07
GO:BP	GO:0009566	fertilization	82	212	1.224e-07
GO:BP	GO:0002922	positive regulation of humoral immune response	18	22	1.277e-07
GO:BP	GO:0002366	leukocyte activation involved in immune response	108	305	1.387e-07
GO:BP	GO:0002263	cell activation involved in immune response	109	309	1.481e-07
GO:BP	GO:0048609	multicellular organismal reproductive process	279	980	1.719e-07
GO:BP	GO:1990868	response to chemokine	47	99	1.942e-07
GO:BP	GO:1990869	cellular response to chemokine	47	99	1.942e-07
GO:BP	GO:0072677	eosinophil migration	22	31	2.001e-07
GO:BP	GO:0050776	regulation of immune response	258	897	2.436e-07
GO:BP	GO:0050832	defense response to fungus	33	59	2.445e-07
GO:BP	GO:0071216	cellular response to biotic stimulus	92	251	2.903e-07
GO:BP	GO:0048245	eosinophil chemotaxis	20	27	3.121e-07
GO:BP	GO:0071715	icosanoid transport	35	65	3.122e-07
GO:BP	GO:0050727	regulation of inflammatory response	127	381	3.701e-07
GO:BP	GO:0032649	regulation of type II interferon production	52	117	4.698e-07
GO:BP	GO:0050670	regulation of lymphocyte proliferation	87	236	5.335e-07
GO:BP	GO:0022600	digestive system process	48	105	5.726e-07
GO:BP	GO:0032944	regulation of mononuclear cell proliferation	88	240	5.813e-07
GO:BP	GO:0060294	cilium movement involved in cell motility	67	167	5.832e-07
GO:BP	GO:0030317	flagellated sperm motility	61	147	5.861e-07
GO:BP	GO:0097722	sperm motility	61	147	5.861e-07
GO:BP	GO:0032609	type II interferon production	52	118	6.345e-07
GO:BP	GO:0031341	regulation of cell killing	48	106	7.977e-07
GO:BP	GO:0002706	regulation of lymphocyte mediated immunity	71	182	8.191e-07
GO:BP	GO:0002443	leukocyte mediated immunity	146	461	1.138e-06
GO:BP	GO:0033139	regulation of peptidyl-serine phosphorylation of STAT protein	18	24	1.242e-06
GO:BP	GO:0006953	acute-phase response	28	49	1.763e-06
GO:BP	GO:0048247	lymphocyte chemotaxis	33	63	1.893e-06
GO:BP	GO:0001539	cilium or flagellum-dependent cell motility	67	172	2.139e-06
GO:BP	GO:0060285	cilium-dependent cell motility	67	172	2.139e-06
GO:BP	GO:0001909	leukocyte mediated cytotoxicity	56	135	2.223e-06
GO:BP	GO:0002274	myeloid leukocyte activation	86	240	2.612e-06
GO:BP	GO:0007188	adenylate cyclase-modulating G protein-coupled receptor signaling pathway	88	248	3.047e-06
GO:BP	GO:0032689	negative regulation of type II interferon production	25	42	3.066e-06
GO:BP	GO:0042501	serine phosphorylation of STAT protein	18	25	3.341e-06
GO:BP	GO:0022412	cellular process involved in reproduction in multicellular organism	130	408	4.288e-06
GO:BP	GO:0007276	gamete generation	233	822	4.345e-06
GO:BP	GO:0050778	positive regulation of immune response	211	732	4.554e-06
GO:BP	GO:0019953	sexual reproduction	300	1103	4.591e-06
GO:BP	GO:0048240	sperm capacitation	21	33	6.936e-06
GO:BP	GO:0001819	positive regulation of cytokine production	149	486	7.167e-06
GO:BP	GO:0006063	uronic acid metabolic process	18	26	8.268e-06
GO:BP	GO:0019585	glucuronate metabolic process	18	26	8.268e-06
GO:BP	GO:0140975	disruption of cellular anatomical structure in another organism	10	10	8.941e-06
GO:BP	GO:0002775	antimicrobial peptide production	10	10	8.941e-06
GO:BP	GO:0007259	cell surface receptor signaling pathway via JAK-STAT	64	168	1.011e-05
GO:BP	GO:0043588	skin development	106	322	1.071e-05
GO:BP	GO:0001817	regulation of cytokine production	217	765	1.076e-05
GO:BP	GO:0009620	response to fungus	34	70	1.121e-05
GO:BP	GO:0050953	sensory perception of light stimulus	79	222	1.129e-05
GO:BP	GO:0030101	natural killer cell activation	42	95	1.209e-05
GO:BP	GO:0097696	cell surface receptor signaling pathway via STAT	66	176	1.246e-05
GO:BP	GO:0007601	visual perception	78	219	1.267e-05
GO:BP	GO:0051873	killing by host of symbiont cells	19	29	1.312e-05
GO:BP	GO:0042129	regulation of T cell proliferation	67	180	1.371e-05
GO:BP	GO:0001816	cytokine production	218	772	1.391e-05
GO:BP	GO:0006690	icosanoid metabolic process	50	122	1.557e-05
GO:BP	GO:0002920	regulation of humoral immune response	25	45	1.684e-05
GO:BP	GO:0007631	feeding behavior	45	106	1.805e-05
GO:BP	GO:0007286	spermatid development	76	214	1.968e-05
GO:BP	GO:0042531	positive regulation of tyrosine phosphorylation of STAT protein	31	63	2.471e-05
GO:BP	GO:0019755	one-carbon compound transport	17	25	2.471e-05
GO:BP	GO:0002251	organ or tissue specific immune response	24	43	2.511e-05
GO:BP	GO:0042330	taxis	141	465	2.686e-05
GO:BP	GO:0072676	lymphocyte migration	50	124	2.686e-05
GO:BP	GO:0007342	fusion of sperm to egg plasma membrane involved in single fertilization	19	30	2.686e-05
GO:BP	GO:0001910	regulation of leukocyte mediated cytotoxicity	40	92	3.619e-05
GO:BP	GO:0010468	regulation of gene expression	1268	5515	3.899e-05
GO:BP	GO:0002285	lymphocyte activation involved in immune response	75	214	4.009e-05
GO:BP	GO:0048515	spermatid differentiation	77	222	4.556e-05
GO:BP	GO:0036230	granulocyte activation	26	50	5.085e-05
GO:BP	GO:0050865	regulation of cell activation	177	616	5.147e-05
GO:BP	GO:0015718	monocarboxylic acid transport	65	179	5.147e-05
GO:BP	GO:0002385	mucosal immune response	22	39	5.559e-05
GO:BP	GO:0006935	chemotaxis	139	463	5.666e-05
GO:BP	GO:0007204	positive regulation of cytosolic calcium ion concentration	62	169	5.956e-05
GO:BP	GO:0042119	neutrophil activation	23	42	6.327e-05
GO:BP	GO:0015670	carbon dioxide transport	12	15	7.547e-05
GO:BP	GO:0070665	positive regulation of leukocyte proliferation	60	163	7.610e-05
GO:BP	GO:0015732	prostaglandin transport	18	29	7.651e-05
GO:BP	GO:0002286	T cell activation involved in immune response	49	125	8.455e-05
GO:BP	GO:0002694	regulation of leukocyte activation	162	561	1.007e-04
GO:BP	GO:0009584	detection of visible light	19	32	1.007e-04
GO:BP	GO:0042102	positive regulation of T cell proliferation	42	102	1.008e-04
GO:BP	GO:0002705	positive regulation of leukocyte mediated immunity	55	147	1.102e-04
GO:BP	GO:0050729	positive regulation of inflammatory response	55	147	1.102e-04
GO:BP	GO:0046649	lymphocyte activation	216	787	1.227e-04
GO:BP	GO:0002698	negative regulation of immune effector process	47	120	1.352e-04
GO:BP	GO:0032612	interleukin-1 production	44	110	1.426e-04
GO:BP	GO:0032652	regulation of interleukin-1 production	44	110	1.426e-04
GO:BP	GO:0042509	regulation of tyrosine phosphorylation of STAT protein	33	74	1.494e-04
GO:BP	GO:0002784	regulation of antimicrobial peptide production	8	8	1.574e-04
GO:BP	GO:0002760	positive regulation of antimicrobial humoral response	8	8	1.574e-04
GO:BP	GO:0002778	antibacterial peptide production	8	8	1.574e-04
GO:BP	GO:0009583	detection of light stimulus	31	68	1.638e-04
GO:BP	GO:0051249	regulation of lymphocyte activation	145	497	1.739e-04
GO:BP	GO:0002673	regulation of acute inflammatory response	24	47	1.755e-04
GO:BP	GO:0032653	regulation of interleukin-10 production	28	59	1.790e-04
GO:BP	GO:0032613	interleukin-10 production	28	59	1.790e-04
GO:BP	GO:0015908	fatty acid transport	46	118	1.873e-04
GO:BP	GO:0003006	developmental process involved in reproduction	270	1022	1.873e-04
GO:BP	GO:0098586	cellular response to virus	34	78	1.884e-04
GO:BP	GO:0071346	cellular response to type II interferon	48	125	1.893e-04
GO:BP	GO:0003341	cilium movement	72	212	2.016e-04
GO:BP	GO:0050671	positive regulation of lymphocyte proliferation	53	143	2.099e-04
GO:BP	GO:0071674	mononuclear cell migration	78	235	2.183e-04
GO:BP	GO:0034341	response to type II interferon	54	147	2.310e-04
GO:BP	GO:0030855	epithelial cell differentiation	203	741	2.510e-04
GO:BP	GO:0042110	T cell activation	159	558	2.519e-04
GO:BP	GO:0060295	regulation of cilium movement involved in cell motility	18	31	2.536e-04
GO:BP	GO:1902019	regulation of cilium-dependent cell motility	18	31	2.536e-04
GO:BP	GO:0007159	leukocyte cell-cell adhesion	121	404	2.574e-04
GO:BP	GO:0032309	icosanoid secretion	24	48	2.602e-04
GO:BP	GO:0007602	phototransduction	24	48	2.602e-04
GO:BP	GO:0042363	fat-soluble vitamin catabolic process	10	12	2.649e-04
GO:BP	GO:0007260	tyrosine phosphorylation of STAT protein	33	76	2.691e-04
GO:BP	GO:0051250	negative regulation of lymphocyte activation	57	159	2.915e-04
GO:BP	GO:0045026	plasma membrane fusion	19	34	2.933e-04
GO:BP	GO:0002822	regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	65	189	3.360e-04
GO:BP	GO:0002819	regulation of adaptive immune response	69	204	3.426e-04
GO:BP	GO:0031347	regulation of defense response	212	783	3.438e-04
GO:BP	GO:0032946	positive regulation of mononuclear cell proliferation	53	146	3.899e-04
GO:BP	GO:0006805	xenobiotic metabolic process	47	125	4.184e-04
GO:BP	GO:0006691	leukotriene metabolic process	18	32	4.408e-04
GO:BP	GO:0032945	negative regulation of mononuclear cell proliferation	36	88	5.148e-04
GO:BP	GO:1903037	regulation of leukocyte cell-cell adhesion	110	366	5.277e-04
GO:BP	GO:0007281	germ cell development	111	370	5.277e-04
GO:BP	GO:0002709	regulation of T cell mediated immunity	38	95	5.492e-04
GO:BP	GO:0032722	positive regulation of chemokine production	31	72	5.902e-04
GO:BP	GO:0002685	regulation of leukocyte migration	75	230	5.911e-04
GO:BP	GO:0050863	regulation of T cell activation	112	375	5.911e-04
GO:BP	GO:0007200	phospholipase C-activating G protein-coupled receptor signaling pathway	44	116	5.911e-04
GO:BP	GO:1901317	regulation of flagellated sperm motility	14	22	5.951e-04
GO:BP	GO:0010556	regulation of macromolecule biosynthetic process	1276	5633	6.069e-04
GO:BP	GO:0002695	negative regulation of leukocyte activation	63	185	6.100e-04
GO:BP	GO:0002225	positive regulation of antimicrobial peptide production	7	7	6.253e-04
GO:BP	GO:0052697	xenobiotic glucuronidation	7	7	6.253e-04
GO:BP	GO:0002704	negative regulation of leukocyte mediated immunity	29	66	6.637e-04
GO:BP	GO:0032101	regulation of response to external stimulus	277	1071	6.802e-04
GO:BP	GO:0032602	chemokine production	38	96	6.874e-04
GO:BP	GO:0032642	regulation of chemokine production	38	96	6.874e-04
GO:BP	GO:0070664	negative regulation of leukocyte proliferation	38	96	6.874e-04
GO:BP	GO:0032757	positive regulation of interleukin-8 production	28	63	6.970e-04
GO:BP	GO:0009581	detection of external stimulus	51	142	7.251e-04
GO:BP	GO:0002449	lymphocyte mediated immunity	108	361	7.251e-04
GO:BP	GO:0002687	positive regulation of leukocyte migration	54	153	7.362e-04
GO:BP	GO:0042113	B cell activation	88	282	7.362e-04
GO:BP	GO:0032677	regulation of interleukin-8 production	34	83	7.764e-04
GO:BP	GO:0032637	interleukin-8 production	34	83	7.764e-04
GO:BP	GO:0042098	T cell proliferation	70	213	7.789e-04
GO:BP	GO:0002444	myeloid leukocyte mediated immunity	43	114	7.950e-04
GO:BP	GO:0002544	chronic inflammatory response	13	20	8.066e-04
GO:BP	GO:0050868	negative regulation of T cell activation	46	125	8.673e-04
GO:BP	GO:0070374	positive regulation of ERK1 and ERK2 cascade	69	210	8.811e-04
GO:BP	GO:0002759	regulation of antimicrobial humoral response	9	11	9.070e-04
GO:BP	GO:1903038	negative regulation of leukocyte cell-cell adhesion	49	136	9.078e-04
GO:BP	GO:0050672	negative regulation of lymphocyte proliferation	35	87	9.094e-04
GO:BP	GO:0002227	innate immune response in mucosa	16	28	9.123e-04
GO:BP	GO:0032103	positive regulation of response to external stimulus	170	619	9.807e-04
GO:BP	GO:0015669	gas transport	14	23	1.100e-03
GO:BP	GO:0030277	maintenance of gastrointestinal epithelium	14	23	1.100e-03
GO:BP	GO:0032735	positive regulation of interleukin-12 production	21	43	1.271e-03
GO:BP	GO:0071345	cellular response to cytokine stimulus	222	843	1.273e-03
GO:BP	GO:1904892	regulation of receptor signaling pathway via STAT	40	106	1.418e-03
GO:BP	GO:0046425	regulation of receptor signaling pathway via JAK-STAT	38	99	1.418e-03
GO:BP	GO:0060046	regulation of acrosome reaction	11	16	1.565e-03
GO:BP	GO:0001818	negative regulation of cytokine production	88	288	1.624e-03
GO:BP	GO:0002825	regulation of T-helper 1 type immune response	17	32	1.754e-03
GO:BP	GO:0002715	regulation of natural killer cell mediated immunity	23	50	1.781e-03
GO:BP	GO:0002228	natural killer cell mediated immunity	31	76	1.797e-03
GO:BP	GO:0002700	regulation of production of molecular mediator of immune response	62	188	1.837e-03
GO:BP	GO:0007189	adenylate cyclase-activating G protein-coupled receptor signaling pathway	54	158	1.843e-03
GO:BP	GO:0002701	negative regulation of production of molecular mediator of immune response	21	44	1.881e-03
GO:BP	GO:0001523	retinoid metabolic process	33	83	1.899e-03
GO:BP	GO:0031343	positive regulation of cell killing	30	73	1.961e-03
GO:BP	GO:0009889	regulation of biosynthetic process	1302	5795	1.992e-03
GO:BP	GO:0009111	vitamin catabolic process	10	14	2.062e-03
GO:BP	GO:0070942	neutrophil mediated cytotoxicity	10	14	2.062e-03
GO:BP	GO:0042445	hormone metabolic process	76	243	2.132e-03
GO:BP	GO:0048519	negative regulation of biological process	1316	5865	2.239e-03
GO:BP	GO:0042832	defense response to protozoan	15	27	2.350e-03
GO:BP	GO:0000270	peptidoglycan metabolic process	6	6	2.505e-03
GO:BP	GO:0009253	peptidoglycan catabolic process	6	6	2.505e-03
GO:BP	GO:0051552	flavone metabolic process	6	6	2.505e-03
GO:BP	GO:0051673	disruption of plasma membrane integrity in another organism	6	6	2.505e-03
GO:BP	GO:0002786	regulation of antibacterial peptide production	6	6	2.505e-03
GO:BP	GO:0009582	detection of abiotic stimulus	50	145	2.505e-03
GO:BP	GO:0070943	neutrophil-mediated killing of symbiont cell	9	12	2.622e-03
GO:BP	GO:0032680	regulation of tumor necrosis factor production	55	164	2.649e-03
GO:BP	GO:0032640	tumor necrosis factor production	55	164	2.649e-03
GO:BP	GO:0031349	positive regulation of defense response	135	484	2.649e-03
GO:BP	GO:0016101	diterpenoid metabolic process	34	88	2.739e-03
GO:BP	GO:0030431	sleep	13	22	2.927e-03
GO:BP	GO:0120254	olefinic compound metabolic process	54	161	3.006e-03
GO:BP	GO:0002456	T cell mediated immunity	44	124	3.006e-03
GO:BP	GO:0050866	negative regulation of cell activation	66	207	3.129e-03
GO:BP	GO:0002707	negative regulation of lymphocyte mediated immunity	24	55	3.173e-03
GO:BP	GO:0002768	immune response-regulating cell surface receptor signaling pathway	98	334	3.194e-03
GO:BP	GO:0008228	opsonization	11	17	3.205e-03
GO:BP	GO:0071706	tumor necrosis factor superfamily cytokine production	56	169	3.205e-03
GO:BP	GO:1903555	regulation of tumor necrosis factor superfamily cytokine production	56	169	3.205e-03
GO:BP	GO:0006968	cellular defense response	23	52	3.364e-03
GO:BP	GO:0032615	interleukin-12 production	26	62	3.618e-03
GO:BP	GO:0032655	regulation of interleukin-12 production	26	62	3.618e-03
GO:BP	GO:0051607	defense response to virus	92	311	3.618e-03
GO:BP	GO:0002708	positive regulation of lymphocyte mediated immunity	44	125	3.618e-03
GO:BP	GO:0002710	negative regulation of T cell mediated immunity	15	28	3.752e-03
GO:BP	GO:0002275	myeloid cell activation involved in immune response	37	100	3.763e-03
GO:BP	GO:0032611	interleukin-1 beta production	35	93	3.806e-03
GO:BP	GO:0032651	regulation of interleukin-1 beta production	35	93	3.806e-03
GO:BP	GO:0030183	B cell differentiation	53	159	3.943e-03
GO:BP	GO:0071466	cellular response to xenobiotic stimulus	62	194	4.400e-03
GO:BP	GO:0034097	response to cytokine	239	937	4.901e-03
GO:BP	GO:0060259	regulation of feeding behavior	14	26	5.747e-03
GO:BP	GO:0032760	positive regulation of tumor necrosis factor production	37	102	5.854e-03
GO:BP	GO:0046456	icosanoid biosynthetic process	24	57	5.854e-03
GO:BP	GO:0032733	positive regulation of interleukin-10 production	19	41	5.913e-03
GO:BP	GO:0009072	aromatic amino acid metabolic process	19	41	5.913e-03
GO:BP	GO:0010817	regulation of hormone levels	148	548	5.969e-03
GO:BP	GO:0042755	eating behavior	18	38	6.100e-03
GO:BP	GO:0050482	arachidonate secretion	16	32	6.178e-03
GO:BP	GO:1903963	arachidonate transport	16	32	6.178e-03
GO:BP	GO:1903557	positive regulation of tumor necrosis factor superfamily cytokine production	38	106	6.239e-03
GO:BP	GO:0071347	cellular response to interleukin-1	38	106	6.239e-03
GO:BP	GO:0002440	production of molecular mediator of immune response	68	220	6.306e-03
GO:BP	GO:1901652	response to peptide	241	950	6.306e-03
GO:BP	GO:0032732	positive regulation of interleukin-1 production	28	71	6.656e-03
GO:BP	GO:0002820	negative regulation of adaptive immune response	25	61	6.970e-03
GO:BP	GO:0050795	regulation of behavior	29	75	7.694e-03
GO:BP	GO:0070944	neutrophil-mediated killing of bacterium	8	11	8.362e-03
GO:BP	GO:1903027	regulation of opsonization	8	11	8.362e-03
GO:BP	GO:0044058	regulation of digestive system process	18	39	8.822e-03
GO:BP	GO:0034374	low-density lipoprotein particle remodeling	10	16	9.089e-03
GO:BP	GO:0002675	positive regulation of acute inflammatory response	14	27	9.089e-03
GO:BP	GO:0015671	oxygen transport	10	16	9.089e-03
GO:BP	GO:0002719	negative regulation of cytokine production involved in immune response	16	33	9.254e-03
GO:BP	GO:0050891	multicellular organismal-level water homeostasis	16	33	9.254e-03
GO:BP	GO:0001562	response to protozoan	15	30	9.254e-03
GO:BP	GO:0050766	positive regulation of phagocytosis	27	69	9.556e-03
GO:BP	GO:0002688	regulation of leukocyte chemotaxis	42	123	9.628e-03
GO:BP	GO:0022407	regulation of cell-cell adhesion	130	478	9.660e-03
GO:BP	GO:0052696	flavonoid glucuronidation	5	5	1.015e-02
GO:BP	GO:0002803	positive regulation of antibacterial peptide production	5	5	1.015e-02
GO:BP	GO:1903028	positive regulation of opsonization	7	9	1.047e-02
GO:BP	GO:0001912	positive regulation of leukocyte mediated cytotoxicity	26	66	1.060e-02
GO:BP	GO:0042267	natural killer cell mediated cytotoxicity	28	73	1.081e-02
GO:BP	GO:0002827	positive regulation of T-helper 1 type immune response	11	19	1.105e-02
GO:BP	GO:0019370	leukotriene biosynthetic process	11	19	1.105e-02
GO:BP	GO:0007187	G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger	23	56	1.105e-02
GO:BP	GO:0035743	CD4-positive, alpha-beta T cell cytokine production	11	19	1.105e-02
GO:BP	GO:0002823	negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	23	56	1.105e-02
GO:BP	GO:0007198	adenylate cyclase-inhibiting serotonin receptor signaling pathway	6	7	1.179e-02
GO:BP	GO:0043299	leukocyte degranulation	31	84	1.180e-02
GO:BP	GO:0002683	negative regulation of immune system process	135	502	1.204e-02
GO:BP	GO:0035036	sperm-egg recognition	22	53	1.204e-02
GO:BP	GO:0050867	positive regulation of cell activation	104	372	1.216e-02
GO:BP	GO:0070555	response to interleukin-1	44	132	1.220e-02
GO:BP	GO:0002446	neutrophil mediated immunity	17	37	1.269e-02
GO:BP	GO:0010273	detoxification of copper ion	9	14	1.269e-02
GO:BP	GO:0002430	complement receptor mediated signaling pathway	9	14	1.269e-02
GO:BP	GO:1990169	stress response to copper ion	9	14	1.269e-02
GO:BP	GO:0072678	T cell migration	28	74	1.338e-02
GO:BP	GO:1902221	erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process	14	28	1.358e-02
GO:BP	GO:0055078	sodium ion homeostasis	20	47	1.432e-02
GO:BP	GO:0009988	cell-cell recognition	28	75	1.695e-02
GO:BP	GO:0008037	cell recognition	50	157	1.695e-02
GO:BP	GO:0044706	multi-multicellular organism process	64	212	1.695e-02
GO:BP	GO:0043330	response to exogenous dsRNA	21	51	1.764e-02
GO:BP	GO:0032621	interleukin-18 production	8	12	1.828e-02
GO:BP	GO:0016056	G protein-coupled opsin signaling pathway	8	12	1.828e-02
GO:BP	GO:0032661	regulation of interleukin-18 production	8	12	1.828e-02
GO:BP	GO:0009812	flavonoid metabolic process	8	12	1.828e-02
GO:BP	GO:0022408	negative regulation of cell-cell adhesion	58	189	1.862e-02
GO:BP	GO:0042130	negative regulation of T cell proliferation	27	72	1.900e-02
GO:BP	GO:0006775	fat-soluble vitamin metabolic process	20	48	1.924e-02
GO:BP	GO:0018149	peptide cross-linking	14	29	2.049e-02
GO:BP	GO:0006910	phagocytosis, recognition	14	29	2.049e-02
GO:BP	GO:0098581	detection of external biotic stimulus	13	26	2.058e-02
GO:BP	GO:0032729	positive regulation of type II interferon production	28	76	2.093e-02
GO:BP	GO:0048523	negative regulation of cellular process	1251	5646	2.251e-02
GO:BP	GO:0030098	lymphocyte differentiation	118	438	2.292e-02
GO:BP	GO:0046006	regulation of activated T cell proliferation	18	42	2.298e-02
GO:BP	GO:0044703	multi-organism reproductive process	61	203	2.426e-02
GO:BP	GO:0141005	transposable element silencing by heterochromatin formation	9	15	2.437e-02
GO:BP	GO:0007340	acrosome reaction	17	39	2.484e-02
GO:BP	GO:0002690	positive regulation of leukocyte chemotaxis	33	95	2.484e-02
GO:BP	GO:0032635	interleukin-6 production	48	152	2.487e-02
GO:BP	GO:0032675	regulation of interleukin-6 production	48	152	2.487e-02
GO:BP	GO:0002361	CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation	7	10	2.492e-02
GO:BP	GO:0008343	adult feeding behavior	7	10	2.492e-02
GO:BP	GO:0002696	positive regulation of leukocyte activation	98	355	2.492e-02
GO:BP	GO:0002676	regulation of chronic inflammatory response	7	10	2.492e-02
GO:BP	GO:0002765	immune response-inhibiting signal transduction	7	10	2.492e-02
GO:BP	GO:0002821	positive regulation of adaptive immune response	42	129	2.492e-02
GO:BP	GO:0071947	protein deubiquitination involved in ubiquitin-dependent protein catabolic process	7	10	2.492e-02
GO:BP	GO:0035747	natural killer cell chemotaxis	7	10	2.492e-02
GO:BP	GO:0006869	lipid transport	116	431	2.510e-02
GO:BP	GO:0002437	inflammatory response to antigenic stimulus	28	77	2.522e-02
GO:BP	GO:0006721	terpenoid metabolic process	34	99	2.549e-02
GO:BP	GO:0002764	immune response-regulating signaling pathway	133	504	2.619e-02
GO:BP	GO:0042269	regulation of natural killer cell mediated cytotoxicity	19	46	2.740e-02
GO:BP	GO:0034369	plasma lipoprotein particle remodeling	15	33	2.741e-02
GO:BP	GO:0042573	retinoic acid metabolic process	15	33	2.741e-02
GO:BP	GO:0034368	protein-lipid complex remodeling	15	33	2.741e-02
GO:BP	GO:0010669	epithelial structure maintenance	15	33	2.741e-02
GO:BP	GO:0007603	phototransduction, visible light	10	18	2.741e-02
GO:BP	GO:0002523	leukocyte migration involved in inflammatory response	11	21	2.925e-02
GO:BP	GO:0042745	circadian sleep/wake cycle	11	21	2.925e-02
GO:BP	GO:0043950	positive regulation of cAMP-mediated signaling	11	21	2.925e-02
GO:BP	GO:0002577	regulation of antigen processing and presentation	11	21	2.925e-02
GO:BP	GO:0032731	positive regulation of interleukin-1 beta production	23	60	2.925e-02
GO:BP	GO:0003352	regulation of cilium movement	18	43	2.957e-02
GO:BP	GO:0002438	acute inflammatory response to antigenic stimulus	13	27	2.957e-02
GO:BP	GO:0046634	regulation of alpha-beta T cell activation	38	115	2.962e-02
GO:BP	GO:0009074	aromatic amino acid family catabolic process	12	24	2.967e-02
GO:BP	GO:0002367	cytokine production involved in immune response	39	119	3.047e-02
GO:BP	GO:0002718	regulation of cytokine production involved in immune response	39	119	3.047e-02
GO:BP	GO:0002824	positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	40	123	3.138e-02
GO:BP	GO:0042088	T-helper 1 type immune response	20	50	3.165e-02
GO:BP	GO:2000501	regulation of natural killer cell chemotaxis	6	8	3.222e-02
GO:BP	GO:1903039	positive regulation of leukocyte cell-cell adhesion	77	271	3.222e-02
GO:BP	GO:0019369	arachidonate metabolic process	22	57	3.222e-02
GO:BP	GO:0070268	cornification	6	8	3.222e-02
GO:BP	GO:0032714	negative regulation of interleukin-5 production	6	8	3.222e-02
GO:BP	GO:0032741	positive regulation of interleukin-18 production	6	8	3.222e-02
GO:BP	GO:0014061	regulation of norepinephrine secretion	8	13	3.369e-02
GO:BP	GO:0046541	saliva secretion	8	13	3.369e-02
GO:BP	GO:0035745	T-helper 2 cell cytokine production	8	13	3.369e-02
GO:BP	GO:2000551	regulation of T-helper 2 cell cytokine production	8	13	3.369e-02
GO:BP	GO:0060456	positive regulation of digestive system process	8	13	3.369e-02
GO:BP	GO:0032720	negative regulation of tumor necrosis factor production	23	61	3.613e-02
GO:BP	GO:0032692	negative regulation of interleukin-1 production	15	34	3.738e-02
GO:BP	GO:0002702	positive regulation of production of molecular mediator of immune response	43	136	3.774e-02
GO:BP	GO:0042320	regulation of circadian sleep/wake cycle, REM sleep	4	4	3.774e-02
GO:BP	GO:0036101	leukotriene B4 catabolic process	4	4	3.774e-02
GO:BP	GO:0042376	phylloquinone catabolic process	4	4	3.774e-02
GO:BP	GO:0042377	vitamin K catabolic process	4	4	3.774e-02
GO:BP	GO:0042374	phylloquinone metabolic process	4	4	3.774e-02
GO:BP	GO:2000851	positive regulation of glucocorticoid secretion	4	4	3.774e-02
GO:BP	GO:0042747	circadian sleep/wake cycle, REM sleep	4	4	3.774e-02
GO:BP	GO:0002325	natural killer cell differentiation involved in immune response	4	4	3.774e-02
GO:BP	GO:0045938	positive regulation of circadian sleep/wake cycle, sleep	4	4	3.774e-02
GO:BP	GO:0002429	immune response-activating cell surface receptor signaling pathway	85	306	3.774e-02
GO:BP	GO:0060480	lung goblet cell differentiation	4	4	3.774e-02
GO:BP	GO:0032826	regulation of natural killer cell differentiation involved in immune response	4	4	3.774e-02
GO:BP	GO:0044278	disruption of cell wall in another organism	4	4	3.774e-02
GO:BP	GO:0051464	positive regulation of cortisol secretion	4	4	3.774e-02
GO:BP	GO:0002507	tolerance induction	14	31	3.812e-02
GO:BP	GO:0051969	regulation of transmission of nerve impulse	9	16	3.812e-02
GO:BP	GO:0034382	chylomicron remnant clearance	5	6	3.812e-02
GO:BP	GO:2000503	positive regulation of natural killer cell chemotaxis	5	6	3.812e-02
GO:BP	GO:0036100	leukotriene catabolic process	5	6	3.812e-02
GO:BP	GO:0010901	regulation of very-low-density lipoprotein particle remodeling	5	6	3.812e-02
GO:BP	GO:0035821	modulation of process of another organism	9	16	3.812e-02
GO:BP	GO:0097272	ammonium homeostasis	5	6	3.812e-02
GO:BP	GO:0022409	positive regulation of cell-cell adhesion	88	319	3.812e-02
GO:BP	GO:0072378	blood coagulation, fibrin clot formation	9	16	3.812e-02
GO:BP	GO:0046942	carboxylic acid transport	94	344	3.812e-02
GO:BP	GO:0042744	hydrogen peroxide catabolic process	14	31	3.812e-02
GO:BP	GO:0050731	positive regulation of peptidyl-tyrosine phosphorylation	50	164	3.908e-02
GO:BP	GO:0015849	organic acid transport	94	345	4.079e-02
GO:BP	GO:0032693	negative regulation of interleukin-10 production	10	19	4.083e-02
GO:BP	GO:0072376	protein activation cascade	10	19	4.083e-02
GO:BP	GO:0097501	stress response to metal ion	10	19	4.083e-02
GO:BP	GO:0022410	circadian sleep/wake cycle process	10	19	4.083e-02
GO:BP	GO:0098543	detection of other organism	10	19	4.083e-02
GO:BP	GO:0042749	regulation of circadian sleep/wake cycle	10	19	4.083e-02
GO:BP	GO:0048520	positive regulation of behavior	12	25	4.100e-02
GO:BP	GO:0042430	indole-containing compound metabolic process	12	25	4.100e-02
GO:BP	GO:0002833	positive regulation of response to biotic stimulus	102	379	4.100e-02
GO:BP	GO:1900015	regulation of cytokine production involved in inflammatory response	23	62	4.233e-02
GO:BP	GO:0002534	cytokine production involved in inflammatory response	23	62	4.233e-02
GO:BP	GO:0050878	regulation of body fluid levels	100	371	4.233e-02
GO:BP	GO:2000344	positive regulation of acrosome reaction	7	11	4.646e-02
GO:BP	GO:0034105	positive regulation of tissue remodeling	7	11	4.646e-02
GO:BP	GO:0032375	negative regulation of cholesterol transport	7	11	4.646e-02
GO:BP	GO:0032372	negative regulation of sterol transport	7	11	4.646e-02
GO:BP	GO:0030888	regulation of B cell proliferation	24	66	4.646e-02
GO:BP	GO:0002725	negative regulation of T cell cytokine production	7	11	4.646e-02
GO:BP	GO:0021562	vestibulocochlear nerve development	7	11	4.646e-02
GO:BP	GO:0042116	macrophage activation	35	107	4.681e-02
GO:BP	GO:0046636	negative regulation of alpha-beta T cell activation	18	45	4.681e-02
KEGG	KEGG:04740	Olfactory transduction	369	428	7.883e-179
KEGG	KEGG:04060	Cytokine-cytokine receptor interaction	154	291	2.327e-27
KEGG	KEGG:04080	Neuroactive ligand-receptor interaction	178	365	2.562e-26
KEGG	KEGG:05206	MicroRNAs in cancer	149	310	4.215e-21
KEGG	KEGG:05150	Staphylococcus aureus infection	60	86	1.731e-18
KEGG	KEGG:04061	Viral protein interaction with cytokine and cytokine receptor	63	98	1.101e-16
KEGG	KEGG:04742	Taste transduction	49	85	2.376e-10
KEGG	KEGG:00830	Retinol metabolism	41	68	1.610e-09
KEGG	KEGG:05320	Autoimmune thyroid disease	32	49	1.071e-08
KEGG	KEGG:05310	Asthma	21	27	8.154e-08
KEGG	KEGG:00980	Metabolism of xenobiotics by cytochrome P450	40	74	1.840e-07
KEGG	KEGG:04640	Hematopoietic cell lineage	46	92	3.330e-07
KEGG	KEGG:05204	Chemical carcinogenesis - DNA adducts	36	67	1.103e-06
KEGG	KEGG:04672	Intestinal immune network for IgA production	26	44	6.383e-06
KEGG	KEGG:00982	Drug metabolism - cytochrome P450	34	68	2.141e-05
KEGG	KEGG:04630	JAK-STAT signaling pathway	64	162	3.107e-05
KEGG	KEGG:05323	Rheumatoid arthritis	40	88	4.815e-05
KEGG	KEGG:00053	Ascorbate and aldarate metabolism	19	30	4.815e-05
KEGG	KEGG:05322	Systemic lupus erythematosus	54	132	4.823e-05
KEGG	KEGG:00140	Steroid hormone biosynthesis	31	62	4.823e-05
KEGG	KEGG:05332	Graft-versus-host disease	21	37	1.440e-04
KEGG	KEGG:04976	Bile secretion	39	89	1.440e-04
KEGG	KEGG:05321	Inflammatory bowel disease	30	62	1.440e-04
KEGG	KEGG:00590	Arachidonic acid metabolism	29	61	2.912e-04
KEGG	KEGG:05144	Malaria	24	49	7.806e-04
KEGG	KEGG:00591	Linoleic acid metabolism	17	30	8.847e-04
KEGG	KEGG:00040	Pentose and glucuronate interconversions	19	36	1.186e-03
KEGG	KEGG:00592	alpha-Linolenic acid metabolism	15	26	1.624e-03
KEGG	KEGG:05330	Allograft rejection	18	34	1.624e-03
KEGG	KEGG:04610	Complement and coagulation cascades	35	86	1.941e-03
KEGG	KEGG:04650	Natural killer cell mediated cytotoxicity	45	124	5.422e-03
KEGG	KEGG:04940	Type I diabetes mellitus	19	40	5.422e-03
KEGG	KEGG:00860	Porphyrin metabolism	20	43	5.422e-03
KEGG	KEGG:04975	Fat digestion and absorption	20	43	5.422e-03
KEGG	KEGG:05340	Primary immunodeficiency	18	37	5.422e-03
KEGG	KEGG:05164	Influenza A	57	167	5.688e-03
KEGG	KEGG:05152	Tuberculosis	59	175	6.375e-03
KEGG	KEGG:05143	African trypanosomiasis	17	36	1.011e-02
KEGG	KEGG:00350	Tyrosine metabolism	17	36	1.011e-02
KEGG	KEGG:04620	Toll-like receptor signaling pathway	38	106	1.465e-02
KEGG	KEGG:00983	Drug metabolism - other enzymes	30	79	1.527e-02
KEGG	KEGG:04514	Cell adhesion molecules	50	153	2.874e-02
KEGG	KEGG:05133	Pertussis	28	76	3.368e-02
KEGG	KEGG:04613	Neutrophil extracellular trap formation	59	188	3.520e-02
KEGG	KEGG:04972	Pancreatic secretion	35	102	4.363e-02
KEGG	KEGG:04657	IL-17 signaling pathway	32	92	4.766e-02

