Recovery RNAseq DOX Data

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Last updated: 2025-04-18

Checks: 6 1

Knit directory: Recovery_5FU/

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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

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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/cormotifARclust_pp.RDS
    Ignored:    data/counts_DE_df_dox.RDS
    Ignored:    data/ensembl_backup_dox.RDS
    Ignored:    data/filt_gene_list_dox.RDS
    Ignored:    data/gene_clustlike_motif.RDS
    Ignored:    data/gene_postprob_motif.RDS
    Ignored:    data/genematrix_dox.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

Untracked files:
    Untracked:  NBL1_motif1_examplegene_1000x600_EMP_250416.png

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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	62c3340	emmapfort	2025-04-18	Updated analysis 25/04/18
Rmd	424626d	emmapfort	2025-04-15	Add In DOX only set
html	be23fa9	emmapfort	2025-04-15	Build site.
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

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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")

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

###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"))

Past versions of "Pull Out Some Cardiac Genes-1.png"

Version	Author	Date
be23fa9	emmapfort	2025-04-15

#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"))

Past versions of "Pull Out Some Cardiac Genes-2.png"

Version	Author	Date
be23fa9	emmapfort	2025-04-15

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"))

Past versions of "Pull Out Some Cardiac Genes-3.png"

Version	Author	Date
be23fa9	emmapfort	2025-04-15

#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

Past versions of "Pull Out Some Cardiac Genes-4.png"

Version	Author	Date
be23fa9	emmapfort	2025-04-15

fungraph_dmso_