#write.csv(tableNR, "output/table_NRmotif.csv")

#GO:BP
tableNR_GOBP_d <- tableNR_d %>% 
  dplyr::filter(source=="GO:BP") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

#saveRDS(tableNR_GOBP, "data/tableNR_GOBP.RDS")

tableNR_GOBP_d %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("No Response Enriched GO:BP Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("GO:BP term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "GO analysis NR Dox only-2.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

#KEGG
tableNR_KEGG_d <- tableNR_d %>% 
  dplyr::filter(source=="KEGG") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

tableNR_KEGG_d %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("No Response Enriched KEGG Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("KEGG term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "GO analysis NR Dox only-3.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

Now let’s do the same thing but with the posterior probability rather than the clustlike

motif_NR_pp <- prob_motif_1

NRmotif_genes_pp <- gost(query = motif_NR_pp,
                      organism = "hsapiens",
                      ordered_query = FALSE,
                      measure_underrepresentation = FALSE,
                      evcodes = FALSE,
                      user_threshold = 0.05,
                      correction_method = c("fdr"),
                      sources = c("GO:BP", "KEGG"))

cormotifNFclust_pp <- gostplot(NRmotif_genes_pp, capped = FALSE, interactive = TRUE)
cormotifNFclust_pp

tableNR_pp <- NRmotif_genes_pp$result %>% 
  dplyr::select(c(source, term_id, term_name, intersection_size, term_size, p_value))

tableNR_pp %>% 
  mutate_at(.vars = 6, .funs = scales::label_scientific(digits=4)) %>% 
  kableExtra::kable(.,) %>% 
  kableExtra::kable_paper("striped", full_width = FALSE) %>% 
  kableExtra::kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "hover")) %>% 
  kableExtra::scroll_box(width = "100%", height = "400px")

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0050907	detection of chemical stimulus involved in sensory perception	389	443	4.186e-215
GO:BP	GO:0035195	miRNA-mediated post-transcriptional gene silencing	470	612	4.158e-211
GO:BP	GO:0050911	detection of chemical stimulus involved in sensory perception of smell	360	397	2.523e-210
GO:BP	GO:0007606	sensory perception of chemical stimulus	412	497	3.411e-208
GO:BP	GO:0035194	regulatory ncRNA-mediated post-transcriptional gene silencing	470	624	4.428e-205
GO:BP	GO:0016441	post-transcriptional gene silencing	471	630	3.359e-203
GO:BP	GO:0009593	detection of chemical stimulus	397	480	8.297e-200
GO:BP	GO:0007608	sensory perception of smell	367	423	2.725e-199
GO:BP	GO:0050906	detection of stimulus involved in sensory perception	410	515	1.984e-194
GO:BP	GO:0031047	regulatory ncRNA-mediated gene silencing	477	686	1.302e-183
GO:BP	GO:0051606	detection of stimulus	447	643	1.824e-171
GO:BP	GO:0007186	G protein-coupled receptor signaling pathway	681	1275	3.713e-171
GO:BP	GO:0007600	sensory perception	541	955	1.249e-148
GO:BP	GO:0050877	nervous system process	630	1489	1.697e-96
GO:BP	GO:0010608	post-transcriptional regulation of gene expression	505	1087	1.021e-93
GO:BP	GO:0003008	system process	775	2266	1.816e-67
GO:BP	GO:0010629	negative regulation of gene expression	609	1640	4.032e-66
GO:BP	GO:0042221	response to chemical	1051	3867	9.768e-37
GO:BP	GO:0065007	biological regulation	2806	12671	1.122e-33
GO:BP	GO:0050789	regulation of biological process	2722	12278	1.450e-31
GO:BP	GO:0042742	defense response to bacterium	156	326	6.334e-29
GO:BP	GO:0050794	regulation of cellular process	2631	11876	1.045e-28
GO:BP	GO:0006959	humoral immune response	131	254	3.440e-28
GO:BP	GO:0010558	negative regulation of macromolecule biosynthetic process	767	2772	1.341e-27
GO:BP	GO:0006952	defense response	543	1809	1.690e-27
GO:BP	GO:0032501	multicellular organismal process	1713	7234	5.059e-27
GO:BP	GO:0009890	negative regulation of biosynthetic process	775	2838	4.943e-26
GO:BP	GO:0031424	keratinization	62	82	1.446e-25
GO:BP	GO:0009617	response to bacterium	260	721	3.796e-24
GO:BP	GO:0019730	antimicrobial humoral response	79	131	1.953e-22
GO:BP	GO:0098542	defense response to other organism	383	1228	5.483e-22
GO:BP	GO:0043207	response to external biotic stimulus	451	1558	6.261e-19
GO:BP	GO:0009607	response to biotic stimulus	458	1593	1.223e-18
GO:BP	GO:0051707	response to other organism	449	1555	1.247e-18
GO:BP	GO:0140546	defense response to symbiont	345	1125	2.595e-18
GO:BP	GO:0007165	signal transduction	1396	5979	3.094e-17
GO:BP	GO:0010605	negative regulation of macromolecule metabolic process	807	3197	1.528e-16
GO:BP	GO:0141060	disruption of anatomical structure in another organism	59	98	1.541e-16
GO:BP	GO:0031640	killing of cells of another organism	55	91	1.746e-15
GO:BP	GO:0141061	disruption of cell in another organism	55	91	1.746e-15
GO:BP	GO:0001906	cell killing	97	219	6.596e-15
GO:BP	GO:0009605	response to external stimulus	616	2367	7.109e-15
GO:BP	GO:0061844	antimicrobial humoral immune response mediated by antimicrobial peptide	51	83	9.354e-15
GO:BP	GO:0045109	intermediate filament organization	47	73	1.045e-14
GO:BP	GO:0030216	keratinocyte differentiation	83	176	1.215e-14
GO:BP	GO:0006954	inflammatory response	262	847	3.704e-14
GO:BP	GO:0009892	negative regulation of metabolic process	838	3418	7.562e-14
GO:BP	GO:0044419	biological process involved in interspecies interaction between organisms	466	1724	9.825e-14
GO:BP	GO:0007154	cell communication	1475	6496	1.041e-13
GO:BP	GO:0023052	signaling	1470	6471	1.041e-13
GO:BP	GO:0006955	immune response	528	2008	2.218e-13
GO:BP	GO:0045087	innate immune response	289	977	5.592e-13
GO:BP	GO:0097530	granulocyte migration	72	156	4.663e-12
GO:BP	GO:1990266	neutrophil migration	63	129	7.202e-12
GO:BP	GO:0030593	neutrophil chemotaxis	55	106	1.134e-11
GO:BP	GO:0009913	epidermal cell differentiation	99	250	1.502e-11
GO:BP	GO:0071621	granulocyte chemotaxis	62	129	2.724e-11
GO:BP	GO:0050896	response to stimulus	1951	8993	3.425e-11
GO:BP	GO:0050909	sensory perception of taste	40	67	6.335e-11
GO:BP	GO:0030595	leukocyte chemotaxis	93	237	1.461e-10
GO:BP	GO:0050829	defense response to Gram-negative bacterium	48	91	1.772e-10
GO:BP	GO:0050830	defense response to Gram-positive bacterium	57	120	4.327e-10
GO:BP	GO:0007586	digestion	62	136	4.646e-10
GO:BP	GO:0045104	intermediate filament cytoskeleton organization	48	94	7.995e-10
GO:BP	GO:0002252	immune effector process	210	703	1.156e-09
GO:BP	GO:0045103	intermediate filament-based process	48	95	1.273e-09
GO:BP	GO:0097529	myeloid leukocyte migration	90	237	2.527e-09
GO:BP	GO:0050913	sensory perception of bitter taste	28	42	4.122e-09
GO:BP	GO:0007218	neuropeptide signaling pathway	52	110	4.324e-09
GO:BP	GO:0002323	natural killer cell activation involved in immune response	25	35	4.440e-09
GO:BP	GO:0070098	chemokine-mediated signaling pathway	45	90	8.242e-09
GO:BP	GO:0050912	detection of chemical stimulus involved in sensory perception of taste	28	43	9.089e-09
GO:BP	GO:0008544	epidermis development	130	394	1.004e-08
GO:BP	GO:0042100	B cell proliferation	50	106	1.056e-08
GO:BP	GO:0033141	positive regulation of peptidyl-serine phosphorylation of STAT protein	18	21	1.250e-08
GO:BP	GO:0052695	cellular glucuronidation	18	21	1.250e-08
GO:BP	GO:0050900	leukocyte migration	130	396	1.390e-08
GO:BP	GO:0071715	icosanoid transport	36	65	1.430e-08
GO:BP	GO:0019731	antibacterial humoral response	37	68	1.565e-08
GO:BP	GO:0002237	response to molecule of bacterial origin	119	355	1.900e-08
GO:BP	GO:0002376	immune system process	667	2796	2.433e-08
GO:BP	GO:0001580	detection of chemical stimulus involved in sensory perception of bitter taste	25	37	2.540e-08
GO:BP	GO:0060326	cell chemotaxis	109	319	3.022e-08
GO:BP	GO:0007338	single fertilization	68	169	3.164e-08
GO:BP	GO:0051716	cellular response to stimulus	1588	7320	5.696e-08
GO:BP	GO:0002697	regulation of immune effector process	124	381	6.115e-08
GO:BP	GO:0002548	monocyte chemotaxis	36	68	6.973e-08
GO:BP	GO:0032496	response to lipopolysaccharide	112	337	1.040e-07
GO:BP	GO:0071219	cellular response to molecule of bacterial origin	82	224	1.165e-07
GO:BP	GO:0048245	eosinophil chemotaxis	20	27	1.165e-07
GO:BP	GO:0007283	spermatogenesis	185	637	1.739e-07
GO:BP	GO:0019221	cytokine-mediated signaling pathway	152	503	2.680e-07
GO:BP	GO:1990869	cellular response to chemokine	45	99	3.137e-07
GO:BP	GO:1990868	response to chemokine	45	99	3.137e-07
GO:BP	GO:0071222	cellular response to lipopolysaccharide	78	214	3.448e-07
GO:BP	GO:0006953	acute-phase response	28	49	5.028e-07
GO:BP	GO:0009566	fertilization	77	212	5.028e-07
GO:BP	GO:0048232	male gamete generation	187	654	5.028e-07
GO:BP	GO:0033139	regulation of peptidyl-serine phosphorylation of STAT protein	18	24	5.301e-07
GO:BP	GO:0072677	eosinophil migration	21	31	5.486e-07
GO:BP	GO:0070661	leukocyte proliferation	113	351	5.932e-07
GO:BP	GO:0046651	lymphocyte proliferation	102	308	6.084e-07
GO:BP	GO:0002526	acute inflammatory response	47	109	1.047e-06
GO:BP	GO:0032943	mononuclear cell proliferation	103	315	1.072e-06
GO:BP	GO:0050832	defense response to fungus	31	59	1.114e-06
GO:BP	GO:0042501	serine phosphorylation of STAT protein	18	25	1.446e-06
GO:BP	GO:0048247	lymphocyte chemotaxis	32	63	1.872e-06
GO:BP	GO:0002366	leukocyte activation involved in immune response	99	305	2.968e-06
GO:BP	GO:0002263	cell activation involved in immune response	100	309	2.972e-06
GO:BP	GO:0043588	skin development	103	322	3.601e-06
GO:BP	GO:0006063	uronic acid metabolic process	18	26	3.636e-06
GO:BP	GO:0019585	glucuronate metabolic process	18	26	3.636e-06
GO:BP	GO:0002682	regulation of immune system process	377	1526	5.573e-06
GO:BP	GO:0140975	disruption of cellular anatomical structure in another organism	10	10	5.853e-06
GO:BP	GO:0071216	cellular response to biotic stimulus	84	251	6.641e-06
GO:BP	GO:0002274	myeloid leukocyte activation	81	240	7.350e-06
GO:BP	GO:0022600	digestive system process	44	105	7.350e-06
GO:BP	GO:0001775	cell activation	282	1098	7.629e-06
GO:BP	GO:0007631	feeding behavior	44	106	1.005e-05
GO:BP	GO:0045321	leukocyte activation	248	951	1.207e-05
GO:BP	GO:0007342	fusion of sperm to egg plasma membrane involved in single fertilization	19	30	1.236e-05
GO:BP	GO:0015718	monocarboxylic acid transport	64	179	1.471e-05
GO:BP	GO:0015908	fatty acid transport	47	118	1.634e-05
GO:BP	GO:0002699	positive regulation of immune effector process	83	253	1.921e-05
GO:BP	GO:0070663	regulation of leukocyte proliferation	86	265	1.986e-05
GO:BP	GO:0048609	multicellular organismal reproductive process	253	980	2.108e-05
GO:BP	GO:0060294	cilium movement involved in cell motility	60	167	2.767e-05
GO:BP	GO:0032309	icosanoid secretion	25	48	2.884e-05
GO:BP	GO:0007188	adenylate cyclase-modulating G protein-coupled receptor signaling pathway	81	248	3.140e-05
GO:BP	GO:0042330	taxis	134	465	3.356e-05
GO:BP	GO:0009620	response to fungus	32	70	3.454e-05
GO:BP	GO:0015732	prostaglandin transport	18	29	3.738e-05
GO:BP	GO:0097722	sperm motility	54	147	4.387e-05
GO:BP	GO:0030317	flagellated sperm motility	54	147	4.387e-05
GO:BP	GO:0002922	positive regulation of humoral immune response	15	22	5.627e-05
GO:BP	GO:0010468	regulation of gene expression	1192	5515	5.627e-05
GO:BP	GO:0006935	chemotaxis	132	463	7.290e-05
GO:BP	GO:0031341	regulation of cell killing	42	106	7.393e-05
GO:BP	GO:0022414	reproductive process	375	1556	7.399e-05
GO:BP	GO:0007259	cell surface receptor signaling pathway via JAK-STAT	59	168	7.451e-05
GO:BP	GO:0007286	spermatid development	71	214	7.509e-05
GO:BP	GO:0072676	lymphocyte migration	47	124	7.625e-05
GO:BP	GO:0060285	cilium-dependent cell motility	60	172	7.625e-05
GO:BP	GO:0001539	cilium or flagellum-dependent cell motility	60	172	7.625e-05
GO:BP	GO:0097696	cell surface receptor signaling pathway via STAT	61	176	7.939e-05
GO:BP	GO:0048240	sperm capacitation	19	33	8.393e-05
GO:BP	GO:0006690	icosanoid metabolic process	46	122	1.140e-04
GO:BP	GO:0002684	positive regulation of immune system process	267	1066	1.218e-04
GO:BP	GO:0045026	plasma membrane fusion	19	34	1.525e-04
GO:BP	GO:0048515	spermatid differentiation	72	222	1.525e-04
GO:BP	GO:0007200	phospholipase C-activating G protein-coupled receptor signaling pathway	44	116	1.529e-04
GO:BP	GO:0030101	natural killer cell activation	38	95	1.628e-04
GO:BP	GO:0098586	cellular response to virus	33	78	1.685e-04
GO:BP	GO:0071674	mononuclear cell migration	75	235	1.819e-04
GO:BP	GO:0002775	antimicrobial peptide production	9	10	1.836e-04
GO:BP	GO:0022412	cellular process involved in reproduction in multicellular organism	117	408	1.878e-04
GO:BP	GO:0042363	fat-soluble vitamin catabolic process	10	12	1.905e-04
GO:BP	GO:0032649	regulation of type II interferon production	44	117	1.905e-04
GO:BP	GO:0051873	killing by host of symbiont cells	17	29	1.988e-04
GO:BP	GO:0050670	regulation of lymphocyte proliferation	75	236	2.075e-04
GO:BP	GO:0032944	regulation of mononuclear cell proliferation	76	240	2.075e-04
GO:BP	GO:0050776	regulation of immune response	228	897	2.112e-04
GO:BP	GO:0006805	xenobiotic metabolic process	46	125	2.224e-04
GO:BP	GO:0009584	detection of visible light	18	32	2.247e-04
GO:BP	GO:0019953	sexual reproduction	273	1103	2.289e-04
GO:BP	GO:0032609	type II interferon production	44	118	2.339e-04
GO:BP	GO:0007276	gamete generation	211	822	2.339e-04
GO:BP	GO:0002703	regulation of leukocyte mediated immunity	76	243	3.303e-04
GO:BP	GO:0007204	positive regulation of cytosolic calcium ion concentration	57	169	3.870e-04
GO:BP	GO:0001909	leukocyte mediated cytotoxicity	48	135	3.987e-04
GO:BP	GO:1904892	regulation of receptor signaling pathway via STAT	40	106	4.371e-04
GO:BP	GO:0046425	regulation of receptor signaling pathway via JAK-STAT	38	99	4.562e-04
GO:BP	GO:0034341	response to type II interferon	51	147	4.595e-04
GO:BP	GO:0019755	one-carbon compound transport	15	25	4.622e-04
GO:BP	GO:0015670	carbon dioxide transport	11	15	4.622e-04
GO:BP	GO:0071346	cellular response to type II interferon	45	125	5.064e-04
GO:BP	GO:0001819	positive regulation of cytokine production	133	486	5.159e-04
GO:BP	GO:0052697	xenobiotic glucuronidation	7	7	5.160e-04
GO:BP	GO:0002285	lymphocyte activation involved in immune response	68	214	5.185e-04
GO:BP	GO:0002251	organ or tissue specific immune response	21	43	6.395e-04
GO:BP	GO:0050727	regulation of inflammatory response	108	381	6.607e-04
GO:BP	GO:0036230	granulocyte activation	23	50	8.576e-04
GO:BP	GO:0010556	regulation of macromolecule biosynthetic process	1199	5633	8.576e-04
GO:BP	GO:0002443	leukocyte mediated immunity	126	461	8.939e-04
GO:BP	GO:0050953	sensory perception of light stimulus	69	222	9.835e-04
GO:BP	GO:0070374	positive regulation of ERK1 and ERK2 cascade	66	210	9.894e-04
GO:BP	GO:0006691	leukotriene metabolic process	17	32	1.002e-03
GO:BP	GO:1903963	arachidonate transport	17	32	1.002e-03
GO:BP	GO:0050482	arachidonate secretion	17	32	1.002e-03
GO:BP	GO:0001817	regulation of cytokine production	194	765	1.089e-03
GO:BP	GO:0002286	T cell activation involved in immune response	44	125	1.110e-03
GO:BP	GO:0007601	visual perception	68	219	1.123e-03
GO:BP	GO:0032602	chemokine production	36	96	1.250e-03
GO:BP	GO:0032642	regulation of chemokine production	36	96	1.250e-03
GO:BP	GO:0001816	cytokine production	195	772	1.302e-03
GO:BP	GO:0007602	phototransduction	22	48	1.303e-03
GO:BP	GO:0030855	epithelial cell differentiation	188	741	1.360e-03
GO:BP	GO:0002920	regulation of humoral immune response	21	45	1.395e-03
GO:BP	GO:0050865	regulation of cell activation	160	616	1.423e-03
GO:BP	GO:0032689	negative regulation of type II interferon production	20	42	1.467e-03
GO:BP	GO:0042119	neutrophil activation	20	42	1.467e-03
GO:BP	GO:0009111	vitamin catabolic process	10	14	1.518e-03
GO:BP	GO:0032722	positive regulation of chemokine production	29	72	1.518e-03
GO:BP	GO:0002385	mucosal immune response	19	39	1.518e-03
GO:BP	GO:0048519	negative regulation of biological process	1241	5865	1.549e-03
GO:BP	GO:0007189	adenylate cyclase-activating G protein-coupled receptor signaling pathway	52	158	1.661e-03
GO:BP	GO:0032677	regulation of interleukin-8 production	32	83	1.693e-03
GO:BP	GO:0032637	interleukin-8 production	32	83	1.693e-03
GO:BP	GO:0050778	positive regulation of immune response	185	732	1.868e-03
GO:BP	GO:0070665	positive regulation of leukocyte proliferation	53	163	1.997e-03
GO:BP	GO:0051552	flavone metabolic process	6	6	2.215e-03
GO:BP	GO:0032757	positive regulation of interleukin-8 production	26	63	2.215e-03
GO:BP	GO:0042531	positive regulation of tyrosine phosphorylation of STAT protein	26	63	2.215e-03
GO:BP	GO:0051673	disruption of plasma membrane integrity in another organism	6	6	2.215e-03
GO:BP	GO:0002694	regulation of leukocyte activation	146	561	2.589e-03
GO:BP	GO:0001910	regulation of leukocyte mediated cytotoxicity	34	92	2.617e-03
GO:BP	GO:0002687	positive regulation of leukocyte migration	50	153	2.698e-03
GO:BP	GO:0002784	regulation of antimicrobial peptide production	7	8	2.774e-03
GO:BP	GO:0002778	antibacterial peptide production	7	8	2.774e-03
GO:BP	GO:0002760	positive regulation of antimicrobial humoral response	7	8	2.774e-03
GO:BP	GO:0002685	regulation of leukocyte migration	69	230	2.869e-03
GO:BP	GO:0002544	chronic inflammatory response	12	20	2.963e-03
GO:BP	GO:0009889	regulation of biosynthetic process	1222	5795	3.169e-03
GO:BP	GO:0071466	cellular response to xenobiotic stimulus	60	194	3.177e-03
GO:BP	GO:0002706	regulation of lymphocyte mediated immunity	57	182	3.215e-03
GO:BP	GO:0009583	detection of light stimulus	27	68	3.381e-03
GO:BP	GO:0015669	gas transport	13	23	3.404e-03
GO:BP	GO:0042755	eating behavior	18	38	3.473e-03
GO:BP	GO:0042113	B cell activation	81	282	3.646e-03
GO:BP	GO:0060259	regulation of feeding behavior	14	26	3.658e-03
GO:BP	GO:0051250	negative regulation of lymphocyte activation	51	159	3.697e-03
GO:BP	GO:0042129	regulation of T cell proliferation	56	180	4.370e-03
GO:BP	GO:0051249	regulation of lymphocyte activation	130	497	4.639e-03
GO:BP	GO:0071347	cellular response to interleukin-1	37	106	4.745e-03
GO:BP	GO:0006968	cellular defense response	22	52	4.802e-03
GO:BP	GO:0002444	myeloid leukocyte mediated immunity	39	114	5.104e-03
GO:BP	GO:0044058	regulation of digestive system process	18	39	5.104e-03
GO:BP	GO:0071345	cellular response to cytokine stimulus	206	843	5.201e-03
GO:BP	GO:0050891	multicellular organismal-level water homeostasis	16	33	5.739e-03
GO:BP	GO:0007187	G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger	23	56	5.739e-03
GO:BP	GO:0042509	regulation of tyrosine phosphorylation of STAT protein	28	74	6.331e-03
GO:BP	GO:0035036	sperm-egg recognition	22	53	6.523e-03
GO:BP	GO:0007159	leukocyte cell-cell adhesion	108	404	6.635e-03
GO:BP	GO:0002759	regulation of antimicrobial humoral response	8	11	6.837e-03
GO:BP	GO:0015671	oxygen transport	10	16	6.866e-03
GO:BP	GO:0050671	positive regulation of lymphocyte proliferation	46	143	6.903e-03
GO:BP	GO:0003341	cilium movement	63	212	6.916e-03
GO:BP	GO:0030183	B cell differentiation	50	159	6.916e-03
GO:BP	GO:0070555	response to interleukin-1	43	132	7.954e-03
GO:BP	GO:0050795	regulation of behavior	28	75	7.954e-03
GO:BP	GO:0002673	regulation of acute inflammatory response	20	47	8.172e-03
GO:BP	GO:0055078	sodium ion homeostasis	20	47	8.172e-03
GO:BP	GO:0060295	regulation of cilium movement involved in cell motility	15	31	8.874e-03
GO:BP	GO:0030431	sleep	12	22	8.874e-03
GO:BP	GO:1901317	regulation of flagellated sperm motility	12	22	8.874e-03
GO:BP	GO:0046649	lymphocyte activation	192	787	8.874e-03
GO:BP	GO:1902019	regulation of cilium-dependent cell motility	15	31	8.874e-03
GO:BP	GO:0002695	negative regulation of leukocyte activation	56	185	8.874e-03
GO:BP	GO:0001523	retinoid metabolic process	30	83	9.045e-03
GO:BP	GO:0120254	olefinic compound metabolic process	50	161	9.224e-03
GO:BP	GO:0042102	positive regulation of T cell proliferation	35	102	9.331e-03
GO:BP	GO:0052696	flavonoid glucuronidation	5	5	9.336e-03
GO:BP	GO:0007260	tyrosine phosphorylation of STAT protein	28	76	9.778e-03
GO:BP	GO:1990169	stress response to copper ion	9	14	1.000e-02
GO:BP	GO:0070942	neutrophil mediated cytotoxicity	9	14	1.000e-02
GO:BP	GO:0010273	detoxification of copper ion	9	14	1.000e-02
GO:BP	GO:0002225	positive regulation of antimicrobial peptide production	6	7	1.032e-02
GO:BP	GO:0007198	adenylate cyclase-inhibiting serotonin receptor signaling pathway	6	7	1.032e-02
GO:BP	GO:0009581	detection of external stimulus	45	142	1.068e-02
GO:BP	GO:0032946	positive regulation of mononuclear cell proliferation	46	146	1.068e-02
GO:BP	GO:0031343	positive regulation of cell killing	27	73	1.124e-02
GO:BP	GO:0016101	diterpenoid metabolic process	31	88	1.160e-02
GO:BP	GO:0002688	regulation of leukocyte chemotaxis	40	123	1.228e-02
GO:BP	GO:0002705	positive regulation of leukocyte mediated immunity	46	147	1.247e-02
GO:BP	GO:0003006	developmental process involved in reproduction	241	1022	1.293e-02
GO:BP	GO:0002275	myeloid cell activation involved in immune response	34	100	1.300e-02
GO:BP	GO:0018149	peptide cross-linking	14	29	1.355e-02
GO:BP	GO:0032680	regulation of tumor necrosis factor production	50	164	1.393e-02
GO:BP	GO:0032640	tumor necrosis factor production	50	164	1.393e-02
GO:BP	GO:0030277	maintenance of gastrointestinal epithelium	12	23	1.409e-02
GO:BP	GO:1903038	negative regulation of leukocyte cell-cell adhesion	43	136	1.452e-02
GO:BP	GO:0070943	neutrophil-mediated killing of symbiont cell	8	12	1.472e-02
GO:BP	GO:0007281	germ cell development	98	370	1.557e-02
GO:BP	GO:0071706	tumor necrosis factor superfamily cytokine production	51	169	1.569e-02
GO:BP	GO:1903555	regulation of tumor necrosis factor superfamily cytokine production	51	169	1.569e-02
GO:BP	GO:0034097	response to cytokine	222	937	1.587e-02
GO:BP	GO:1903037	regulation of leukocyte cell-cell adhesion	97	366	1.598e-02
GO:BP	GO:0050863	regulation of T cell activation	99	375	1.621e-02
GO:BP	GO:0050868	negative regulation of T cell activation	40	125	1.673e-02
GO:BP	GO:0009988	cell-cell recognition	27	75	1.726e-02
GO:BP	GO:0042573	retinoic acid metabolic process	15	33	1.819e-02
GO:BP	GO:0032735	positive regulation of interleukin-12 production	18	43	1.820e-02
GO:BP	GO:0019369	arachidonate metabolic process	22	57	1.824e-02
GO:BP	GO:0032760	positive regulation of tumor necrosis factor production	34	102	1.838e-02
GO:BP	GO:1903557	positive regulation of tumor necrosis factor superfamily cytokine production	35	106	1.870e-02
GO:BP	GO:1901652	response to peptide	224	950	1.909e-02
GO:BP	GO:0048523	negative regulation of cellular process	1178	5646	1.923e-02
GO:BP	GO:0042832	defense response to protozoan	13	27	2.085e-02
GO:BP	GO:0071947	protein deubiquitination involved in ubiquitin-dependent protein catabolic process	7	10	2.095e-02
GO:BP	GO:0002690	positive regulation of leukocyte chemotaxis	32	95	2.095e-02
GO:BP	GO:0035747	natural killer cell chemotaxis	7	10	2.095e-02
GO:BP	GO:0008343	adult feeding behavior	7	10	2.095e-02
GO:BP	GO:0050729	positive regulation of inflammatory response	45	147	2.190e-02
GO:BP	GO:0032945	negative regulation of mononuclear cell proliferation	30	88	2.394e-02
GO:BP	GO:0043330	response to exogenous dsRNA	20	51	2.416e-02
GO:BP	GO:0070664	negative regulation of leukocyte proliferation	32	96	2.517e-02
GO:BP	GO:0032615	interleukin-12 production	23	62	2.521e-02
GO:BP	GO:0032655	regulation of interleukin-12 production	23	62	2.521e-02
GO:BP	GO:0002698	negative regulation of immune effector process	38	120	2.651e-02
GO:BP	GO:0009072	aromatic amino acid metabolic process	17	41	2.750e-02
GO:BP	GO:0006775	fat-soluble vitamin metabolic process	19	48	2.776e-02
GO:BP	GO:0060456	positive regulation of digestive system process	8	13	2.869e-02
GO:BP	GO:2000501	regulation of natural killer cell chemotaxis	6	8	2.914e-02
GO:BP	GO:0032653	regulation of interleukin-10 production	22	59	2.914e-02
GO:BP	GO:0009582	detection of abiotic stimulus	44	145	2.914e-02
GO:BP	GO:0070268	cornification	6	8	2.914e-02
GO:BP	GO:0032613	interleukin-10 production	22	59	2.914e-02
GO:BP	GO:1902221	erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process	13	28	2.994e-02
GO:BP	GO:0002227	innate immune response in mucosa	13	28	2.994e-02
GO:BP	GO:0051969	regulation of transmission of nerve impulse	9	16	3.206e-02
GO:BP	GO:0048520	positive regulation of behavior	12	25	3.206e-02
GO:BP	GO:0060046	regulation of acrosome reaction	9	16	3.206e-02
GO:BP	GO:0034374	low-density lipoprotein particle remodeling	9	16	3.206e-02
GO:BP	GO:0072378	blood coagulation, fibrin clot formation	9	16	3.206e-02
GO:BP	GO:0035821	modulation of process of another organism	9	16	3.206e-02
GO:BP	GO:0097501	stress response to metal ion	10	19	3.338e-02
GO:BP	GO:0019370	leukotriene biosynthetic process	10	19	3.338e-02
GO:BP	GO:0072376	protein activation cascade	10	19	3.338e-02
GO:BP	GO:0050878	regulation of body fluid levels	96	371	3.435e-02
GO:BP	GO:0045938	positive regulation of circadian sleep/wake cycle, sleep	4	4	3.626e-02
GO:BP	GO:0032826	regulation of natural killer cell differentiation involved in immune response	4	4	3.626e-02
GO:BP	GO:0036100	leukotriene catabolic process	5	6	3.626e-02
GO:BP	GO:0002325	natural killer cell differentiation involved in immune response	4	4	3.626e-02
GO:BP	GO:0002786	regulation of antibacterial peptide production	5	6	3.626e-02
GO:BP	GO:0051464	positive regulation of cortisol secretion	4	4	3.626e-02
GO:BP	GO:0001818	negative regulation of cytokine production	77	288	3.626e-02
GO:BP	GO:0036101	leukotriene B4 catabolic process	4	4	3.626e-02
GO:BP	GO:0097272	ammonium homeostasis	5	6	3.626e-02
GO:BP	GO:2000503	positive regulation of natural killer cell chemotaxis	5	6	3.626e-02
GO:BP	GO:0060480	lung goblet cell differentiation	4	4	3.626e-02
GO:BP	GO:0042110	T cell activation	137	558	3.626e-02
GO:BP	GO:2000851	positive regulation of glucocorticoid secretion	4	4	3.626e-02
GO:BP	GO:0042747	circadian sleep/wake cycle, REM sleep	4	4	3.626e-02
GO:BP	GO:0042377	vitamin K catabolic process	4	4	3.626e-02
GO:BP	GO:0044278	disruption of cell wall in another organism	4	4	3.626e-02
GO:BP	GO:0042374	phylloquinone metabolic process	4	4	3.626e-02
GO:BP	GO:0042320	regulation of circadian sleep/wake cycle, REM sleep	4	4	3.626e-02
GO:BP	GO:0042376	phylloquinone catabolic process	4	4	3.626e-02
GO:BP	GO:0002825	regulation of T-helper 1 type immune response	14	32	3.641e-02
GO:BP	GO:0050672	negative regulation of lymphocyte proliferation	29	87	3.754e-02
GO:BP	GO:0042116	macrophage activation	34	107	3.950e-02
GO:BP	GO:0046456	icosanoid biosynthetic process	21	57	4.023e-02
GO:BP	GO:0070944	neutrophil-mediated killing of bacterium	7	11	4.089e-02
GO:BP	GO:0021562	vestibulocochlear nerve development	7	11	4.089e-02
GO:BP	GO:0050866	negative regulation of cell activation	58	207	4.102e-02
GO:BP	GO:0002228	natural killer cell mediated immunity	26	76	4.169e-02
GO:BP	GO:0002768	immune response-regulating cell surface receptor signaling pathway	87	334	4.214e-02
GO:BP	GO:0002715	regulation of natural killer cell mediated immunity	19	50	4.274e-02
GO:BP	GO:0098581	detection of external biotic stimulus	12	26	4.398e-02
GO:BP	GO:0046427	positive regulation of receptor signaling pathway via JAK-STAT	17	43	4.437e-02
GO:BP	GO:0008037	cell recognition	46	157	4.438e-02
GO:BP	GO:0010817	regulation of hormone levels	134	548	4.551e-02
GO:BP	GO:0046942	carboxylic acid transport	89	344	4.588e-02
GO:BP	GO:0034116	positive regulation of heterotypic cell-cell adhesion	8	14	4.751e-02
GO:BP	GO:0002430	complement receptor mediated signaling pathway	8	14	4.751e-02
GO:BP	GO:0042098	T cell proliferation	59	213	4.886e-02
GO:BP	GO:0015849	organic acid transport	89	345	4.971e-02
GO:BP	GO:0008228	opsonization	9	17	4.984e-02
KEGG	KEGG:04740	Olfactory transduction	367	428	4.270e-187
KEGG	KEGG:04060	Cytokine-cytokine receptor interaction	146	291	7.455e-26
KEGG	KEGG:04080	Neuroactive ligand-receptor interaction	167	365	4.428e-24
KEGG	KEGG:05206	MicroRNAs in cancer	146	310	1.499e-22
KEGG	KEGG:05150	Staphylococcus aureus infection	57	86	2.620e-17
KEGG	KEGG:04061	Viral protein interaction with cytokine and cytokine receptor	59	98	4.701e-15
KEGG	KEGG:05320	Autoimmune thyroid disease	32	49	2.255e-09
KEGG	KEGG:00830	Retinol metabolism	39	68	4.976e-09
KEGG	KEGG:04742	Taste transduction	45	85	6.461e-09
KEGG	KEGG:00980	Metabolism of xenobiotics by cytochrome P450	38	74	4.653e-07
KEGG	KEGG:04640	Hematopoietic cell lineage	43	92	1.754e-06
KEGG	KEGG:05310	Asthma	19	27	1.993e-06
KEGG	KEGG:05204	Chemical carcinogenesis - DNA adducts	34	67	3.014e-06
KEGG	KEGG:00982	Drug metabolism - cytochrome P450	33	68	1.630e-05
KEGG	KEGG:00053	Ascorbate and aldarate metabolism	19	30	1.996e-05
KEGG	KEGG:05323	Rheumatoid arthritis	39	88	2.714e-05
KEGG	KEGG:04672	Intestinal immune network for IgA production	24	44	3.152e-05
KEGG	KEGG:05332	Graft-versus-host disease	21	37	5.696e-05
KEGG	KEGG:04630	JAK-STAT signaling pathway	60	162	6.796e-05
KEGG	KEGG:04976	Bile secretion	38	89	8.880e-05
KEGG	KEGG:05322	Systemic lupus erythematosus	50	132	1.899e-04
KEGG	KEGG:00590	Arachidonic acid metabolism	28	61	2.694e-04
KEGG	KEGG:05144	Malaria	24	49	2.694e-04
KEGG	KEGG:00140	Steroid hormone biosynthesis	28	62	3.647e-04
KEGG	KEGG:00591	Linoleic acid metabolism	17	30	3.743e-04
KEGG	KEGG:00040	Pentose and glucuronate interconversions	19	36	4.713e-04
KEGG	KEGG:00592	alpha-Linolenic acid metabolism	15	26	7.805e-04
KEGG	KEGG:05321	Inflammatory bowel disease	27	62	9.482e-04
KEGG	KEGG:05330	Allograft rejection	17	34	2.548e-03
KEGG	KEGG:04650	Natural killer cell mediated cytotoxicity	44	124	2.548e-03
KEGG	KEGG:00983	Drug metabolism - other enzymes	30	79	6.442e-03
KEGG	KEGG:04610	Complement and coagulation cascades	32	86	6.442e-03
KEGG	KEGG:04975	Fat digestion and absorption	19	43	7.038e-03
KEGG	KEGG:00860	Porphyrin metabolism	19	43	7.038e-03
KEGG	KEGG:04940	Type I diabetes mellitus	18	40	7.204e-03
KEGG	KEGG:05340	Primary immunodeficiency	17	37	7.299e-03
KEGG	KEGG:05152	Tuberculosis	55	175	1.191e-02
KEGG	KEGG:00350	Tyrosine metabolism	16	36	1.478e-02
KEGG	KEGG:05143	African trypanosomiasis	16	36	1.478e-02
KEGG	KEGG:04972	Pancreatic secretion	35	102	1.573e-02
KEGG	KEGG:04620	Toll-like receptor signaling pathway	36	106	1.634e-02
KEGG	KEGG:05164	Influenza A	52	167	1.752e-02
KEGG	KEGG:04514	Cell adhesion molecules	48	153	2.096e-02
KEGG	KEGG:04950	Maturity onset diabetes of the young	12	26	3.351e-02
KEGG	KEGG:04657	IL-17 signaling pathway	31	92	3.373e-02
KEGG	KEGG:00565	Ether lipid metabolism	19	50	4.195e-02

#write.csv(tableNR, "output/table_NRmotif.csv")

#GO:BP
tableNR_GOBP_pp <- tableNR_pp %>% 
  dplyr::filter(source=="GO:BP") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

#saveRDS(tableNR_GOBP_pp, "data/tableNR_GOBP_postprob.RDS")

tableNR_GOBP_pp %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("No Response Enriched GO:BP Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("GO:BP term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "No Response Motif Genes Post Prob-2.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

#KEGG
tableNR_KEGG_pp <- tableNR_pp %>% 
  dplyr::filter(source=="KEGG") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

tableNR_KEGG_pp %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("No Response Enriched KEGG Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("KEGG term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "No Response Motif Genes Post Prob-3.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

The Acute Response had no genes pop up for clustlike at the cutoff of > 0.5 However, when we changed the cutoff and used post prob we got some genes, so let’s use them for GO analysis This is from motif 2, where there is a light gray box in the first study (DOX 24hr)

motif_AR_pp <- prob_motif_2

ARmotif_genes_pp <- gost(query = motif_AR_pp,
                      organism = "hsapiens",
                      ordered_query = FALSE,
                      measure_underrepresentation = FALSE,
                      evcodes = FALSE,
                      user_threshold = 0.05,
                      correction_method = c("fdr"),
                      sources = c("GO:BP", "KEGG"))

cormotifARclust_pp <- gostplot(ARmotif_genes_pp, capped = FALSE, interactive = TRUE)
cormotifARclust_pp

tableAR_pp <- ARmotif_genes_pp$result %>% 
  dplyr::select(c(source, term_id, term_name, intersection_size, term_size, p_value))

tableAR_pp %>% 
  mutate_at(.vars = 6, .funs = scales::label_scientific(digits=4)) %>% 
  kableExtra::kable(.,) %>% 
  kableExtra::kable_paper("striped", full_width = FALSE) %>% 
  kableExtra::kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "hover")) %>% 
  kableExtra::scroll_box(width = "100%", height = "400px")

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0032501	multicellular organismal process	557	7234	7.251e-14
GO:BP	GO:0032502	developmental process	488	6478	1.846e-09
GO:BP	GO:0022414	reproductive process	156	1556	9.758e-09
GO:BP	GO:0048856	anatomical structure development	448	5924	1.088e-08
GO:BP	GO:0006952	defense response	172	1809	3.330e-08
GO:BP	GO:0009605	response to external stimulus	207	2367	3.880e-07
GO:BP	GO:0048513	animal organ development	253	3047	3.993e-07
GO:BP	GO:0045165	cell fate commitment	46	291	3.993e-07
GO:BP	GO:0002684	positive regulation of immune system process	111	1066	6.467e-07
GO:BP	GO:0050670	regulation of lymphocyte proliferation	39	236	1.851e-06
GO:BP	GO:0032944	regulation of mononuclear cell proliferation	39	240	2.746e-06
GO:BP	GO:0006954	inflammatory response	91	847	3.922e-06
GO:BP	GO:0070663	regulation of leukocyte proliferation	41	265	4.091e-06
GO:BP	GO:0007423	sensory organ development	71	612	7.712e-06
GO:BP	GO:0048663	neuron fate commitment	19	73	9.422e-06
GO:BP	GO:0002682	regulation of immune system process	140	1526	9.422e-06
GO:BP	GO:0042129	regulation of T cell proliferation	31	180	1.720e-05
GO:BP	GO:0050727	regulation of inflammatory response	50	381	1.873e-05
GO:BP	GO:0002706	regulation of lymphocyte mediated immunity	31	182	1.902e-05
GO:BP	GO:0003008	system process	190	2266	1.902e-05
GO:BP	GO:0002703	regulation of leukocyte mediated immunity	37	243	2.066e-05
GO:BP	GO:0002819	regulation of adaptive immune response	33	204	2.343e-05
GO:BP	GO:0050729	positive regulation of inflammatory response	27	147	2.389e-05
GO:BP	GO:0098542	defense response to other organism	116	1228	2.482e-05
GO:BP	GO:0140546	defense response to symbiont	108	1125	3.060e-05
GO:BP	GO:0003006	developmental process involved in reproduction	100	1022	3.624e-05
GO:BP	GO:0051239	regulation of multicellular organismal process	232	2928	3.828e-05
GO:BP	GO:0045087	innate immune response	96	977	4.823e-05
GO:BP	GO:0046651	lymphocyte proliferation	42	308	4.823e-05
GO:BP	GO:0042098	T cell proliferation	33	213	4.880e-05
GO:BP	GO:0009582	detection of abiotic stimulus	26	145	5.036e-05
GO:BP	GO:0002697	regulation of immune effector process	48	381	6.727e-05
GO:BP	GO:0050776	regulation of immune response	89	897	7.659e-05
GO:BP	GO:0032943	mononuclear cell proliferation	42	315	7.659e-05
GO:BP	GO:0045321	leukocyte activation	93	951	7.729e-05
GO:BP	GO:0048562	embryonic organ morphogenesis	41	305	7.831e-05
GO:BP	GO:0002822	regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	30	189	8.037e-05
GO:BP	GO:0006690	icosanoid metabolic process	23	122	8.037e-05
GO:BP	GO:0019953	sexual reproduction	104	1103	8.040e-05
GO:BP	GO:0007275	multicellular organism development	340	4658	8.040e-05
GO:BP	GO:0009581	detection of external stimulus	25	142	9.037e-05
GO:BP	GO:0046456	icosanoid biosynthetic process	15	57	9.037e-05
GO:BP	GO:0051707	response to other organism	136	1555	9.037e-05
GO:BP	GO:0043207	response to external biotic stimulus	136	1558	9.679e-05
GO:BP	GO:0050671	positive regulation of lymphocyte proliferation	25	143	9.679e-05
GO:BP	GO:0070665	positive regulation of leukocyte proliferation	27	163	1.040e-04
GO:BP	GO:0050896	response to stimulus	600	8993	1.238e-04
GO:BP	GO:0009887	animal organ morphogenesis	98	1037	1.273e-04
GO:BP	GO:0031347	regulation of defense response	79	783	1.273e-04
GO:BP	GO:0032946	positive regulation of mononuclear cell proliferation	25	146	1.301e-04
GO:BP	GO:0070661	leukocyte proliferation	44	351	1.491e-04
GO:BP	GO:0007601	visual perception	32	219	1.620e-04
GO:BP	GO:0042102	positive regulation of T cell proliferation	20	102	1.652e-04
GO:BP	GO:0009607	response to biotic stimulus	137	1593	1.652e-04
GO:BP	GO:0071695	anatomical structure maturation	37	274	1.666e-04
GO:BP	GO:0007155	cell adhesion	131	1511	1.819e-04
GO:BP	GO:0048731	system development	294	3985	1.946e-04
GO:BP	GO:0050953	sensory perception of light stimulus	32	222	1.952e-04
GO:BP	GO:0051240	positive regulation of multicellular organismal process	140	1644	1.952e-04
GO:BP	GO:0050778	positive regulation of immune response	74	732	2.151e-04
GO:BP	GO:0090596	sensory organ morphogenesis	38	290	2.283e-04
GO:BP	GO:0032101	regulation of response to external stimulus	99	1071	2.358e-04
GO:BP	GO:0031349	positive regulation of defense response	54	484	3.011e-04
GO:BP	GO:0019226	transmission of nerve impulse	16	73	3.411e-04
GO:BP	GO:0032649	regulation of type II interferon production	21	117	3.411e-04
GO:BP	GO:0055085	transmembrane transport	131	1538	3.795e-04
GO:BP	GO:0032609	type II interferon production	21	118	3.795e-04
GO:BP	GO:0002699	positive regulation of immune effector process	34	253	3.983e-04
GO:BP	GO:0009617	response to bacterium	72	721	3.987e-04
GO:BP	GO:0032103	positive regulation of response to external stimulus	64	619	4.421e-04
GO:BP	GO:0048609	multicellular organismal reproductive process	91	980	4.486e-04
GO:BP	GO:0007186	G protein-coupled receptor signaling pathway	112	1275	4.767e-04
GO:BP	GO:0001775	cell activation	99	1098	5.829e-04
GO:BP	GO:0001819	positive regulation of cytokine production	53	486	6.151e-04
GO:BP	GO:0001708	cell fate specification	20	113	6.192e-04
GO:BP	GO:0046649	lymphocyte activation	76	787	6.625e-04
GO:BP	GO:0048880	sensory system development	47	414	6.795e-04
GO:BP	GO:0002456	T cell mediated immunity	21	124	6.948e-04
GO:BP	GO:0030154	cell differentiation	314	4381	6.948e-04
GO:BP	GO:0021700	developmental maturation	41	343	6.948e-04
GO:BP	GO:0002696	positive regulation of leukocyte activation	42	355	6.948e-04
GO:BP	GO:0032098	regulation of appetite	8	20	6.948e-04
GO:BP	GO:0048869	cellular developmental process	314	4382	6.948e-04
GO:BP	GO:0001817	regulation of cytokine production	74	765	7.456e-04
GO:BP	GO:0065007	biological regulation	802	12671	7.513e-04
GO:BP	GO:0007631	feeding behavior	19	106	7.513e-04
GO:BP	GO:0009653	anatomical structure morphogenesis	206	2692	7.513e-04
GO:BP	GO:0048469	cell maturation	29	208	7.582e-04
GO:BP	GO:0030856	regulation of epithelial cell differentiation	24	156	8.155e-04
GO:BP	GO:0042531	positive regulation of tyrosine phosphorylation of STAT protein	14	63	8.495e-04
GO:BP	GO:0150063	visual system development	46	408	8.572e-04
GO:BP	GO:0006811	monoatomic ion transport	109	1256	8.577e-04
GO:BP	GO:0050867	positive regulation of cell activation	43	372	8.706e-04
GO:BP	GO:0002694	regulation of leukocyte activation	58	561	9.090e-04
GO:BP	GO:0001816	cytokine production	74	772	9.090e-04
GO:BP	GO:0030858	positive regulation of epithelial cell differentiation	14	64	9.657e-04
GO:BP	GO:0003341	cilium movement	29	212	9.964e-04
GO:BP	GO:0002821	positive regulation of adaptive immune response	21	129	1.080e-03
GO:BP	GO:0043010	camera-type eye development	41	352	1.081e-03
GO:BP	GO:0071715	icosanoid transport	14	65	1.119e-03
GO:BP	GO:0044703	multi-organism reproductive process	28	203	1.145e-03
GO:BP	GO:0048584	positive regulation of response to stimulus	178	2293	1.269e-03
GO:BP	GO:0001654	eye development	45	404	1.269e-03
GO:BP	GO:0030855	epithelial cell differentiation	71	741	1.269e-03
GO:BP	GO:0050877	nervous system process	124	1489	1.285e-03
GO:BP	GO:0044419	biological process involved in interspecies interaction between organisms	140	1724	1.285e-03
GO:BP	GO:0006955	immune response	159	2008	1.299e-03
GO:BP	GO:0021515	cell differentiation in spinal cord	12	50	1.307e-03
GO:BP	GO:0009988	cell-cell recognition	15	75	1.319e-03
GO:BP	GO:0042110	T cell activation	57	558	1.319e-03
GO:BP	GO:0007610	behavior	65	665	1.428e-03
GO:BP	GO:0022412	cellular process involved in reproduction in multicellular organism	45	408	1.499e-03
GO:BP	GO:0002824	positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	20	123	1.509e-03
GO:BP	GO:0050865	regulation of cell activation	61	616	1.683e-03
GO:BP	GO:0002443	leukocyte mediated immunity	49	461	1.715e-03
GO:BP	GO:0022600	digestive system process	18	105	1.785e-03
GO:BP	GO:0060041	retina development in camera-type eye	24	166	1.785e-03
GO:BP	GO:0042127	regulation of cell population proliferation	136	1682	1.883e-03
GO:BP	GO:0060294	cilium movement involved in cell motility	24	167	1.939e-03
GO:BP	GO:0098609	cell-cell adhesion	85	948	1.993e-03
GO:BP	GO:0007154	cell communication	438	6496	2.114e-03
GO:BP	GO:0035036	sperm-egg recognition	12	53	2.114e-03
GO:BP	GO:0015718	monocarboxylic acid transport	25	179	2.114e-03
GO:BP	GO:0002705	positive regulation of leukocyte mediated immunity	22	147	2.114e-03
GO:BP	GO:0009566	fertilization	28	212	2.114e-03
GO:BP	GO:0007166	cell surface receptor signaling pathway	209	2803	2.284e-03
GO:BP	GO:0007188	adenylate cyclase-modulating G protein-coupled receptor signaling pathway	31	248	2.357e-03
GO:BP	GO:0021953	central nervous system neuron differentiation	27	203	2.434e-03
GO:BP	GO:0051249	regulation of lymphocyte activation	51	497	2.680e-03
GO:BP	GO:0060285	cilium-dependent cell motility	24	172	2.861e-03
GO:BP	GO:0001539	cilium or flagellum-dependent cell motility	24	172	2.861e-03
GO:BP	GO:0034220	monoatomic ion transmembrane transport	89	1017	2.886e-03
GO:BP	GO:0032612	interleukin-1 production	18	110	2.927e-03
GO:BP	GO:0032652	regulation of interleukin-1 production	18	110	2.927e-03
GO:BP	GO:0051251	positive regulation of lymphocyte activation	37	324	3.090e-03
GO:BP	GO:0007165	signal transduction	405	5979	3.115e-03
GO:BP	GO:0019317	fucose catabolic process	5	9	3.314e-03
GO:BP	GO:0042355	L-fucose catabolic process	5	9	3.314e-03
GO:BP	GO:0042742	defense response to bacterium	37	326	3.392e-03
GO:BP	GO:0002252	immune effector process	66	703	3.392e-03
GO:BP	GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	41	376	3.458e-03
GO:BP	GO:0002253	activation of immune response	54	543	3.458e-03
GO:BP	GO:0032494	response to peptidoglycan	6	14	3.564e-03
GO:BP	GO:0042509	regulation of tyrosine phosphorylation of STAT protein	14	74	3.576e-03
GO:BP	GO:0007267	cell-cell signaling	109	1316	3.805e-03
GO:BP	GO:0045088	regulation of innate immune response	45	430	4.079e-03
GO:BP	GO:0051241	negative regulation of multicellular organismal process	93	1088	4.187e-03
GO:BP	GO:0002237	response to molecule of bacterial origin	39	355	4.204e-03
GO:BP	GO:0023052	signaling	433	6471	4.318e-03
GO:BP	GO:0044706	multi-multicellular organism process	27	212	4.412e-03
GO:BP	GO:0008544	epidermis development	42	394	4.424e-03
GO:BP	GO:0002376	immune system process	206	2796	4.424e-03
GO:BP	GO:0002708	positive regulation of lymphocyte mediated immunity	19	125	4.522e-03
GO:BP	GO:0007260	tyrosine phosphorylation of STAT protein	14	76	4.525e-03
GO:BP	GO:0002709	regulation of T cell mediated immunity	16	95	4.526e-03
GO:BP	GO:0008037	cell recognition	22	157	4.539e-03
GO:BP	GO:0046006	regulation of activated T cell proliferation	10	42	4.658e-03
GO:BP	GO:0032689	negative regulation of type II interferon production	10	42	4.658e-03
GO:BP	GO:0007586	digestion	20	136	4.658e-03
GO:BP	GO:0030317	flagellated sperm motility	21	147	4.741e-03
GO:BP	GO:0097722	sperm motility	21	147	4.741e-03
GO:BP	GO:0032653	regulation of interleukin-10 production	12	59	4.923e-03
GO:BP	GO:0032613	interleukin-10 production	12	59	4.923e-03
GO:BP	GO:0031341	regulation of cell killing	17	106	4.923e-03
GO:BP	GO:0048870	cell motility	135	1716	5.050e-03
GO:BP	GO:0002831	regulation of response to biotic stimulus	51	515	5.133e-03
GO:BP	GO:0042354	L-fucose metabolic process	5	10	5.185e-03
GO:BP	GO:0008343	adult feeding behavior	5	10	5.185e-03
GO:BP	GO:0002449	lymphocyte mediated immunity	39	361	5.257e-03
GO:BP	GO:0002757	immune response-activating signaling pathway	48	477	5.370e-03
GO:BP	GO:0007389	pattern specification process	48	478	5.612e-03
GO:BP	GO:0048608	reproductive structure development	35	313	5.756e-03
GO:BP	GO:0048232	male gamete generation	61	654	6.054e-03
GO:BP	GO:1904158	axonemal central apparatus assembly	4	6	6.054e-03
GO:BP	GO:0035082	axoneme assembly	16	99	6.612e-03
GO:BP	GO:0007159	leukocyte cell-cell adhesion	42	404	6.638e-03
GO:BP	GO:0042445	hormone metabolic process	29	243	6.644e-03
GO:BP	GO:0048646	anatomical structure formation involved in morphogenesis	98	1181	6.644e-03
GO:BP	GO:1903037	regulation of leukocyte cell-cell adhesion	39	366	6.644e-03
GO:BP	GO:0015721	bile acid and bile salt transport	8	29	6.664e-03
GO:BP	GO:0002833	positive regulation of response to biotic stimulus	40	379	6.664e-03
GO:BP	GO:0048598	embryonic morphogenesis	58	617	6.798e-03
GO:BP	GO:0006869	lipid transport	44	431	6.798e-03
GO:BP	GO:0061458	reproductive system development	35	317	6.894e-03
GO:BP	GO:0007218	neuropeptide signaling pathway	17	110	6.944e-03
GO:BP	GO:0002534	cytokine production involved in inflammatory response	12	62	6.977e-03
GO:BP	GO:0046661	male sex differentiation	23	175	6.977e-03
GO:BP	GO:0032732	positive regulation of interleukin-1 production	13	71	6.977e-03
GO:BP	GO:1900015	regulation of cytokine production involved in inflammatory response	12	62	6.977e-03
GO:BP	GO:1901246	regulation of lung ciliated cell differentiation	3	3	6.977e-03
GO:BP	GO:0050789	regulation of biological process	768	12278	6.977e-03
GO:BP	GO:0060429	epithelium development	101	1229	7.025e-03
GO:BP	GO:0045089	positive regulation of innate immune response	38	356	7.139e-03
GO:BP	GO:0043583	ear development	28	234	7.416e-03
GO:BP	GO:0003002	regionalization	44	434	7.416e-03
GO:BP	GO:0042471	ear morphogenesis	19	132	7.416e-03
GO:BP	GO:0009888	tissue development	153	2012	7.417e-03
GO:BP	GO:1903039	positive regulation of leukocyte cell-cell adhesion	31	271	7.833e-03
GO:BP	GO:0007342	fusion of sperm to egg plasma membrane involved in single fertilization	8	30	7.850e-03
GO:BP	GO:0030277	maintenance of gastrointestinal epithelium	7	23	7.878e-03
GO:BP	GO:0007283	spermatogenesis	59	637	8.036e-03
GO:BP	GO:0050798	activated T cell proliferation	10	46	8.182e-03
GO:BP	GO:0001910	regulation of leukocyte mediated cytotoxicity	15	92	8.182e-03
GO:BP	GO:0048568	embryonic organ development	46	463	8.182e-03
GO:BP	GO:0050870	positive regulation of T cell activation	29	248	8.194e-03
GO:BP	GO:0002764	immune response-regulating signaling pathway	49	504	8.603e-03
GO:BP	GO:0022407	regulation of cell-cell adhesion	47	478	8.791e-03
GO:BP	GO:0030155	regulation of cell adhesion	69	779	8.838e-03
GO:BP	GO:0007276	gamete generation	72	822	9.046e-03
GO:BP	GO:0008283	cell population proliferation	152	2009	9.212e-03
GO:BP	GO:0007338	single fertilization	22	169	9.846e-03
GO:BP	GO:0007187	G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger	11	56	1.001e-02
GO:BP	GO:0071224	cellular response to peptidoglycan	4	7	1.095e-02
GO:BP	GO:0042327	positive regulation of phosphorylation	57	620	1.153e-02
GO:BP	GO:0019369	arachidonate metabolic process	11	57	1.154e-02
GO:BP	GO:0042363	fat-soluble vitamin catabolic process	5	12	1.154e-02
GO:BP	GO:0006691	leukotriene metabolic process	8	32	1.167e-02
GO:BP	GO:0098655	monoatomic cation transmembrane transport	72	832	1.229e-02
GO:BP	GO:0048839	inner ear development	25	207	1.230e-02
GO:BP	GO:0050794	regulation of cellular process	742	11876	1.233e-02
GO:BP	GO:0001934	positive regulation of protein phosphorylation	55	595	1.233e-02
GO:BP	GO:0042104	positive regulation of activated T cell proliferation	7	25	1.255e-02
GO:BP	GO:0001578	microtubule bundle formation	18	128	1.255e-02
GO:BP	GO:0007281	germ cell development	38	370	1.324e-02
GO:BP	GO:0033993	response to lipid	78	921	1.326e-02
GO:BP	GO:0050672	negative regulation of lymphocyte proliferation	14	87	1.338e-02
GO:BP	GO:0051716	cellular response to stimulus	477	7320	1.338e-02
GO:BP	GO:0010562	positive regulation of phosphorus metabolic process	60	667	1.339e-02
GO:BP	GO:0045937	positive regulation of phosphate metabolic process	60	667	1.339e-02
GO:BP	GO:0048240	sperm capacitation	8	33	1.363e-02
GO:BP	GO:0032673	regulation of interleukin-4 production	8	33	1.363e-02
GO:BP	GO:0010669	epithelial structure maintenance	8	33	1.363e-02
GO:BP	GO:0032633	interleukin-4 production	8	33	1.363e-02
GO:BP	GO:0009583	detection of light stimulus	12	68	1.386e-02
GO:BP	GO:0002715	regulation of natural killer cell mediated immunity	10	50	1.445e-02
GO:BP	GO:0032945	negative regulation of mononuclear cell proliferation	14	88	1.450e-02
GO:BP	GO:0050731	positive regulation of peptidyl-tyrosine phosphorylation	21	164	1.483e-02
GO:BP	GO:0010628	positive regulation of gene expression	96	1189	1.483e-02
GO:BP	GO:0019370	leukotriene biosynthetic process	6	19	1.501e-02
GO:BP	GO:0050830	defense response to Gram-positive bacterium	17	120	1.531e-02
GO:BP	GO:0010876	lipid localization	46	480	1.531e-02
GO:BP	GO:0050766	positive regulation of phagocytosis	12	69	1.539e-02
GO:BP	GO:0050863	regulation of T cell activation	38	375	1.578e-02
GO:BP	GO:0071219	cellular response to molecule of bacterial origin	26	224	1.578e-02
GO:BP	GO:0045026	plasma membrane fusion	8	34	1.610e-02
GO:BP	GO:0032496	response to lipopolysaccharide	35	337	1.626e-02
GO:BP	GO:0006812	monoatomic cation transport	85	1032	1.626e-02
GO:BP	GO:0009952	anterior/posterior pattern specification	26	225	1.656e-02
GO:BP	GO:0042221	response to chemical	267	3867	1.656e-02
GO:BP	GO:0045860	positive regulation of protein kinase activity	29	262	1.674e-02
GO:BP	GO:0098660	inorganic ion transmembrane transport	76	903	1.679e-02
GO:BP	GO:1901700	response to oxygen-containing compound	125	1632	1.725e-02
GO:BP	GO:0042472	inner ear morphogenesis	16	111	1.725e-02
GO:BP	GO:0046394	carboxylic acid biosynthetic process	34	326	1.741e-02
GO:BP	GO:1901750	leukotriene D4 biosynthetic process	4	8	1.746e-02
GO:BP	GO:0032735	positive regulation of interleukin-12 production	9	43	1.777e-02
GO:BP	GO:0002820	negative regulation of adaptive immune response	11	61	1.780e-02
GO:BP	GO:0043032	positive regulation of macrophage activation	7	27	1.785e-02
GO:BP	GO:0021510	spinal cord development	15	101	1.785e-02
GO:BP	GO:0034308	primary alcohol metabolic process	15	101	1.785e-02
GO:BP	GO:0016048	detection of temperature stimulus	7	27	1.785e-02
GO:BP	GO:0006629	lipid metabolic process	108	1379	1.822e-02
GO:BP	GO:0060005	vestibular reflex	3	4	1.932e-02
GO:BP	GO:0061141	lung ciliated cell differentiation	3	4	1.932e-02
GO:BP	GO:0048871	multicellular organismal-level homeostasis	69	809	1.959e-02
GO:BP	GO:0016053	organic acid biosynthetic process	34	329	1.959e-02
GO:BP	GO:0007565	female pregnancy	22	181	1.998e-02
GO:BP	GO:0001909	leukocyte mediated cytotoxicity	18	135	1.998e-02
GO:BP	GO:0046631	alpha-beta T cell activation	22	181	1.998e-02
GO:BP	GO:0007600	sensory perception	79	955	2.025e-02
GO:BP	GO:0033674	positive regulation of kinase activity	30	279	2.025e-02
GO:BP	GO:0046638	positive regulation of alpha-beta T cell differentiation	10	53	2.026e-02
GO:BP	GO:0042130	negative regulation of T cell proliferation	12	72	2.027e-02
GO:BP	GO:0098662	inorganic cation transmembrane transport	69	811	2.031e-02
GO:BP	GO:0009111	vitamin catabolic process	5	14	2.064e-02
GO:BP	GO:0034341	response to type II interferon	19	147	2.064e-02
GO:BP	GO:0046942	carboxylic acid transport	35	344	2.092e-02
GO:BP	GO:0002702	positive regulation of production of molecular mediator of immune response	18	136	2.098e-02
GO:BP	GO:1900017	positive regulation of cytokine production involved in inflammatory response	7	28	2.117e-02
GO:BP	GO:0070887	cellular response to chemical stimulus	160	2186	2.134e-02
GO:BP	GO:0032611	interleukin-1 beta production	14	93	2.134e-02
GO:BP	GO:0008284	positive regulation of cell population proliferation	79	958	2.134e-02
GO:BP	GO:0032651	regulation of interleukin-1 beta production	14	93	2.134e-02
GO:BP	GO:0022409	positive regulation of cell-cell adhesion	33	319	2.135e-02
GO:BP	GO:0015849	organic acid transport	35	345	2.141e-02
GO:BP	GO:0009799	specification of symmetry	19	148	2.154e-02
GO:BP	GO:0009855	determination of bilateral symmetry	19	148	2.154e-02
GO:BP	GO:0001523	retinoid metabolic process	13	83	2.169e-02
GO:BP	GO:0032674	regulation of interleukin-5 production	6	21	2.217e-02
GO:BP	GO:0032634	interleukin-5 production	6	21	2.217e-02
GO:BP	GO:0060749	mammary gland alveolus development	6	21	2.217e-02
GO:BP	GO:0002920	regulation of humoral immune response	9	45	2.217e-02
GO:BP	GO:0061377	mammary gland lobule development	6	21	2.217e-02
GO:BP	GO:0010817	regulation of hormone levels	50	548	2.223e-02
GO:BP	GO:0015850	organic hydroxy compound transport	30	283	2.339e-02
GO:BP	GO:0120254	olefinic compound metabolic process	20	161	2.343e-02
GO:BP	GO:0021545	cranial nerve development	11	64	2.343e-02
GO:BP	GO:0018108	peptidyl-tyrosine phosphorylation	28	258	2.347e-02
GO:BP	GO:0072678	T cell migration	12	74	2.378e-02
GO:BP	GO:0009312	oligosaccharide biosynthetic process	7	29	2.459e-02
GO:BP	GO:0015732	prostaglandin transport	7	29	2.459e-02
GO:BP	GO:0021879	forebrain neuron differentiation	9	46	2.491e-02
GO:BP	GO:0048541	Peyer’s patch development	4	9	2.491e-02
GO:BP	GO:0048537	mucosa-associated lymphoid tissue development	4	9	2.491e-02
GO:BP	GO:0021517	ventral spinal cord development	9	46	2.491e-02
GO:BP	GO:0007368	determination of left/right symmetry	18	139	2.491e-02
GO:BP	GO:0009629	response to gravity	4	9	2.491e-02
GO:BP	GO:0008217	regulation of blood pressure	22	186	2.502e-02
GO:BP	GO:0048706	embryonic skeletal system development	17	128	2.502e-02
GO:BP	GO:0048518	positive regulation of biological process	408	6235	2.524e-02
GO:BP	GO:0018212	peptidyl-tyrosine modification	28	260	2.527e-02
GO:BP	GO:0008584	male gonad development	19	151	2.527e-02
GO:BP	GO:0072044	collecting duct development	5	15	2.601e-02
GO:BP	GO:0070664	negative regulation of leukocyte proliferation	14	96	2.643e-02
GO:BP	GO:0030431	sleep	6	22	2.687e-02
GO:BP	GO:0015908	fatty acid transport	16	118	2.687e-02
GO:BP	GO:0048709	oligodendrocyte differentiation	15	107	2.687e-02
GO:BP	GO:0046546	development of primary male sexual characteristics	19	152	2.687e-02
GO:BP	GO:0021872	forebrain generation of neurons	10	56	2.697e-02
GO:BP	GO:0098916	anterograde trans-synaptic signaling	64	753	2.710e-02
GO:BP	GO:0007268	chemical synaptic transmission	64	753	2.710e-02
GO:BP	GO:0002228	natural killer cell mediated immunity	12	76	2.799e-02
GO:BP	GO:0051093	negative regulation of developmental process	76	928	2.799e-02
GO:BP	GO:0021522	spinal cord motor neuron differentiation	7	30	2.833e-02
GO:BP	GO:0071222	cellular response to lipopolysaccharide	24	214	3.058e-02
GO:BP	GO:0002260	lymphocyte homeostasis	12	77	3.117e-02
GO:BP	GO:0050909	sensory perception of taste	11	67	3.136e-02
GO:BP	GO:0001676	long-chain fatty acid metabolic process	15	109	3.141e-02
GO:BP	GO:0032309	icosanoid secretion	9	48	3.174e-02
GO:BP	GO:0050900	leukocyte migration	38	396	3.191e-02
GO:BP	GO:0099537	trans-synaptic signaling	64	759	3.191e-02
GO:BP	GO:0007548	sex differentiation	30	291	3.227e-02
GO:BP	GO:0050793	regulation of developmental process	175	2453	3.252e-02
GO:BP	GO:2000026	regulation of multicellular organismal development	108	1413	3.252e-02
GO:BP	GO:0016101	diterpenoid metabolic process	13	88	3.252e-02
GO:BP	GO:0098664	G protein-coupled serotonin receptor signaling pathway	6	23	3.257e-02
GO:BP	GO:0006004	fucose metabolic process	5	16	3.338e-02
GO:BP	GO:0051969	regulation of transmission of nerve impulse	5	16	3.338e-02
GO:BP	GO:0001754	eye photoreceptor cell differentiation	10	58	3.350e-02
GO:BP	GO:0098742	cell-cell adhesion via plasma-membrane adhesion molecules	29	280	3.486e-02
GO:BP	GO:0002429	immune response-activating cell surface receptor signaling pathway	31	306	3.497e-02
GO:BP	GO:1901748	leukotriene D4 metabolic process	4	10	3.516e-02
GO:BP	GO:0002420	natural killer cell mediated cytotoxicity directed against tumor cell target	4	10	3.516e-02
GO:BP	GO:0045188	regulation of circadian sleep/wake cycle, non-REM sleep	3	5	3.516e-02
GO:BP	GO:0006702	androgen biosynthetic process	4	10	3.516e-02
GO:BP	GO:0072205	metanephric collecting duct development	4	10	3.516e-02
GO:BP	GO:0030718	germ-line stem cell population maintenance	3	5	3.516e-02
GO:BP	GO:0060972	left/right pattern formation	18	145	3.520e-02
GO:BP	GO:0048592	eye morphogenesis	20	169	3.617e-02
GO:BP	GO:0042592	homeostatic process	127	1711	3.627e-02
GO:BP	GO:0015711	organic anion transport	41	442	3.795e-02
GO:BP	GO:0065008	regulation of biological quality	199	2847	3.811e-02
GO:BP	GO:0001906	cell killing	24	219	3.847e-02
GO:BP	GO:0002825	regulation of T-helper 1 type immune response	7	32	3.875e-02
GO:BP	GO:0050961	detection of temperature stimulus involved in sensory perception	6	24	3.890e-02
GO:BP	GO:0021871	forebrain regionalization	6	24	3.890e-02
GO:BP	GO:0048468	cell development	198	2833	3.890e-02
GO:BP	GO:0042088	T-helper 1 type immune response	9	50	3.921e-02
GO:BP	GO:0035295	tube development	86	1092	3.921e-02
GO:BP	GO:0006633	fatty acid biosynthetic process	19	159	4.018e-02
GO:BP	GO:0032733	positive regulation of interleukin-10 production	8	41	4.018e-02
GO:BP	GO:0050829	defense response to Gram-negative bacterium	13	91	4.078e-02
GO:BP	GO:0032731	positive regulation of interleukin-1 beta production	10	60	4.078e-02
GO:BP	GO:0036065	fucosylation	5	17	4.184e-02
GO:BP	GO:0071346	cellular response to type II interferon	16	125	4.300e-02
GO:BP	GO:0019221	cytokine-mediated signaling pathway	45	503	4.585e-02
GO:BP	GO:0050913	sensory perception of bitter taste	8	42	4.639e-02
GO:BP	GO:0042430	indole-containing compound metabolic process	6	25	4.726e-02
GO:BP	GO:0006334	nucleosome assembly	15	115	4.779e-02
GO:BP	GO:0002423	natural killer cell mediated immune response to tumor cell	4	11	4.865e-02
GO:BP	GO:0097267	omega-hydroxylase P450 pathway	4	11	4.865e-02
GO:BP	GO:0001818	negative regulation of cytokine production	29	288	4.865e-02
GO:BP	GO:0072173	metanephric tubule morphogenesis	4	11	4.865e-02
GO:BP	GO:0021562	vestibulocochlear nerve development	4	11	4.865e-02
GO:BP	GO:1903027	regulation of opsonization	4	11	4.865e-02
GO:BP	GO:0003014	renal system process	16	127	4.913e-02
KEGG	KEGG:04080	Neuroactive ligand-receptor interaction	66	365	2.487e-13
KEGG	KEGG:04060	Cytokine-cytokine receptor interaction	39	291	3.591e-04
KEGG	KEGG:04742	Taste transduction	18	85	3.591e-04
KEGG	KEGG:04672	Intestinal immune network for IgA production	12	44	7.297e-04
KEGG	KEGG:05322	Systemic lupus erythematosus	22	132	8.976e-04
KEGG	KEGG:00590	Arachidonic acid metabolism	14	61	8.976e-04
KEGG	KEGG:00601	Glycosphingolipid biosynthesis - lacto and neolacto series	9	28	1.304e-03
KEGG	KEGG:04726	Serotonergic synapse	18	112	6.243e-03
KEGG	KEGG:04613	Neutrophil extracellular trap formation	25	188	7.755e-03
KEGG	KEGG:04913	Ovarian steroidogenesis	10	51	2.964e-02
KEGG	KEGG:04020	Calcium signaling pathway	28	251	4.381e-02
KEGG	KEGG:05340	Primary immunodeficiency	8	37	4.381e-02
KEGG	KEGG:00591	Linoleic acid metabolism	7	30	4.592e-02

#write.csv(tableNR, "output/table_NRmotif.csv")

#GO:BP
tableNR_GOBP_pp <- tableNR_pp %>% 
  dplyr::filter(source=="GO:BP") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

#saveRDS(tableNR_GOBP_pp, "data/tableNR_GOBP_postprob.RDS")

tableNR_GOBP_pp %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("No Response Enriched GO:BP Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("GO:BP term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "Acute Response GO Analysis KEGG terms-2.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

#KEGG
tableNR_KEGG_pp <- tableNR_pp %>% 
  dplyr::filter(source=="KEGG") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

tableNR_KEGG_pp %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("No Response Enriched KEGG Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("KEGG term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "Acute Response GO Analysis KEGG terms-3.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

Next, we’ll look at the Late Response (motif 3)

motif_LD_d <- clust3_d


LDmotif_genes_d <- gost(query = motif_LD_d,
                      organism = "hsapiens",
                      ordered_query = FALSE,
                      measure_underrepresentation = FALSE,
                      evcodes = FALSE,
                      user_threshold = 0.05,
                      correction_method = c("fdr"),
                      sources = c("GO:BP", "KEGG"))

cormotifLDclust_d <- gostplot(LDmotif_genes_d, capped = FALSE, interactive = TRUE)
cormotifLDclust_d

tableLD_d <- LDmotif_genes_d$result %>% 
  dplyr::select(c(source, term_id, term_name, intersection_size, term_size, p_value))

tableLD_d %>% 
  mutate_at(.vars = 6, .funs = scales::label_scientific(digits=4)) %>% 
  kableExtra::kable(.,) %>% 
  kableExtra::kable_paper("striped", full_width = FALSE) %>% 
  kableExtra::kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "hover")) %>% 
  kableExtra::scroll_box(width = "100%", height = "400px")

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0006811	monoatomic ion transport	76	1256	1.859e-16
GO:BP	GO:0034220	monoatomic ion transmembrane transport	66	1017	1.150e-15
GO:BP	GO:0055085	transmembrane transport	81	1538	1.275e-14
GO:BP	GO:0098660	inorganic ion transmembrane transport	59	903	4.056e-14
GO:BP	GO:0015698	inorganic anion transport	25	165	6.202e-13
GO:BP	GO:0006820	monoatomic anion transport	25	167	6.916e-13
GO:BP	GO:0006821	chloride transport	20	122	8.036e-11
GO:BP	GO:0098661	inorganic anion transmembrane transport	20	127	1.544e-10
GO:BP	GO:0006812	monoatomic cation transport	56	1032	3.213e-10
GO:BP	GO:0030001	metal ion transport	50	875	8.778e-10
GO:BP	GO:0098656	monoatomic anion transmembrane transport	20	142	9.669e-10
GO:BP	GO:1902476	chloride transmembrane transport	17	107	5.174e-09
GO:BP	GO:0098655	monoatomic cation transmembrane transport	47	832	5.174e-09
GO:BP	GO:0006810	transport	137	4341	8.659e-09
GO:BP	GO:0050896	response to stimulus	229	8993	7.328e-08
GO:BP	GO:0098662	inorganic cation transmembrane transport	44	811	7.328e-08
GO:BP	GO:0048869	cellular developmental process	133	4382	2.366e-07
GO:BP	GO:0030154	cell differentiation	133	4381	2.366e-07
GO:BP	GO:0032502	developmental process	177	6478	3.165e-07
GO:BP	GO:0032501	multicellular organismal process	191	7234	6.618e-07
GO:BP	GO:0051234	establishment of localization	140	4869	2.283e-06
GO:BP	GO:0048468	cell development	94	2833	2.327e-06
GO:BP	GO:0065008	regulation of biological quality	94	2847	2.843e-06
GO:BP	GO:0035725	sodium ion transmembrane transport	17	169	3.857e-06
GO:BP	GO:0007267	cell-cell signaling	54	1316	7.714e-06
GO:BP	GO:0007188	adenylate cyclase-modulating G protein-coupled receptor signaling pathway	20	248	8.700e-06
GO:BP	GO:0006814	sodium ion transport	19	235	1.747e-05
GO:BP	GO:0048856	anatomical structure development	158	5924	2.143e-05
GO:BP	GO:0030003	intracellular monoatomic cation homeostasis	29	521	3.048e-05
GO:BP	GO:0007193	adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway	11	79	3.777e-05
GO:BP	GO:0006873	intracellular monoatomic ion homeostasis	29	530	4.076e-05
GO:BP	GO:0051179	localization	148	5521	4.773e-05
GO:BP	GO:0055080	monoatomic cation homeostasis	31	598	4.781e-05
GO:BP	GO:0002521	leukocyte differentiation	32	632	5.022e-05
GO:BP	GO:0050801	monoatomic ion homeostasis	31	608	6.443e-05
GO:BP	GO:0006813	potassium ion transport	18	238	7.650e-05
GO:BP	GO:0098771	inorganic ion homeostasis	28	531	1.150e-04
GO:BP	GO:0055074	calcium ion homeostasis	21	326	1.192e-04
GO:BP	GO:0015711	organic anion transport	25	442	1.210e-04
GO:BP	GO:0006874	intracellular calcium ion homeostasis	20	302	1.341e-04
GO:BP	GO:0023052	signaling	165	6471	1.385e-04
GO:BP	GO:0065007	biological regulation	281	12671	1.491e-04
GO:BP	GO:0002429	immune response-activating cell surface receptor signaling pathway	20	306	1.529e-04
GO:BP	GO:0007154	cell communication	165	6496	1.673e-04
GO:BP	GO:0099536	synaptic signaling	35	783	1.918e-04
GO:BP	GO:0050877	nervous system process	54	1489	2.051e-04
GO:BP	GO:0055082	intracellular chemical homeostasis	33	723	2.347e-04
GO:BP	GO:0007155	cell adhesion	54	1511	3.030e-04
GO:BP	GO:0042592	homeostatic process	59	1711	3.030e-04
GO:BP	GO:0050851	antigen receptor-mediated signaling pathway	15	192	3.228e-04
GO:BP	GO:0048878	chemical homeostasis	41	1026	3.612e-04
GO:BP	GO:0002768	immune response-regulating cell surface receptor signaling pathway	20	334	4.779e-04
GO:BP	GO:0048232	male gamete generation	30	654	5.513e-04
GO:BP	GO:0099537	trans-synaptic signaling	33	759	5.699e-04
GO:BP	GO:0022414	reproductive process	54	1556	6.223e-04
GO:BP	GO:0050957	equilibrioception	4	8	6.636e-04
GO:BP	GO:0071805	potassium ion transmembrane transport	15	213	9.978e-04
GO:BP	GO:0051480	regulation of cytosolic calcium ion concentration	8	59	1.073e-03
GO:BP	GO:0098916	anterograde trans-synaptic signaling	32	753	1.104e-03
GO:BP	GO:0007186	G protein-coupled receptor signaling pathway	46	1275	1.104e-03
GO:BP	GO:0007268	chemical synaptic transmission	32	753	1.104e-03
GO:BP	GO:0019725	cellular homeostasis	34	826	1.131e-03
GO:BP	GO:0009605	response to external stimulus	72	2367	1.429e-03
GO:BP	GO:0003006	developmental process involved in reproduction	39	1022	1.436e-03
GO:BP	GO:0098609	cell-cell adhesion	37	948	1.439e-03
GO:BP	GO:0010951	negative regulation of endopeptidase activity	6	31	1.439e-03
GO:BP	GO:0051716	cellular response to stimulus	176	7320	1.444e-03
GO:BP	GO:0007275	multicellular organism development	122	4658	1.472e-03
GO:BP	GO:1903131	mononuclear cell differentiation	25	529	1.557e-03
GO:BP	GO:0006816	calcium ion transport	22	433	1.614e-03
GO:BP	GO:0009410	response to xenobiotic stimulus	22	436	1.767e-03
GO:BP	GO:0007283	spermatogenesis	28	637	1.793e-03
GO:BP	GO:0048731	system development	107	3985	1.988e-03
GO:BP	GO:0015747	urate transport	4	11	2.264e-03
GO:BP	GO:0042221	response to chemical	104	3867	2.455e-03
GO:BP	GO:0010817	regulation of hormone levels	25	548	2.522e-03
GO:BP	GO:1902105	regulation of leukocyte differentiation	18	325	2.672e-03
GO:BP	GO:0006968	cellular defense response	7	52	2.928e-03
GO:BP	GO:0050853	B cell receptor signaling pathway	8	71	3.113e-03
GO:BP	GO:1901700	response to oxygen-containing compound	53	1632	3.186e-03
GO:BP	GO:0060004	reflex	5	23	3.275e-03
GO:BP	GO:0007200	phospholipase C-activating G protein-coupled receptor signaling pathway	10	116	3.665e-03
GO:BP	GO:0019722	calcium-mediated signaling	14	218	3.665e-03
GO:BP	GO:0050805	negative regulation of synaptic transmission	7	55	3.931e-03
GO:BP	GO:0060348	bone development	14	220	3.948e-03
GO:BP	GO:0009581	detection of external stimulus	11	142	4.080e-03
GO:BP	GO:0030098	lymphocyte differentiation	21	438	4.545e-03
GO:BP	GO:0030217	T cell differentiation	17	312	4.635e-03
GO:BP	GO:0009582	detection of abiotic stimulus	11	145	4.761e-03
GO:BP	GO:0140013	meiotic nuclear division	13	198	4.891e-03
GO:BP	GO:0002253	activation of immune response	24	543	4.891e-03
GO:BP	GO:0002757	immune response-activating signaling pathway	22	477	5.142e-03
GO:BP	GO:0019953	sexual reproduction	39	1103	5.143e-03
GO:BP	GO:0060078	regulation of postsynaptic membrane potential	11	148	5.417e-03
GO:BP	GO:0007600	sensory perception	35	955	5.823e-03
GO:BP	GO:0007610	behavior	27	665	6.963e-03
GO:BP	GO:0042110	T cell activation	24	558	6.963e-03
GO:BP	GO:0050789	regulation of biological process	264	12278	7.266e-03
GO:BP	GO:0006817	phosphate ion transport	5	28	7.266e-03
GO:BP	GO:0046631	alpha-beta T cell activation	12	181	7.448e-03
GO:BP	GO:0003008	system process	66	2266	7.662e-03
GO:BP	GO:0007276	gamete generation	31	822	8.125e-03
GO:BP	GO:0010466	negative regulation of peptidase activity	6	45	8.188e-03
GO:BP	GO:0006869	lipid transport	20	431	8.627e-03
GO:BP	GO:0048609	multicellular organismal reproductive process	35	980	8.638e-03
GO:BP	GO:0042391	regulation of membrane potential	20	433	8.859e-03
GO:BP	GO:0042445	hormone metabolic process	14	243	8.859e-03
GO:BP	GO:0021879	forebrain neuron differentiation	6	46	8.859e-03
GO:BP	GO:0002366	leukocyte activation involved in immune response	16	305	9.166e-03
GO:BP	GO:0045588	positive regulation of gamma-delta T cell differentiation	3	7	9.166e-03
GO:BP	GO:0002764	immune response-regulating signaling pathway	22	504	9.211e-03
GO:BP	GO:0014070	response to organic cyclic compound	33	909	9.211e-03
GO:BP	GO:1902107	positive regulation of leukocyte differentiation	12	189	9.684e-03
GO:BP	GO:1903708	positive regulation of hemopoiesis	12	189	9.684e-03
GO:BP	GO:0070588	calcium ion transmembrane transport	17	339	9.684e-03
GO:BP	GO:0002263	cell activation involved in immune response	16	309	1.006e-02
GO:BP	GO:0050870	positive regulation of T cell activation	14	248	1.008e-02
GO:BP	GO:0007601	visual perception	13	219	1.008e-02
GO:BP	GO:0035249	synaptic transmission, glutamatergic	9	112	1.008e-02
GO:BP	GO:1903046	meiotic cell cycle process	13	220	1.045e-02
GO:BP	GO:0098657	import into cell	33	921	1.071e-02
GO:BP	GO:0046942	carboxylic acid transport	17	344	1.071e-02
GO:BP	GO:0002923	regulation of humoral immune response mediated by circulating immunoglobulin	4	18	1.086e-02
GO:BP	GO:0050852	T cell receptor signaling pathway	10	139	1.086e-02
GO:BP	GO:0032604	granulocyte macrophage colony-stimulating factor production	4	18	1.086e-02
GO:BP	GO:0032645	regulation of granulocyte macrophage colony-stimulating factor production	4	18	1.086e-02
GO:BP	GO:0050953	sensory perception of light stimulus	13	222	1.086e-02
GO:BP	GO:0015849	organic acid transport	17	345	1.086e-02
GO:BP	GO:0050778	positive regulation of immune response	28	732	1.086e-02
GO:BP	GO:0008283	cell population proliferation	59	2009	1.123e-02
GO:BP	GO:0021630	olfactory nerve maturation	2	2	1.163e-02
GO:BP	GO:0009628	response to abiotic stimulus	38	1130	1.163e-02
GO:BP	GO:0036368	cone photoresponse recovery	2	2	1.163e-02
GO:BP	GO:0015913	short-chain fatty acid transmembrane transport	2	2	1.163e-02
GO:BP	GO:0030573	bile acid catabolic process	2	2	1.163e-02
GO:BP	GO:0046645	positive regulation of gamma-delta T cell activation	3	8	1.163e-02
GO:BP	GO:0048513	animal organ development	82	3047	1.163e-02
GO:BP	GO:0030097	hemopoiesis	34	971	1.163e-02
GO:BP	GO:0015741	fumarate transport	2	2	1.163e-02
GO:BP	GO:2000471	regulation of hematopoietic stem cell migration	2	2	1.163e-02
GO:BP	GO:2000473	positive regulation of hematopoietic stem cell migration	2	2	1.163e-02
GO:BP	GO:0045055	regulated exocytosis	13	229	1.290e-02
GO:BP	GO:0001775	cell activation	37	1098	1.290e-02
GO:BP	GO:0045582	positive regulation of T cell differentiation	9	119	1.295e-02
GO:BP	GO:0042127	regulation of cell population proliferation	51	1682	1.295e-02
GO:BP	GO:0046649	lymphocyte activation	29	787	1.338e-02
GO:BP	GO:0051321	meiotic cell cycle	15	294	1.437e-02
GO:BP	GO:0007165	signal transduction	142	5979	1.448e-02
GO:BP	GO:0070372	regulation of ERK1 and ERK2 cascade	15	295	1.469e-02
GO:BP	GO:0048518	positive regulation of biological process	147	6235	1.486e-02
GO:BP	GO:0006909	phagocytosis	13	234	1.500e-02
GO:BP	GO:0045321	leukocyte activation	33	951	1.511e-02
GO:BP	GO:0030450	regulation of complement activation, classical pathway	3	9	1.527e-02
GO:BP	GO:0045586	regulation of gamma-delta T cell differentiation	3	9	1.527e-02
GO:BP	GO:0040020	regulation of meiotic nuclear division	5	36	1.571e-02
GO:BP	GO:0002683	negative regulation of immune system process	21	502	1.599e-02
GO:BP	GO:0050982	detection of mechanical stimulus	6	55	1.625e-02
GO:BP	GO:0007140	male meiotic nuclear division	6	55	1.625e-02
GO:BP	GO:0009653	anatomical structure morphogenesis	73	2692	1.769e-02
GO:BP	GO:0021872	forebrain generation of neurons	6	56	1.769e-02
GO:BP	GO:1903039	positive regulation of leukocyte cell-cell adhesion	14	271	1.784e-02
GO:BP	GO:0048871	multicellular organismal-level homeostasis	29	809	1.871e-02
GO:BP	GO:0048485	sympathetic nervous system development	4	22	1.902e-02
GO:BP	GO:0046903	secretion	33	968	1.902e-02
GO:BP	GO:0046629	gamma-delta T cell activation	4	22	1.902e-02
GO:BP	GO:0141124	intracellular signaling cassette	55	1895	1.902e-02
GO:BP	GO:0071695	anatomical structure maturation	14	274	1.915e-02
GO:BP	GO:2001204	regulation of osteoclast development	3	10	1.960e-02
GO:BP	GO:0046643	regulation of gamma-delta T cell activation	3	10	1.960e-02
GO:BP	GO:0007166	cell surface receptor signaling pathway	75	2803	2.028e-02
GO:BP	GO:0010876	lipid localization	20	480	2.066e-02
GO:BP	GO:0050776	regulation of immune response	31	897	2.110e-02
GO:BP	GO:0002064	epithelial cell development	12	217	2.226e-02
GO:BP	GO:0098742	cell-cell adhesion via plasma-membrane adhesion molecules	14	280	2.269e-02
GO:BP	GO:0007127	meiosis I	9	132	2.275e-02
GO:BP	GO:0051932	synaptic transmission, GABAergic	6	60	2.330e-02
GO:BP	GO:0010481	epidermal cell division	2	3	2.428e-02
GO:BP	GO:0009888	tissue development	57	2012	2.428e-02
GO:BP	GO:0015850	organic hydroxy compound transport	14	283	2.428e-02
GO:BP	GO:0070543	response to linoleic acid	2	3	2.428e-02
GO:BP	GO:1903706	regulation of hemopoiesis	18	420	2.428e-02
GO:BP	GO:0071486	cellular response to high light intensity	2	3	2.428e-02
GO:BP	GO:1903306	negative regulation of regulated secretory pathway	4	24	2.428e-02
GO:BP	GO:0015912	short-chain fatty acid transport	2	3	2.428e-02
GO:BP	GO:0006959	humoral immune response	13	254	2.428e-02
GO:BP	GO:0070371	ERK1 and ERK2 cascade	15	318	2.428e-02
GO:BP	GO:0010482	regulation of epidermal cell division	2	3	2.428e-02
GO:BP	GO:0050954	sensory perception of mechanical stimulus	11	190	2.428e-02
GO:BP	GO:0021605	cranial nerve maturation	2	3	2.428e-02
GO:BP	GO:0072313	metanephric glomerular epithelial cell development	2	3	2.428e-02
GO:BP	GO:0032663	regulation of interleukin-2 production	6	62	2.428e-02
GO:BP	GO:0032623	interleukin-2 production	6	62	2.428e-02
GO:BP	GO:0045621	positive regulation of lymphocyte differentiation	9	134	2.428e-02
GO:BP	GO:0072312	metanephric glomerular epithelial cell differentiation	2	3	2.428e-02
GO:BP	GO:0072249	metanephric podocyte development	2	3	2.428e-02
GO:BP	GO:0072248	metanephric podocyte differentiation	2	3	2.428e-02
GO:BP	GO:0072244	metanephric glomerular epithelium development	2	3	2.428e-02
GO:BP	GO:0033563	dorsal/ventral axon guidance	2	3	2.428e-02
GO:BP	GO:1903977	positive regulation of glial cell migration	3	11	2.428e-02
GO:BP	GO:0006311	meiotic gene conversion	2	3	2.428e-02
GO:BP	GO:0048522	positive regulation of cellular process	138	5886	2.428e-02
GO:BP	GO:0009887	animal organ morphogenesis	34	1037	2.505e-02
GO:BP	GO:0043408	regulation of MAPK cascade	24	645	2.620e-02
GO:BP	GO:0007605	sensory perception of sound	10	166	2.660e-02
GO:BP	GO:0001501	skeletal system development	21	536	2.785e-02
GO:BP	GO:0044341	sodium-dependent phosphate transport	3	12	2.867e-02
GO:BP	GO:0043410	positive regulation of MAPK cascade	19	465	2.882e-02
GO:BP	GO:0021895	cerebral cortex neuron differentiation	4	26	2.925e-02
GO:BP	GO:0045494	photoreceptor cell maintenance	5	44	2.972e-02
GO:BP	GO:0050794	regulation of cellular process	251	11876	2.996e-02
GO:BP	GO:0061982	meiosis I cell cycle process	9	141	3.006e-02
GO:BP	GO:0009266	response to temperature stimulus	10	170	3.063e-02
GO:BP	GO:0035270	endocrine system development	9	142	3.128e-02
GO:BP	GO:0046634	regulation of alpha-beta T cell activation	8	115	3.144e-02
GO:BP	GO:0002704	negative regulation of leukocyte mediated immunity	6	66	3.152e-02
GO:BP	GO:0001894	tissue homeostasis	13	264	3.164e-02
GO:BP	GO:0060249	anatomical structure homeostasis	13	264	3.164e-02
GO:BP	GO:0007263	nitric oxide mediated signal transduction	4	27	3.228e-02
GO:BP	GO:0021953	central nervous system neuron differentiation	11	203	3.372e-02
GO:BP	GO:0043383	negative T cell selection	3	13	3.411e-02
GO:BP	GO:0043301	negative regulation of leukocyte degranulation	3	13	3.411e-02
GO:BP	GO:0042492	gamma-delta T cell differentiation	3	13	3.411e-02
GO:BP	GO:0051446	positive regulation of meiotic cell cycle	4	28	3.628e-02
GO:BP	GO:0050867	positive regulation of cell activation	16	372	3.730e-02
GO:BP	GO:0046633	alpha-beta T cell proliferation	5	47	3.730e-02
GO:BP	GO:0050848	regulation of calcium-mediated signaling	7	93	3.730e-02
GO:BP	GO:0014074	response to purine-containing compound	9	147	3.730e-02
GO:BP	GO:0051445	regulation of meiotic cell cycle	6	69	3.736e-02
GO:BP	GO:0045597	positive regulation of cell differentiation	29	866	3.736e-02
GO:BP	GO:2001205	negative regulation of osteoclast development	2	4	3.794e-02
GO:BP	GO:0141006	transposable element silencing by piRNA-mediated heterochromatin formation	2	4	3.794e-02
GO:BP	GO:1903942	positive regulation of respiratory gaseous exchange	2	4	3.794e-02
GO:BP	GO:0140966	piRNA-mediated heterochromatin formation	2	4	3.794e-02
GO:BP	GO:0071639	positive regulation of monocyte chemotactic protein-1 production	3	14	3.794e-02
GO:BP	GO:1990834	response to odorant	2	4	3.794e-02
GO:BP	GO:0000165	MAPK cascade	26	749	3.794e-02
GO:BP	GO:0042475	odontogenesis of dentin-containing tooth	7	95	3.794e-02
GO:BP	GO:0042403	thyroid hormone metabolic process	4	29	3.794e-02
GO:BP	GO:0010520	regulation of reciprocal meiotic recombination	2	4	3.794e-02
GO:BP	GO:0035822	gene conversion	2	4	3.794e-02
GO:BP	GO:0035589	G protein-coupled purinergic nucleotide receptor signaling pathway	3	14	3.794e-02
GO:BP	GO:0045728	respiratory burst after phagocytosis	2	4	3.794e-02
GO:BP	GO:0046305	alkanesulfonate biosynthetic process	2	4	3.794e-02
GO:BP	GO:0046352	disaccharide catabolic process	2	4	3.794e-02
GO:BP	GO:0007214	gamma-aminobutyric acid signaling pathway	4	29	3.794e-02
GO:BP	GO:0042412	taurine biosynthetic process	2	4	3.794e-02
GO:BP	GO:0048562	embryonic organ morphogenesis	14	305	3.794e-02
GO:BP	GO:0048806	genitalia development	5	48	3.794e-02
GO:BP	GO:0048870	cell motility	49	1716	3.794e-02
GO:BP	GO:0021682	nerve maturation	2	4	3.794e-02
GO:BP	GO:0010845	positive regulation of reciprocal meiotic recombination	2	4	3.794e-02
GO:BP	GO:0060117	auditory receptor cell development	4	29	3.794e-02
GO:BP	GO:0043266	regulation of potassium ion transport	7	94	3.794e-02
GO:BP	GO:0021700	developmental maturation	15	343	3.902e-02
GO:BP	GO:0002703	regulation of leukocyte mediated immunity	12	243	3.953e-02
GO:BP	GO:0008277	regulation of G protein-coupled receptor signaling pathway	9	151	3.974e-02
GO:BP	GO:0009566	fertilization	11	212	4.027e-02
GO:BP	GO:0003341	cilium movement	11	212	4.027e-02
GO:BP	GO:1904888	cranial skeletal system development	6	72	4.099e-02
GO:BP	GO:0002706	regulation of lymphocyte mediated immunity	10	182	4.121e-02
GO:BP	GO:0050764	regulation of phagocytosis	7	97	4.121e-02
GO:BP	GO:0030900	forebrain development	17	417	4.129e-02
GO:BP	GO:0006911	phagocytosis, engulfment	5	50	4.206e-02
GO:BP	GO:0045580	regulation of T cell differentiation	10	183	4.216e-02
GO:BP	GO:1903530	regulation of secretion by cell	21	567	4.216e-02
GO:BP	GO:0007626	locomotory behavior	11	214	4.216e-02
GO:BP	GO:0070887	cellular response to chemical stimulus	59	2186	4.216e-02
GO:BP	GO:0046635	positive regulation of alpha-beta T cell activation	6	73	4.231e-02
GO:BP	GO:0051239	regulation of multicellular organismal process	75	2928	4.231e-02
GO:BP	GO:0045471	response to ethanol	8	125	4.231e-02
GO:BP	GO:0023061	signal release	19	493	4.260e-02
GO:BP	GO:0045619	regulation of lymphocyte differentiation	11	215	4.260e-02
GO:BP	GO:0006955	immune response	55	2008	4.263e-02
GO:BP	GO:1902358	sulfate transmembrane transport	3	15	4.277e-02
GO:BP	GO:1901698	response to nitrogen compound	32	1010	4.350e-02
GO:BP	GO:0002065	columnar/cuboidal epithelial cell differentiation	8	126	4.350e-02
GO:BP	GO:0051346	negative regulation of hydrolase activity	7	99	4.350e-02
GO:BP	GO:0046632	alpha-beta T cell differentiation	8	128	4.751e-02
GO:BP	GO:0022409	positive regulation of cell-cell adhesion	14	319	4.770e-02
GO:BP	GO:0001906	cell killing	11	219	4.770e-02
GO:BP	GO:0060429	epithelium development	37	1229	4.838e-02
GO:BP	GO:0002696	positive regulation of leukocyte activation	15	355	4.871e-02
GO:BP	GO:0007189	adenylate cyclase-activating G protein-coupled receptor signaling pathway	9	158	4.881e-02
GO:BP	GO:0006957	complement activation, alternative pathway	3	16	4.947e-02
GO:BP	GO:0007194	negative regulation of adenylate cyclase activity	3	16	4.947e-02
GO:BP	GO:0061101	neuroendocrine cell differentiation	3	16	4.947e-02
GO:BP	GO:0043374	CD8-positive, alpha-beta T cell differentiation	3	16	4.947e-02
GO:BP	GO:0042102	positive regulation of T cell proliferation	7	102	4.947e-02
GO:BP	GO:0030183	B cell differentiation	9	159	4.985e-02
KEGG	KEGG:04080	Neuroactive ligand-receptor interaction	29	365	1.040e-06
KEGG	KEGG:00430	Taurine and hypotaurine metabolism	5	16	2.720e-03

#write.csv(tableLD, "output/table_LateDOXmotif.csv")

#GO:BP
tableLD_GOBP_d <- tableLD_d %>% 
  dplyr::filter(source=="GO:BP") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

#saveRDS(tableLD_GOBP, "data/tableLD_GOBP.RDS")

tableLD_GOBP_d %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("Late Response Enriched GO:BP Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("GO:BP term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "Late DOX Response Motif Genes-2.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

#KEGG
tableLD_KEGG_d <- tableLD_d %>% 
  dplyr::filter(source=="KEGG") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

tableLD_KEGG_d %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("Late Response Enriched KEGG Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("KEGG term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "Late DOX Response Motif Genes-3.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

Now let’s look at this motif 3 (Late Response) with the posterior probability

motif_LR_pp <- prob_motif_3

LRmotif_genes_pp <- gost(query = motif_LR_pp,
                      organism = "hsapiens",
                      ordered_query = FALSE,
                      measure_underrepresentation = FALSE,
                      evcodes = FALSE,
                      user_threshold = 0.05,
                      correction_method = c("fdr"),
                      sources = c("GO:BP", "KEGG"))

cormotifLRclust_pp <- gostplot(LRmotif_genes_pp, capped = FALSE, interactive = TRUE)
cormotifLRclust_pp

tableLR_pp <- LRmotif_genes_pp$result %>% 
  dplyr::select(c(source, term_id, term_name, intersection_size, term_size, p_value))

tableLR_pp %>% 
  mutate_at(.vars = 6, .funs = scales::label_scientific(digits=4)) %>% 
  kableExtra::kable(.,) %>% 
  kableExtra::kable_paper("striped", full_width = FALSE) %>% 
  kableExtra::kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "hover")) %>% 
  kableExtra::scroll_box(width = "100%", height = "400px")

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0006811	monoatomic ion transport	60	1256	6.212e-11
GO:BP	GO:0034220	monoatomic ion transmembrane transport	52	1017	1.681e-10
GO:BP	GO:0055085	transmembrane transport	65	1538	4.113e-10
GO:BP	GO:0098660	inorganic ion transmembrane transport	45	903	1.161e-08
GO:BP	GO:0015698	inorganic anion transport	18	165	1.375e-07
GO:BP	GO:0006820	monoatomic anion transport	18	167	1.400e-07
GO:BP	GO:0048869	cellular developmental process	118	4382	2.840e-07
GO:BP	GO:0030154	cell differentiation	118	4381	2.840e-07
GO:BP	GO:0006810	transport	117	4341	2.971e-07
GO:BP	GO:0006821	chloride transport	15	122	4.430e-07
GO:BP	GO:0032501	multicellular organismal process	167	7234	1.046e-06
GO:BP	GO:0006812	monoatomic cation transport	43	1032	2.823e-06
GO:BP	GO:0098656	monoatomic anion transmembrane transport	15	142	2.844e-06
GO:BP	GO:0032502	developmental process	152	6478	3.014e-06
GO:BP	GO:0048468	cell development	83	2833	4.124e-06
GO:BP	GO:1902476	chloride transmembrane transport	13	107	4.238e-06
GO:BP	GO:0098655	monoatomic cation transmembrane transport	37	832	4.606e-06
GO:BP	GO:0050896	response to stimulus	193	8993	4.865e-06
GO:BP	GO:0030001	metal ion transport	38	875	4.881e-06
GO:BP	GO:0007193	adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway	11	79	1.047e-05
GO:BP	GO:0007267	cell-cell signaling	48	1316	1.298e-05
GO:BP	GO:0051234	establishment of localization	120	4869	1.533e-05
GO:BP	GO:0065008	regulation of biological quality	81	2847	1.552e-05
GO:BP	GO:0065007	biological regulation	247	12671	1.617e-05
GO:BP	GO:0007188	adenylate cyclase-modulating G protein-coupled receptor signaling pathway	18	248	1.781e-05
GO:BP	GO:0098661	inorganic anion transmembrane transport	13	127	2.060e-05
GO:BP	GO:0098662	inorganic cation transmembrane transport	34	811	4.571e-05
GO:BP	GO:0048856	anatomical structure development	136	5924	7.416e-05
GO:BP	GO:0022414	reproductive process	51	1556	9.471e-05
GO:BP	GO:0051179	localization	127	5521	2.049e-04
GO:BP	GO:0006813	potassium ion transport	16	238	2.050e-04
GO:BP	GO:0015711	organic anion transport	22	442	3.627e-04
GO:BP	GO:0023052	signaling	142	6471	4.510e-04
GO:BP	GO:0051480	regulation of cytosolic calcium ion concentration	8	59	5.282e-04
GO:BP	GO:0007154	cell communication	142	6496	5.345e-04
GO:BP	GO:0048232	male gamete generation	27	654	8.075e-04
GO:BP	GO:0003006	developmental process involved in reproduction	36	1022	8.341e-04
GO:BP	GO:0010817	regulation of hormone levels	24	548	9.563e-04
GO:BP	GO:0071805	potassium ion transmembrane transport	14	213	9.594e-04
GO:BP	GO:0002521	leukocyte differentiation	26	632	1.150e-03
GO:BP	GO:0007186	G protein-coupled receptor signaling pathway	41	1275	1.504e-03
GO:BP	GO:0050789	regulation of biological process	232	12278	1.750e-03
GO:BP	GO:0035725	sodium ion transmembrane transport	12	169	1.750e-03
GO:BP	GO:0007275	multicellular organism development	107	4658	1.750e-03
GO:BP	GO:0099536	synaptic signaling	29	783	2.264e-03
GO:BP	GO:0007283	spermatogenesis	25	637	3.208e-03
GO:BP	GO:0030003	intracellular monoatomic cation homeostasis	22	521	3.208e-03
GO:BP	GO:0019953	sexual reproduction	36	1103	3.281e-03
GO:BP	GO:0055082	intracellular chemical homeostasis	27	723	3.477e-03
GO:BP	GO:0042592	homeostatic process	49	1711	3.593e-03
GO:BP	GO:0006873	intracellular monoatomic ion homeostasis	22	530	3.743e-03
GO:BP	GO:0048731	system development	93	3985	3.743e-03
GO:BP	GO:0098771	inorganic ion homeostasis	22	531	3.776e-03
GO:BP	GO:0050877	nervous system process	44	1489	4.173e-03
GO:BP	GO:0055074	calcium ion homeostasis	16	326	5.815e-03
GO:BP	GO:0140013	meiotic nuclear division	12	198	6.435e-03
GO:BP	GO:0021879	forebrain neuron differentiation	6	46	6.491e-03
GO:BP	GO:0099537	trans-synaptic signaling	27	759	6.655e-03
GO:BP	GO:0035270	endocrine system development	10	142	6.926e-03
GO:BP	GO:0055080	monoatomic cation homeostasis	23	598	6.926e-03
GO:BP	GO:0048609	multicellular organismal reproductive process	32	980	7.045e-03
GO:BP	GO:0007200	phospholipase C-activating G protein-coupled receptor signaling pathway	9	116	7.045e-03
GO:BP	GO:0048878	chemical homeostasis	33	1026	7.079e-03
GO:BP	GO:0006814	sodium ion transport	13	235	7.216e-03
GO:BP	GO:0006874	intracellular calcium ion homeostasis	15	302	7.216e-03
GO:BP	GO:0010951	negative regulation of endopeptidase activity	5	31	7.902e-03
GO:BP	GO:0050801	monoatomic ion homeostasis	23	608	7.924e-03
GO:BP	GO:0002429	immune response-activating cell surface receptor signaling pathway	15	306	7.976e-03
GO:BP	GO:0007276	gamete generation	28	822	8.608e-03
GO:BP	GO:0042445	hormone metabolic process	13	243	9.261e-03
GO:BP	GO:0001775	cell activation	34	1098	1.012e-02
GO:BP	GO:0046903	secretion	31	968	1.091e-02
GO:BP	GO:0051716	cellular response to stimulus	148	7320	1.099e-02
GO:BP	GO:0007268	chemical synaptic transmission	26	753	1.099e-02
GO:BP	GO:0098916	anterograde trans-synaptic signaling	26	753	1.099e-02
GO:BP	GO:0042221	response to chemical	88	3867	1.099e-02
GO:BP	GO:0019722	calcium-mediated signaling	12	218	1.157e-02
GO:BP	GO:1901700	response to oxygen-containing compound	45	1632	1.161e-02
GO:BP	GO:0050957	equilibrioception	3	8	1.165e-02
GO:BP	GO:0060348	bone development	12	220	1.196e-02
GO:BP	GO:1903046	meiotic cell cycle process	12	220	1.196e-02
GO:BP	GO:0009410	response to xenobiotic stimulus	18	436	1.232e-02
GO:BP	GO:0007140	male meiotic nuclear division	6	55	1.232e-02
GO:BP	GO:0021630	olfactory nerve maturation	2	2	1.261e-02
GO:BP	GO:0042110	T cell activation	21	558	1.261e-02
GO:BP	GO:0021872	forebrain generation of neurons	6	56	1.261e-02
GO:BP	GO:0030098	lymphocyte differentiation	18	438	1.261e-02
GO:BP	GO:0036368	cone photoresponse recovery	2	2	1.261e-02
GO:BP	GO:0040020	regulation of meiotic nuclear division	5	36	1.261e-02
GO:BP	GO:0050851	antigen receptor-mediated signaling pathway	11	192	1.285e-02
GO:BP	GO:0051321	meiotic cell cycle	14	294	1.330e-02
GO:BP	GO:0098609	cell-cell adhesion	30	948	1.330e-02
GO:BP	GO:0007155	cell adhesion	42	1511	1.363e-02
GO:BP	GO:0045321	leukocyte activation	30	951	1.372e-02
GO:BP	GO:0021536	diencephalon development	7	81	1.409e-02
GO:BP	GO:0007600	sensory perception	30	955	1.413e-02
GO:BP	GO:0002768	immune response-regulating cell surface receptor signaling pathway	15	334	1.413e-02
GO:BP	GO:0045055	regulated exocytosis	12	229	1.413e-02
GO:BP	GO:0030450	regulation of complement activation, classical pathway	3	9	1.413e-02
GO:BP	GO:1903131	mononuclear cell differentiation	20	529	1.475e-02
GO:BP	GO:0019725	cellular homeostasis	27	826	1.487e-02
GO:BP	GO:0048485	sympathetic nervous system development	4	22	1.570e-02
GO:BP	GO:0046649	lymphocyte activation	26	787	1.582e-02
GO:BP	GO:0048732	gland development	18	454	1.582e-02
GO:BP	GO:0051932	synaptic transmission, GABAergic	6	60	1.582e-02
GO:BP	GO:0002366	leukocyte activation involved in immune response	14	305	1.666e-02
GO:BP	GO:0050794	regulation of cellular process	219	11876	1.689e-02
GO:BP	GO:0021953	central nervous system neuron differentiation	11	203	1.722e-02
GO:BP	GO:0046942	carboxylic acid transport	15	344	1.746e-02
GO:BP	GO:0015849	organic acid transport	15	345	1.783e-02
GO:BP	GO:0009581	detection of external stimulus	9	142	1.795e-02
GO:BP	GO:0002263	cell activation involved in immune response	14	309	1.795e-02
GO:BP	GO:0030217	T cell differentiation	14	312	1.958e-02
GO:BP	GO:1903306	negative regulation of regulated secretory pathway	4	24	1.990e-02
GO:BP	GO:0009582	detection of abiotic stimulus	9	145	2.023e-02
GO:BP	GO:0003008	system process	56	2266	2.064e-02
GO:BP	GO:0009888	tissue development	51	2012	2.112e-02
GO:BP	GO:0006869	lipid transport	17	431	2.155e-02
GO:BP	GO:1903977	positive regulation of glial cell migration	3	11	2.180e-02
GO:BP	GO:0015747	urate transport	3	11	2.180e-02
GO:BP	GO:0003341	cilium movement	11	212	2.195e-02
GO:BP	GO:0042391	regulation of membrane potential	17	433	2.195e-02
GO:BP	GO:0046631	alpha-beta T cell activation	10	181	2.355e-02
GO:BP	GO:0050848	regulation of calcium-mediated signaling	7	93	2.463e-02
GO:BP	GO:0006311	meiotic gene conversion	2	3	2.463e-02
GO:BP	GO:0010466	negative regulation of peptidase activity	5	45	2.463e-02
GO:BP	GO:0010481	epidermal cell division	2	3	2.463e-02
GO:BP	GO:0010482	regulation of epidermal cell division	2	3	2.463e-02
GO:BP	GO:0071486	cellular response to high light intensity	2	3	2.463e-02
GO:BP	GO:0033563	dorsal/ventral axon guidance	2	3	2.463e-02
GO:BP	GO:0021605	cranial nerve maturation	2	3	2.463e-02
GO:BP	GO:0021895	cerebral cortex neuron differentiation	4	26	2.463e-02
GO:BP	GO:1902105	regulation of leukocyte differentiation	14	325	2.463e-02
GO:BP	GO:0002064	epithelial cell development	11	217	2.463e-02
GO:BP	GO:0051445	regulation of meiotic cell cycle	6	69	2.584e-02
GO:BP	GO:0048513	animal organ development	70	3047	2.597e-02
GO:BP	GO:0030097	hemopoiesis	29	971	2.827e-02
GO:BP	GO:1903708	positive regulation of hemopoiesis	10	189	2.899e-02
GO:BP	GO:1902107	positive regulation of leukocyte differentiation	10	189	2.899e-02
GO:BP	GO:0002065	columnar/cuboidal epithelial cell differentiation	8	126	2.899e-02
GO:BP	GO:0008283	cell population proliferation	50	2009	2.927e-02
GO:BP	GO:0051446	positive regulation of meiotic cell cycle	4	28	2.927e-02
GO:BP	GO:0006817	phosphate ion transport	4	28	2.927e-02
GO:BP	GO:0048806	genitalia development	5	48	2.927e-02
GO:BP	GO:0009653	anatomical structure morphogenesis	63	2692	2.952e-02
GO:BP	GO:1904888	cranial skeletal system development	6	72	2.992e-02
GO:BP	GO:0001501	skeletal system development	19	536	3.011e-02
GO:BP	GO:0043301	negative regulation of leukocyte degranulation	3	13	3.011e-02
GO:BP	GO:0042403	thyroid hormone metabolic process	4	29	3.176e-02
GO:BP	GO:0007214	gamma-aminobutyric acid signaling pathway	4	29	3.176e-02
GO:BP	GO:0060249	anatomical structure homeostasis	12	264	3.206e-02
GO:BP	GO:0001894	tissue homeostasis	12	264	3.206e-02
GO:BP	GO:0030900	forebrain development	16	417	3.206e-02
GO:BP	GO:0060429	epithelium development	34	1229	3.455e-02
GO:BP	GO:0007127	meiosis I	8	132	3.539e-02
GO:BP	GO:0140352	export from cell	27	901	3.547e-02
GO:BP	GO:0035589	G protein-coupled purinergic nucleotide receptor signaling pathway	3	14	3.548e-02
GO:BP	GO:0048518	positive regulation of biological process	125	6235	3.604e-02
GO:BP	GO:0043410	positive regulation of MAPK cascade	17	465	3.669e-02
GO:BP	GO:0014070	response to organic cyclic compound	27	909	3.791e-02
GO:BP	GO:0006968	cellular defense response	5	52	3.791e-02
GO:BP	GO:0046352	disaccharide catabolic process	2	4	3.791e-02
GO:BP	GO:0010845	positive regulation of reciprocal meiotic recombination	2	4	3.791e-02
GO:BP	GO:0060294	cilium movement involved in cell motility	9	167	3.791e-02
GO:BP	GO:0021682	nerve maturation	2	4	3.791e-02
GO:BP	GO:0035822	gene conversion	2	4	3.791e-02
GO:BP	GO:0141006	transposable element silencing by piRNA-mediated heterochromatin formation	2	4	3.791e-02
GO:BP	GO:0140966	piRNA-mediated heterochromatin formation	2	4	3.791e-02
GO:BP	GO:0010520	regulation of reciprocal meiotic recombination	2	4	3.791e-02
GO:BP	GO:0045728	respiratory burst after phagocytosis	2	4	3.791e-02
GO:BP	GO:1990834	response to odorant	2	4	3.791e-02
GO:BP	GO:0009605	response to external stimulus	56	2367	3.880e-02
GO:BP	GO:0071695	anatomical structure maturation	12	274	3.887e-02
GO:BP	GO:0006816	calcium ion transport	16	433	4.134e-02
GO:BP	GO:0007165	signal transduction	120	5979	4.180e-02
GO:BP	GO:0007399	nervous system development	59	2541	4.341e-02
GO:BP	GO:2000241	regulation of reproductive process	10	206	4.341e-02
GO:BP	GO:0060285	cilium-dependent cell motility	9	172	4.341e-02
GO:BP	GO:0001539	cilium or flagellum-dependent cell motility	9	172	4.341e-02
GO:BP	GO:0030855	epithelial cell differentiation	23	741	4.442e-02
GO:BP	GO:0032940	secretion by cell	25	832	4.442e-02
GO:BP	GO:0007218	neuropeptide signaling pathway	7	110	4.452e-02
GO:BP	GO:0006957	complement activation, alternative pathway	3	16	4.452e-02
GO:BP	GO:0007194	negative regulation of adenylate cyclase activity	3	16	4.452e-02
GO:BP	GO:0010876	lipid localization	17	480	4.452e-02
GO:BP	GO:0061982	meiosis I cell cycle process	8	141	4.452e-02
GO:BP	GO:0061101	neuroendocrine cell differentiation	3	16	4.452e-02
GO:BP	GO:0043374	CD8-positive, alpha-beta T cell differentiation	3	16	4.452e-02
GO:BP	GO:0048522	positive regulation of cellular process	118	5886	4.481e-02
GO:BP	GO:1903530	regulation of secretion by cell	19	567	4.481e-02
GO:BP	GO:0003382	epithelial cell morphogenesis	4	34	4.481e-02
GO:BP	GO:0043270	positive regulation of monoatomic ion transport	10	209	4.481e-02
GO:BP	GO:0010526	transposable element silencing	4	34	4.481e-02
GO:BP	GO:0015701	bicarbonate transport	4	34	4.481e-02
GO:BP	GO:0045745	positive regulation of G protein-coupled receptor signaling pathway	4	34	4.481e-02
GO:BP	GO:0050870	positive regulation of T cell activation	11	248	4.822e-02
GO:BP	GO:0009566	fertilization	10	212	4.830e-02
GO:BP	GO:0045577	regulation of B cell differentiation	4	35	4.848e-02
GO:BP	GO:0051050	positive regulation of transport	25	844	4.848e-02
GO:BP	GO:0043299	leukocyte degranulation	6	84	4.848e-02
GO:BP	GO:0043949	regulation of cAMP-mediated signaling	4	35	4.848e-02
GO:BP	GO:0002679	respiratory burst involved in defense response	3	17	4.900e-02
GO:BP	GO:0009642	response to light intensity	3	17	4.900e-02
GO:BP	GO:0009628	response to abiotic stimulus	31	1130	4.900e-02
GO:BP	GO:0031280	negative regulation of cyclase activity	3	17	4.900e-02
GO:BP	GO:0045917	positive regulation of complement activation	2	5	4.921e-02
GO:BP	GO:0045920	negative regulation of exocytosis	4	36	4.921e-02
GO:BP	GO:0070995	NADPH oxidation	2	5	4.921e-02
GO:BP	GO:2000611	positive regulation of thyroid hormone generation	2	5	4.921e-02
GO:BP	GO:0032197	retrotransposition	4	36	4.921e-02
GO:BP	GO:0007610	behavior	21	665	4.921e-02
GO:BP	GO:0009644	response to high light intensity	2	5	4.921e-02
GO:BP	GO:0009887	animal organ morphogenesis	29	1037	4.921e-02
GO:BP	GO:0030317	flagellated sperm motility	8	147	4.921e-02
GO:BP	GO:0009914	hormone transport	13	328	4.921e-02
GO:BP	GO:0097722	sperm motility	8	147	4.921e-02
GO:BP	GO:0023061	signal release	17	493	4.921e-02
GO:BP	GO:0071484	cellular response to light intensity	2	5	4.921e-02
GO:BP	GO:0042127	regulation of cell population proliferation	42	1682	4.921e-02
GO:BP	GO:0002434	immune complex clearance	2	5	4.921e-02
GO:BP	GO:0045216	cell-cell junction organization	10	216	4.931e-02
KEGG	KEGG:04080	Neuroactive ligand-receptor interaction	25	365	1.188e-05

#write.csv(tableLR_pp, "output/table_LRmotif.csv")

#GO:BP
tableLR_GOBP_pp <- tableLR_pp %>% 
  dplyr::filter(source=="GO:BP") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

#saveRDS(tableLR_GOBP_pp, "data/tableLR_GOBP_postprob.RDS")

tableLR_GOBP_pp %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("No Response Enriched GO:BP Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("GO:BP term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "Late Response Motif 3 Posterior Probability-2.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

#KEGG
tableLR_KEGG_pp <- tableLR_pp %>% 
  dplyr::filter(source=="KEGG") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

tableLR_KEGG_pp %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("No Response Enriched KEGG Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("KEGG term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "Late Response Motif 3 Posterior Probability-3.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

Now let’s look at motif 4 - Early Sustained Response

motif_ED_d <- clust4_d

EDmotif_genes_d <- gost(query = motif_ED_d,
                      organism = "hsapiens",
                      ordered_query = FALSE,
                      measure_underrepresentation = FALSE,
                      evcodes = FALSE,
                      user_threshold = 0.05,
                      correction_method = c("fdr"),
                      sources = c("GO:BP", "KEGG"))

cormotifEDclust_d <- gostplot(EDmotif_genes_d, capped = FALSE, interactive = TRUE)
cormotifEDclust_d

tableED_d <- EDmotif_genes_d$result %>% 
  dplyr::select(c(source, term_id, term_name, intersection_size, term_size, p_value))

tableED_d %>% 
  mutate_at(.vars = 6, .funs = scales::label_scientific(digits=4)) %>% 
  kableExtra::kable(.,) %>% 
  kableExtra::kable_paper("striped", full_width = FALSE) %>% 
  kableExtra::kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "hover")) %>% 
  kableExtra::scroll_box(width = "100%", height = "400px")

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0032502	developmental process	355	6478	5.420e-13
GO:BP	GO:0048856	anatomical structure development	331	5924	5.420e-13
GO:BP	GO:0032501	multicellular organismal process	372	7234	6.854e-10
GO:BP	GO:0048869	cellular developmental process	249	4382	2.296e-09
GO:BP	GO:0030154	cell differentiation	249	4381	2.296e-09
GO:BP	GO:0045165	cell fate commitment	37	291	1.255e-07
GO:BP	GO:0007275	multicellular organism development	253	4658	1.298e-07
GO:BP	GO:0048731	system development	221	3985	4.809e-07
GO:BP	GO:0003002	regionalization	44	434	2.357e-06
GO:BP	GO:0007389	pattern specification process	45	478	1.363e-05
GO:BP	GO:0001708	cell fate specification	19	113	2.533e-05
GO:BP	GO:0048513	animal organ development	171	3047	2.533e-05
GO:BP	GO:0009891	positive regulation of biosynthetic process	155	2707	3.346e-05
GO:BP	GO:0048663	neuron fate commitment	15	73	3.397e-05
GO:BP	GO:0007399	nervous system development	147	2541	3.675e-05
GO:BP	GO:0009953	dorsal/ventral pattern formation	16	90	8.195e-05
GO:BP	GO:0060429	epithelium development	83	1229	8.195e-05
GO:BP	GO:0009653	anatomical structure morphogenesis	152	2692	8.195e-05
GO:BP	GO:0009887	animal organ morphogenesis	73	1037	8.710e-05
GO:BP	GO:0018958	phenol-containing compound metabolic process	18	116	1.125e-04
GO:BP	GO:0007204	positive regulation of cytosolic calcium ion concentration	22	169	1.341e-04
GO:BP	GO:0009888	tissue development	118	2012	3.034e-04
GO:BP	GO:0033993	response to lipid	65	921	3.055e-04
GO:BP	GO:0007423	sensory organ development	48	612	4.541e-04
GO:BP	GO:0048468	cell development	154	2833	4.613e-04
GO:BP	GO:0034220	monoatomic ion transmembrane transport	69	1017	5.073e-04
GO:BP	GO:0030182	neuron differentiation	89	1434	6.680e-04
GO:BP	GO:0006357	regulation of transcription by RNA polymerase II	141	2572	7.935e-04
GO:BP	GO:0048665	neuron fate specification	9	35	8.914e-04
GO:BP	GO:0007417	central nervous system development	69	1038	8.914e-04
GO:BP	GO:0010557	positive regulation of macromolecule biosynthetic process	141	2604	1.377e-03
GO:BP	GO:0048699	generation of neurons	91	1517	1.699e-03
GO:BP	GO:1901615	organic hydroxy compound metabolic process	42	549	2.643e-03
GO:BP	GO:1901616	organic hydroxy compound catabolic process	11	61	2.797e-03
GO:BP	GO:0030855	epithelial cell differentiation	52	741	2.797e-03
GO:BP	GO:0006366	transcription by RNA polymerase II	143	2698	3.046e-03
GO:BP	GO:0048880	sensory system development	34	414	3.661e-03
GO:BP	GO:0060579	ventral spinal cord interneuron fate commitment	5	11	4.463e-03
GO:BP	GO:0060581	cell fate commitment involved in pattern specification	5	11	4.463e-03
GO:BP	GO:0022008	neurogenesis	99	1746	5.269e-03
GO:BP	GO:0021513	spinal cord dorsal/ventral patterning	6	18	5.269e-03
GO:BP	GO:0150063	visual system development	33	408	5.729e-03
GO:BP	GO:0019336	phenol-containing compound catabolic process	5	12	6.722e-03
GO:BP	GO:0009952	anterior/posterior pattern specification	22	225	6.780e-03
GO:BP	GO:0006952	defense response	101	1809	7.147e-03
GO:BP	GO:0002118	aggressive behavior	4	7	8.370e-03
GO:BP	GO:0006811	monoatomic ion transport	75	1256	8.467e-03
GO:BP	GO:0098660	inorganic ion transmembrane transport	58	903	8.467e-03
GO:BP	GO:0021511	spinal cord patterning	6	20	8.625e-03
GO:BP	GO:0045944	positive regulation of transcription by RNA polymerase II	75	1261	8.709e-03
GO:BP	GO:0060732	positive regulation of inositol phosphate biosynthetic process	5	13	8.709e-03
GO:BP	GO:0001654	eye development	32	404	8.709e-03
GO:BP	GO:0006954	inflammatory response	55	847	8.709e-03
GO:BP	GO:0021514	ventral spinal cord interneuron differentiation	5	13	8.709e-03
GO:BP	GO:0042403	thyroid hormone metabolic process	7	29	8.866e-03
GO:BP	GO:0003407	neural retina development	12	85	8.906e-03
GO:BP	GO:0007281	germ cell development	30	370	8.906e-03
GO:BP	GO:0022412	cellular process involved in reproduction in multicellular organism	32	408	9.645e-03
GO:BP	GO:0035270	endocrine system development	16	142	1.008e-02
GO:BP	GO:0009893	positive regulation of metabolic process	179	3648	1.135e-02
GO:BP	GO:0060040	retinal bipolar neuron differentiation	4	8	1.224e-02
GO:BP	GO:2000179	positive regulation of neural precursor cell proliferation	10	64	1.319e-02
GO:BP	GO:0071542	dopaminergic neuron differentiation	8	42	1.456e-02
GO:BP	GO:0010919	regulation of inositol phosphate biosynthetic process	5	15	1.557e-02
GO:BP	GO:0007267	cell-cell signaling	76	1316	1.589e-02
GO:BP	GO:0009605	response to external stimulus	123	2367	1.634e-02
GO:BP	GO:0035115	embryonic forelimb morphogenesis	7	33	1.744e-02
GO:BP	GO:0043010	camera-type eye development	28	352	1.744e-02
GO:BP	GO:1903409	reactive oxygen species biosynthetic process	9	55	1.768e-02
GO:BP	GO:0042420	dopamine catabolic process	4	9	1.862e-02
GO:BP	GO:0007156	homophilic cell adhesion via plasma membrane adhesion molecules	17	168	1.930e-02
GO:BP	GO:0050793	regulation of developmental process	126	2453	1.952e-02
GO:BP	GO:0042127	regulation of cell population proliferation	92	1682	1.952e-02
GO:BP	GO:0062013	positive regulation of small molecule metabolic process	15	138	1.952e-02
GO:BP	GO:0072330	monocarboxylic acid biosynthetic process	20	218	2.027e-02
GO:BP	GO:1902932	positive regulation of alcohol biosynthetic process	6	25	2.104e-02
GO:BP	GO:0045595	regulation of cell differentiation	87	1577	2.104e-02
GO:BP	GO:0045893	positive regulation of DNA-templated transcription	93	1710	2.104e-02
GO:BP	GO:0051239	regulation of multicellular organismal process	146	2928	2.122e-02
GO:BP	GO:1902680	positive regulation of RNA biosynthetic process	93	1713	2.144e-02
GO:BP	GO:0071396	cellular response to lipid	41	609	2.226e-02
GO:BP	GO:0065007	biological regulation	528	12671	2.357e-02
GO:BP	GO:0003006	developmental process involved in reproduction	61	1022	2.358e-02
GO:BP	GO:0019614	catechol-containing compound catabolic process	4	10	2.479e-02
GO:BP	GO:0042424	catecholamine catabolic process	4	10	2.479e-02
GO:BP	GO:0006633	fatty acid biosynthetic process	16	159	2.560e-02
GO:BP	GO:0051094	positive regulation of developmental process	75	1331	2.715e-02
GO:BP	GO:0062012	regulation of small molecule metabolic process	25	314	2.821e-02
GO:BP	GO:0006334	nucleosome assembly	13	115	2.821e-02
GO:BP	GO:0042759	long-chain fatty acid biosynthetic process	6	27	2.857e-02
GO:BP	GO:0098742	cell-cell adhesion via plasma-membrane adhesion molecules	23	280	2.988e-02
GO:BP	GO:0010628	positive regulation of gene expression	68	1189	3.217e-02
GO:BP	GO:0046069	cGMP catabolic process	3	5	3.232e-02
GO:BP	GO:0060284	regulation of cell development	52	851	3.278e-02
GO:BP	GO:2000049	positive regulation of cell-cell adhesion mediated by cadherin	4	11	3.278e-02
GO:BP	GO:0021515	cell differentiation in spinal cord	8	50	3.278e-02
GO:BP	GO:0010752	regulation of cGMP-mediated signaling	4	11	3.278e-02
GO:BP	GO:0014049	positive regulation of glutamate secretion	4	11	3.278e-02
GO:BP	GO:2000026	regulation of multicellular organismal development	78	1413	3.360e-02
GO:BP	GO:2000177	regulation of neural precursor cell proliferation	12	104	3.422e-02
GO:BP	GO:0042391	regulation of membrane potential	31	433	3.442e-02
GO:BP	GO:0034728	nucleosome organization	14	135	3.596e-02
GO:BP	GO:0051254	positive regulation of RNA metabolic process	97	1844	3.596e-02
GO:BP	GO:0030900	forebrain development	30	417	3.759e-02
GO:BP	GO:0022414	reproductive process	84	1556	3.821e-02
GO:BP	GO:1903426	regulation of reactive oxygen species biosynthetic process	7	40	3.821e-02
GO:BP	GO:0055085	transmembrane transport	83	1538	4.038e-02
GO:BP	GO:0003008	system process	115	2266	4.038e-02
GO:BP	GO:0090596	sensory organ morphogenesis	23	290	4.038e-02
GO:BP	GO:0048598	embryonic morphogenesis	40	617	4.038e-02
GO:BP	GO:0014070	response to organic cyclic compound	54	909	4.145e-02
GO:BP	GO:0035136	forelimb morphogenesis	7	41	4.145e-02
GO:BP	GO:1901654	response to ketone	19	221	4.145e-02
GO:BP	GO:0045597	positive regulation of cell differentiation	52	866	4.145e-02
GO:BP	GO:0052652	cyclic purine nucleotide metabolic process	7	41	4.145e-02
GO:BP	GO:0061351	neural precursor cell proliferation	16	171	4.226e-02
GO:BP	GO:0010604	positive regulation of macromolecule metabolic process	160	3349	4.343e-02
GO:BP	GO:0001819	positive regulation of cytokine production	33	486	4.343e-02
GO:BP	GO:0009187	cyclic nucleotide metabolic process	7	42	4.343e-02
GO:BP	GO:0009713	catechol-containing compound biosynthetic process	5	21	4.343e-02
GO:BP	GO:0060322	head development	48	789	4.343e-02
GO:BP	GO:0060563	neuroepithelial cell differentiation	7	42	4.343e-02
GO:BP	GO:0021536	diencephalon development	10	81	4.343e-02
GO:BP	GO:0048609	multicellular organismal reproductive process	57	980	4.343e-02
GO:BP	GO:0065008	regulation of biological quality	139	2847	4.343e-02
GO:BP	GO:0007218	neuropeptide signaling pathway	12	110	4.343e-02
GO:BP	GO:1903142	positive regulation of establishment of endothelial barrier	3	6	4.343e-02
GO:BP	GO:0042475	odontogenesis of dentin-containing tooth	11	95	4.343e-02
GO:BP	GO:0042423	catecholamine biosynthetic process	5	21	4.343e-02
GO:BP	GO:0007610	behavior	42	665	4.343e-02
GO:BP	GO:0098662	inorganic cation transmembrane transport	49	811	4.343e-02
GO:BP	GO:0048568	embryonic organ development	32	463	4.343e-02
GO:BP	GO:0021554	optic nerve development	5	21	4.343e-02
GO:BP	GO:1901552	positive regulation of endothelial cell development	3	6	4.343e-02
GO:BP	GO:0043132	NAD transport	3	6	4.343e-02
GO:BP	GO:0002065	columnar/cuboidal epithelial cell differentiation	13	126	4.371e-02
GO:BP	GO:0008283	cell population proliferation	103	2009	4.371e-02
GO:BP	GO:0021983	pituitary gland development	7	43	4.596e-02
GO:BP	GO:0007501	mesodermal cell fate specification	4	13	4.663e-02
GO:BP	GO:0036006	cellular response to macrophage colony-stimulating factor stimulus	4	13	4.663e-02
GO:BP	GO:2001141	regulation of RNA biosynthetic process	164	3454	4.663e-02
GO:BP	GO:0045907	positive regulation of vasoconstriction	6	32	4.715e-02
GO:BP	GO:0045723	positive regulation of fatty acid biosynthetic process	5	22	4.864e-02
GO:BP	GO:0008544	epidermis development	28	394	4.864e-02
KEGG	KEGG:04080	Neuroactive ligand-receptor interaction	40	365	3.260e-07
KEGG	KEGG:05322	Systemic lupus erythematosus	22	132	6.042e-07
KEGG	KEGG:05034	Alcoholism	22	187	2.222e-04
KEGG	KEGG:04613	Neutrophil extracellular trap formation	20	188	2.170e-03
KEGG	KEGG:05032	Morphine addiction	12	89	6.221e-03
KEGG	KEGG:04060	Cytokine-cytokine receptor interaction	25	291	6.221e-03
KEGG	KEGG:05202	Transcriptional misregulation in cancer	18	192	1.531e-02

#write.csv(tableED, "output/table_EarlyDOXmotif.csv")


#GO:BP
tableED_GOBP_d <- tableED_d %>% 
  dplyr::filter(source=="GO:BP") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

#saveRDS(tableED_GOBP, "data/tableED_GOBP.RDS")

tableED_GOBP_d %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("Early Sustained Response Enriched GO:BP Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("GO:BP term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "Early Sustained DOX Response Motif Genes-2.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

#KEGG
tableED_KEGG_d <- tableED_d %>% 
  dplyr::filter(source=="KEGG") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

tableED_KEGG_d %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("Early Sustained Response Enriched KEGG Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("KEGG term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "Early Sustained DOX Response Motif Genes-3.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

Now let’s see this with the posterior probability for the Early Sustained Response motif 4

motif_ESR_pp <- prob_motif_4

ESRmotif_genes_pp <- gost(query = motif_ESR_pp,
                      organism = "hsapiens",
                      ordered_query = FALSE,
                      measure_underrepresentation = FALSE,
                      evcodes = FALSE,
                      user_threshold = 0.05,
                      correction_method = c("fdr"),
                      sources = c("GO:BP", "KEGG"))

cormotifESRclust_pp <- gostplot(ESRmotif_genes_pp, capped = FALSE, interactive = TRUE)
cormotifESRclust_pp

tableESR_pp <- LRmotif_genes_pp$result %>% 
  dplyr::select(c(source, term_id, term_name, intersection_size, term_size, p_value))

tableESR_pp %>% 
  mutate_at(.vars = 6, .funs = scales::label_scientific(digits=4)) %>% 
  kableExtra::kable(.,) %>% 
  kableExtra::kable_paper("striped", full_width = FALSE) %>% 
  kableExtra::kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "hover")) %>% 
  kableExtra::scroll_box(width = "100%", height = "400px")

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0006811	monoatomic ion transport	60	1256	6.212e-11
GO:BP	GO:0034220	monoatomic ion transmembrane transport	52	1017	1.681e-10
GO:BP	GO:0055085	transmembrane transport	65	1538	4.113e-10
GO:BP	GO:0098660	inorganic ion transmembrane transport	45	903	1.161e-08
GO:BP	GO:0015698	inorganic anion transport	18	165	1.375e-07
GO:BP	GO:0006820	monoatomic anion transport	18	167	1.400e-07
GO:BP	GO:0048869	cellular developmental process	118	4382	2.840e-07
GO:BP	GO:0030154	cell differentiation	118	4381	2.840e-07
GO:BP	GO:0006810	transport	117	4341	2.971e-07
GO:BP	GO:0006821	chloride transport	15	122	4.430e-07
GO:BP	GO:0032501	multicellular organismal process	167	7234	1.046e-06
GO:BP	GO:0006812	monoatomic cation transport	43	1032	2.823e-06
GO:BP	GO:0098656	monoatomic anion transmembrane transport	15	142	2.844e-06
GO:BP	GO:0032502	developmental process	152	6478	3.014e-06
GO:BP	GO:0048468	cell development	83	2833	4.124e-06
GO:BP	GO:1902476	chloride transmembrane transport	13	107	4.238e-06
GO:BP	GO:0098655	monoatomic cation transmembrane transport	37	832	4.606e-06
GO:BP	GO:0050896	response to stimulus	193	8993	4.865e-06
GO:BP	GO:0030001	metal ion transport	38	875	4.881e-06
GO:BP	GO:0007193	adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway	11	79	1.047e-05
GO:BP	GO:0007267	cell-cell signaling	48	1316	1.298e-05
GO:BP	GO:0051234	establishment of localization	120	4869	1.533e-05
GO:BP	GO:0065008	regulation of biological quality	81	2847	1.552e-05
GO:BP	GO:0065007	biological regulation	247	12671	1.617e-05
GO:BP	GO:0007188	adenylate cyclase-modulating G protein-coupled receptor signaling pathway	18	248	1.781e-05
GO:BP	GO:0098661	inorganic anion transmembrane transport	13	127	2.060e-05
GO:BP	GO:0098662	inorganic cation transmembrane transport	34	811	4.571e-05
GO:BP	GO:0048856	anatomical structure development	136	5924	7.416e-05
GO:BP	GO:0022414	reproductive process	51	1556	9.471e-05
GO:BP	GO:0051179	localization	127	5521	2.049e-04
GO:BP	GO:0006813	potassium ion transport	16	238	2.050e-04
GO:BP	GO:0015711	organic anion transport	22	442	3.627e-04
GO:BP	GO:0023052	signaling	142	6471	4.510e-04
GO:BP	GO:0051480	regulation of cytosolic calcium ion concentration	8	59	5.282e-04
GO:BP	GO:0007154	cell communication	142	6496	5.345e-04
GO:BP	GO:0048232	male gamete generation	27	654	8.075e-04
GO:BP	GO:0003006	developmental process involved in reproduction	36	1022	8.341e-04
GO:BP	GO:0010817	regulation of hormone levels	24	548	9.563e-04
GO:BP	GO:0071805	potassium ion transmembrane transport	14	213	9.594e-04
GO:BP	GO:0002521	leukocyte differentiation	26	632	1.150e-03
GO:BP	GO:0007186	G protein-coupled receptor signaling pathway	41	1275	1.504e-03
GO:BP	GO:0050789	regulation of biological process	232	12278	1.750e-03
GO:BP	GO:0035725	sodium ion transmembrane transport	12	169	1.750e-03
GO:BP	GO:0007275	multicellular organism development	107	4658	1.750e-03
GO:BP	GO:0099536	synaptic signaling	29	783	2.264e-03
GO:BP	GO:0007283	spermatogenesis	25	637	3.208e-03
GO:BP	GO:0030003	intracellular monoatomic cation homeostasis	22	521	3.208e-03
GO:BP	GO:0019953	sexual reproduction	36	1103	3.281e-03
GO:BP	GO:0055082	intracellular chemical homeostasis	27	723	3.477e-03
GO:BP	GO:0042592	homeostatic process	49	1711	3.593e-03
GO:BP	GO:0006873	intracellular monoatomic ion homeostasis	22	530	3.743e-03
GO:BP	GO:0048731	system development	93	3985	3.743e-03
GO:BP	GO:0098771	inorganic ion homeostasis	22	531	3.776e-03
GO:BP	GO:0050877	nervous system process	44	1489	4.173e-03
GO:BP	GO:0055074	calcium ion homeostasis	16	326	5.815e-03
GO:BP	GO:0140013	meiotic nuclear division	12	198	6.435e-03
GO:BP	GO:0021879	forebrain neuron differentiation	6	46	6.491e-03
GO:BP	GO:0099537	trans-synaptic signaling	27	759	6.655e-03
GO:BP	GO:0035270	endocrine system development	10	142	6.926e-03
GO:BP	GO:0055080	monoatomic cation homeostasis	23	598	6.926e-03
GO:BP	GO:0048609	multicellular organismal reproductive process	32	980	7.045e-03
GO:BP	GO:0007200	phospholipase C-activating G protein-coupled receptor signaling pathway	9	116	7.045e-03
GO:BP	GO:0048878	chemical homeostasis	33	1026	7.079e-03
GO:BP	GO:0006814	sodium ion transport	13	235	7.216e-03
GO:BP	GO:0006874	intracellular calcium ion homeostasis	15	302	7.216e-03
GO:BP	GO:0010951	negative regulation of endopeptidase activity	5	31	7.902e-03
GO:BP	GO:0050801	monoatomic ion homeostasis	23	608	7.924e-03
GO:BP	GO:0002429	immune response-activating cell surface receptor signaling pathway	15	306	7.976e-03
GO:BP	GO:0007276	gamete generation	28	822	8.608e-03
GO:BP	GO:0042445	hormone metabolic process	13	243	9.261e-03
GO:BP	GO:0001775	cell activation	34	1098	1.012e-02
GO:BP	GO:0046903	secretion	31	968	1.091e-02
GO:BP	GO:0051716	cellular response to stimulus	148	7320	1.099e-02
GO:BP	GO:0007268	chemical synaptic transmission	26	753	1.099e-02
GO:BP	GO:0098916	anterograde trans-synaptic signaling	26	753	1.099e-02
GO:BP	GO:0042221	response to chemical	88	3867	1.099e-02
GO:BP	GO:0019722	calcium-mediated signaling	12	218	1.157e-02
GO:BP	GO:1901700	response to oxygen-containing compound	45	1632	1.161e-02
GO:BP	GO:0050957	equilibrioception	3	8	1.165e-02
GO:BP	GO:0060348	bone development	12	220	1.196e-02
GO:BP	GO:1903046	meiotic cell cycle process	12	220	1.196e-02
GO:BP	GO:0009410	response to xenobiotic stimulus	18	436	1.232e-02
GO:BP	GO:0007140	male meiotic nuclear division	6	55	1.232e-02
GO:BP	GO:0021630	olfactory nerve maturation	2	2	1.261e-02
GO:BP	GO:0042110	T cell activation	21	558	1.261e-02
GO:BP	GO:0021872	forebrain generation of neurons	6	56	1.261e-02
GO:BP	GO:0030098	lymphocyte differentiation	18	438	1.261e-02
GO:BP	GO:0036368	cone photoresponse recovery	2	2	1.261e-02
GO:BP	GO:0040020	regulation of meiotic nuclear division	5	36	1.261e-02
GO:BP	GO:0050851	antigen receptor-mediated signaling pathway	11	192	1.285e-02
GO:BP	GO:0051321	meiotic cell cycle	14	294	1.330e-02
GO:BP	GO:0098609	cell-cell adhesion	30	948	1.330e-02
GO:BP	GO:0007155	cell adhesion	42	1511	1.363e-02
GO:BP	GO:0045321	leukocyte activation	30	951	1.372e-02
GO:BP	GO:0021536	diencephalon development	7	81	1.409e-02
GO:BP	GO:0007600	sensory perception	30	955	1.413e-02
GO:BP	GO:0002768	immune response-regulating cell surface receptor signaling pathway	15	334	1.413e-02
GO:BP	GO:0045055	regulated exocytosis	12	229	1.413e-02
GO:BP	GO:0030450	regulation of complement activation, classical pathway	3	9	1.413e-02
GO:BP	GO:1903131	mononuclear cell differentiation	20	529	1.475e-02
GO:BP	GO:0019725	cellular homeostasis	27	826	1.487e-02
GO:BP	GO:0048485	sympathetic nervous system development	4	22	1.570e-02
GO:BP	GO:0046649	lymphocyte activation	26	787	1.582e-02
GO:BP	GO:0048732	gland development	18	454	1.582e-02
GO:BP	GO:0051932	synaptic transmission, GABAergic	6	60	1.582e-02
GO:BP	GO:0002366	leukocyte activation involved in immune response	14	305	1.666e-02
GO:BP	GO:0050794	regulation of cellular process	219	11876	1.689e-02
GO:BP	GO:0021953	central nervous system neuron differentiation	11	203	1.722e-02
GO:BP	GO:0046942	carboxylic acid transport	15	344	1.746e-02
GO:BP	GO:0015849	organic acid transport	15	345	1.783e-02
GO:BP	GO:0009581	detection of external stimulus	9	142	1.795e-02
GO:BP	GO:0002263	cell activation involved in immune response	14	309	1.795e-02
GO:BP	GO:0030217	T cell differentiation	14	312	1.958e-02
GO:BP	GO:1903306	negative regulation of regulated secretory pathway	4	24	1.990e-02
GO:BP	GO:0009582	detection of abiotic stimulus	9	145	2.023e-02
GO:BP	GO:0003008	system process	56	2266	2.064e-02
GO:BP	GO:0009888	tissue development	51	2012	2.112e-02
GO:BP	GO:0006869	lipid transport	17	431	2.155e-02
GO:BP	GO:1903977	positive regulation of glial cell migration	3	11	2.180e-02
GO:BP	GO:0015747	urate transport	3	11	2.180e-02
GO:BP	GO:0003341	cilium movement	11	212	2.195e-02
GO:BP	GO:0042391	regulation of membrane potential	17	433	2.195e-02
GO:BP	GO:0046631	alpha-beta T cell activation	10	181	2.355e-02
GO:BP	GO:0050848	regulation of calcium-mediated signaling	7	93	2.463e-02
GO:BP	GO:0006311	meiotic gene conversion	2	3	2.463e-02
GO:BP	GO:0010466	negative regulation of peptidase activity	5	45	2.463e-02
GO:BP	GO:0010481	epidermal cell division	2	3	2.463e-02
GO:BP	GO:0010482	regulation of epidermal cell division	2	3	2.463e-02
GO:BP	GO:0071486	cellular response to high light intensity	2	3	2.463e-02
GO:BP	GO:0033563	dorsal/ventral axon guidance	2	3	2.463e-02
GO:BP	GO:0021605	cranial nerve maturation	2	3	2.463e-02
GO:BP	GO:0021895	cerebral cortex neuron differentiation	4	26	2.463e-02
GO:BP	GO:1902105	regulation of leukocyte differentiation	14	325	2.463e-02
GO:BP	GO:0002064	epithelial cell development	11	217	2.463e-02
GO:BP	GO:0051445	regulation of meiotic cell cycle	6	69	2.584e-02
GO:BP	GO:0048513	animal organ development	70	3047	2.597e-02
GO:BP	GO:0030097	hemopoiesis	29	971	2.827e-02
GO:BP	GO:1903708	positive regulation of hemopoiesis	10	189	2.899e-02
GO:BP	GO:1902107	positive regulation of leukocyte differentiation	10	189	2.899e-02
GO:BP	GO:0002065	columnar/cuboidal epithelial cell differentiation	8	126	2.899e-02
GO:BP	GO:0008283	cell population proliferation	50	2009	2.927e-02
GO:BP	GO:0051446	positive regulation of meiotic cell cycle	4	28	2.927e-02
GO:BP	GO:0006817	phosphate ion transport	4	28	2.927e-02
GO:BP	GO:0048806	genitalia development	5	48	2.927e-02
GO:BP	GO:0009653	anatomical structure morphogenesis	63	2692	2.952e-02
GO:BP	GO:1904888	cranial skeletal system development	6	72	2.992e-02
GO:BP	GO:0001501	skeletal system development	19	536	3.011e-02
GO:BP	GO:0043301	negative regulation of leukocyte degranulation	3	13	3.011e-02
GO:BP	GO:0042403	thyroid hormone metabolic process	4	29	3.176e-02
GO:BP	GO:0007214	gamma-aminobutyric acid signaling pathway	4	29	3.176e-02
GO:BP	GO:0060249	anatomical structure homeostasis	12	264	3.206e-02
GO:BP	GO:0001894	tissue homeostasis	12	264	3.206e-02
GO:BP	GO:0030900	forebrain development	16	417	3.206e-02
GO:BP	GO:0060429	epithelium development	34	1229	3.455e-02
GO:BP	GO:0007127	meiosis I	8	132	3.539e-02
GO:BP	GO:0140352	export from cell	27	901	3.547e-02
GO:BP	GO:0035589	G protein-coupled purinergic nucleotide receptor signaling pathway	3	14	3.548e-02
GO:BP	GO:0048518	positive regulation of biological process	125	6235	3.604e-02
GO:BP	GO:0043410	positive regulation of MAPK cascade	17	465	3.669e-02
GO:BP	GO:0014070	response to organic cyclic compound	27	909	3.791e-02
GO:BP	GO:0006968	cellular defense response	5	52	3.791e-02
GO:BP	GO:0046352	disaccharide catabolic process	2	4	3.791e-02
GO:BP	GO:0010845	positive regulation of reciprocal meiotic recombination	2	4	3.791e-02
GO:BP	GO:0060294	cilium movement involved in cell motility	9	167	3.791e-02
GO:BP	GO:0021682	nerve maturation	2	4	3.791e-02
GO:BP	GO:0035822	gene conversion	2	4	3.791e-02
GO:BP	GO:0141006	transposable element silencing by piRNA-mediated heterochromatin formation	2	4	3.791e-02
GO:BP	GO:0140966	piRNA-mediated heterochromatin formation	2	4	3.791e-02
GO:BP	GO:0010520	regulation of reciprocal meiotic recombination	2	4	3.791e-02
GO:BP	GO:0045728	respiratory burst after phagocytosis	2	4	3.791e-02
GO:BP	GO:1990834	response to odorant	2	4	3.791e-02
GO:BP	GO:0009605	response to external stimulus	56	2367	3.880e-02
GO:BP	GO:0071695	anatomical structure maturation	12	274	3.887e-02
GO:BP	GO:0006816	calcium ion transport	16	433	4.134e-02
GO:BP	GO:0007165	signal transduction	120	5979	4.180e-02
GO:BP	GO:0007399	nervous system development	59	2541	4.341e-02
GO:BP	GO:2000241	regulation of reproductive process	10	206	4.341e-02
GO:BP	GO:0060285	cilium-dependent cell motility	9	172	4.341e-02
GO:BP	GO:0001539	cilium or flagellum-dependent cell motility	9	172	4.341e-02
GO:BP	GO:0030855	epithelial cell differentiation	23	741	4.442e-02
GO:BP	GO:0032940	secretion by cell	25	832	4.442e-02
GO:BP	GO:0007218	neuropeptide signaling pathway	7	110	4.452e-02
GO:BP	GO:0006957	complement activation, alternative pathway	3	16	4.452e-02
GO:BP	GO:0007194	negative regulation of adenylate cyclase activity	3	16	4.452e-02
GO:BP	GO:0010876	lipid localization	17	480	4.452e-02
GO:BP	GO:0061982	meiosis I cell cycle process	8	141	4.452e-02
GO:BP	GO:0061101	neuroendocrine cell differentiation	3	16	4.452e-02
GO:BP	GO:0043374	CD8-positive, alpha-beta T cell differentiation	3	16	4.452e-02
GO:BP	GO:0048522	positive regulation of cellular process	118	5886	4.481e-02
GO:BP	GO:1903530	regulation of secretion by cell	19	567	4.481e-02
GO:BP	GO:0003382	epithelial cell morphogenesis	4	34	4.481e-02
GO:BP	GO:0043270	positive regulation of monoatomic ion transport	10	209	4.481e-02
GO:BP	GO:0010526	transposable element silencing	4	34	4.481e-02
GO:BP	GO:0015701	bicarbonate transport	4	34	4.481e-02
GO:BP	GO:0045745	positive regulation of G protein-coupled receptor signaling pathway	4	34	4.481e-02
GO:BP	GO:0050870	positive regulation of T cell activation	11	248	4.822e-02
GO:BP	GO:0009566	fertilization	10	212	4.830e-02
GO:BP	GO:0045577	regulation of B cell differentiation	4	35	4.848e-02
GO:BP	GO:0051050	positive regulation of transport	25	844	4.848e-02
GO:BP	GO:0043299	leukocyte degranulation	6	84	4.848e-02
GO:BP	GO:0043949	regulation of cAMP-mediated signaling	4	35	4.848e-02
GO:BP	GO:0002679	respiratory burst involved in defense response	3	17	4.900e-02
GO:BP	GO:0009642	response to light intensity	3	17	4.900e-02
GO:BP	GO:0009628	response to abiotic stimulus	31	1130	4.900e-02
GO:BP	GO:0031280	negative regulation of cyclase activity	3	17	4.900e-02
GO:BP	GO:0045917	positive regulation of complement activation	2	5	4.921e-02
GO:BP	GO:0045920	negative regulation of exocytosis	4	36	4.921e-02
GO:BP	GO:0070995	NADPH oxidation	2	5	4.921e-02
GO:BP	GO:2000611	positive regulation of thyroid hormone generation	2	5	4.921e-02
GO:BP	GO:0032197	retrotransposition	4	36	4.921e-02
GO:BP	GO:0007610	behavior	21	665	4.921e-02
GO:BP	GO:0009644	response to high light intensity	2	5	4.921e-02
GO:BP	GO:0009887	animal organ morphogenesis	29	1037	4.921e-02
GO:BP	GO:0030317	flagellated sperm motility	8	147	4.921e-02
GO:BP	GO:0009914	hormone transport	13	328	4.921e-02
GO:BP	GO:0097722	sperm motility	8	147	4.921e-02
GO:BP	GO:0023061	signal release	17	493	4.921e-02
GO:BP	GO:0071484	cellular response to light intensity	2	5	4.921e-02
GO:BP	GO:0042127	regulation of cell population proliferation	42	1682	4.921e-02
GO:BP	GO:0002434	immune complex clearance	2	5	4.921e-02
GO:BP	GO:0045216	cell-cell junction organization	10	216	4.931e-02
KEGG	KEGG:04080	Neuroactive ligand-receptor interaction	25	365	1.188e-05

write.csv(tableESR_pp, "output/table_ESRmotif.csv")

#GO:BP
tableESR_GOBP_pp <- tableESR_pp %>% 
  dplyr::filter(source=="GO:BP") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

#saveRDS(tableESR_GOBP_pp, "data/tableESR_GOBP_postprob.RDS")

tableESR_GOBP_pp %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("No Response Enriched GO:BP Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("GO:BP term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "Early Sustained Response Posterior Probability-2.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

#KEGG
tableESR_KEGG_pp <- tableESR_pp %>% 
  dplyr::filter(source=="KEGG") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

tableESR_KEGG_pp %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("No Response Enriched KEGG Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("KEGG term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "Early Sustained Response Posterior Probability-3.png"

Version	Author	Date
84d5599	emmapfort	2025-04-14

Currently for the posterior probability code - motif 3 and motif 4 are showing up identically

Session information

sessionInfo()

R version 4.4.2 (2024-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22000)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/Chicago
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] gprofiler2_0.2.3            cowplot_1.1.3              
 [3] Rfast_2.1.5.1               RcppParallel_5.1.10        
 [5] zigg_0.0.2                  Rcpp_1.0.13-1              
 [7] RUVSeq_1.40.0               EDASeq_2.40.0              
 [9] ShortRead_1.64.0            GenomicAlignments_1.42.0   
[11] SummarizedExperiment_1.36.0 MatrixGenerics_1.18.1      
[13] matrixStats_1.4.1           Rsamtools_2.22.0           
[15] GenomicRanges_1.58.0        Biostrings_2.74.0          
[17] GenomeInfoDb_1.42.3         XVector_0.46.0             
[19] IRanges_2.40.0              S4Vectors_0.44.0           
[21] BiocParallel_1.40.0         biomaRt_2.62.1             
[23] RColorBrewer_1.1-3          Cormotif_1.52.0            
[25] affy_1.84.0                 Biobase_2.66.0             
[27] BiocGenerics_0.52.0         PCAtools_2.18.0            
[29] ggfortify_0.4.17            pheatmap_1.0.12            
[31] edgeR_4.4.0                 limma_3.62.1               
[33] readxl_1.4.3                edgebundleR_0.1.4          
[35] lubridate_1.9.3             forcats_1.0.0              
[37] stringr_1.5.1               dplyr_1.1.4                
[39] purrr_1.0.2                 readr_2.1.5                
[41] tidyr_1.3.1                 tidyverse_2.0.0            
[43] tibble_3.2.1                hrbrthemes_0.8.7           
[45] reshape2_1.4.4              ggrepel_0.9.6              
[47] ggplot2_3.5.1               workflowr_1.7.1            

loaded via a namespace (and not attached):
  [1] later_1.4.1               BiocIO_1.16.0            
  [3] bitops_1.0-9              filelock_1.0.3           
  [5] R.oo_1.27.0               cellranger_1.1.0         
  [7] preprocessCore_1.68.0     XML_3.99-0.18            
  [9] lifecycle_1.0.4           httr2_1.1.0              
 [11] pwalign_1.2.0             rprojroot_2.0.4          
 [13] MASS_7.3-61               processx_3.8.5           
 [15] lattice_0.22-6            crosstalk_1.2.1          
 [17] magrittr_2.0.3            plotly_4.10.4            
 [19] sass_0.4.9                rmarkdown_2.29           
 [21] jquerylib_0.1.4           yaml_2.3.10              
 [23] httpuv_1.6.15             DBI_1.2.3                
 [25] abind_1.4-8               zlibbioc_1.52.0          
 [27] R.utils_2.12.3            RCurl_1.98-1.16          
 [29] rappdirs_0.3.3            git2r_0.35.0             
 [31] gdtools_0.4.1             GenomeInfoDbData_1.2.13  
 [33] irlba_2.3.5.1             dqrng_0.4.1              
 [35] svglite_2.1.3             DelayedMatrixStats_1.28.1
 [37] codetools_0.2-20          DelayedArray_0.32.0      
 [39] xml2_1.3.6                tidyselect_1.2.1         
 [41] farver_2.1.2              UCSC.utils_1.2.0         
 [43] ScaledMatrix_1.14.0       BiocFileCache_2.14.0     
 [45] jsonlite_1.8.9            systemfonts_1.1.0        
 [47] tools_4.4.2               progress_1.2.3           
 [49] glue_1.8.0                gridExtra_2.3            
 [51] Rttf2pt1_1.3.12           SparseArray_1.6.0        
 [53] xfun_0.49                 withr_3.0.2              
 [55] BiocManager_1.30.25       fastmap_1.2.0            
 [57] latticeExtra_0.6-30       callr_3.7.6              
 [59] digest_0.6.37             rsvd_1.0.5               
 [61] timechange_0.3.0          R6_2.6.1                 
 [63] mime_0.12                 colorspace_2.1-1         
 [65] jpeg_0.1-10               RSQLite_2.3.8            
 [67] R.methodsS3_1.8.2         generics_0.1.3           
 [69] data.table_1.16.4         fontLiberation_0.1.0     
 [71] rtracklayer_1.66.0        prettyunits_1.2.0        
 [73] httr_1.4.7                htmlwidgets_1.6.4        
 [75] S4Arrays_1.6.0            whisker_0.4.1            
 [77] pkgconfig_2.0.3           gtable_0.3.6             
 [79] blob_1.2.4                hwriter_1.3.2.1          
 [81] htmltools_0.5.8.1         fontBitstreamVera_0.1.1  
 [83] kableExtra_1.4.0          scales_1.3.0             
 [85] png_0.1-8                 knitr_1.49               
 [87] rstudioapi_0.17.1         tzdb_0.4.0               
 [89] rjson_0.2.23              curl_6.0.1               
 [91] cachem_1.1.0              parallel_4.4.2           
 [93] extrafont_0.19            AnnotationDbi_1.68.0     
 [95] restfulr_0.0.15           pillar_1.10.1            
 [97] grid_4.4.2                vctrs_0.6.5              
 [99] promises_1.3.2            BiocSingular_1.22.0      
[101] dbplyr_2.5.0              beachmat_2.22.0          
[103] xtable_1.8-4              extrafontdb_1.0          
[105] evaluate_1.0.3            GenomicFeatures_1.58.0   
[107] cli_3.6.3                 locfit_1.5-9.10          
[109] compiler_4.4.2            rlang_1.1.4              
[111] crayon_1.5.3              labeling_0.4.3           
[113] aroma.light_3.36.0        interp_1.1-6             
[115] ps_1.8.1                  getPass_0.2-4            
[117] plyr_1.8.9                fs_1.6.5                 
[119] stringi_1.8.4             viridisLite_0.4.2        
[121] deldir_2.0-4              munsell_0.5.1            
[123] lazyeval_0.2.2            fontquiver_0.2.1         
[125] Matrix_1.7-1              hms_1.1.3                
[127] sparseMatrixStats_1.18.0  bit64_4.5.2              
[129] KEGGREST_1.46.0           statmod_1.5.0            
[131] shiny_1.10.0              igraph_2.1.1             
[133] memoise_2.0.1             affyio_1.76.0            
[135] bslib_0.9.0               bit_4.5.0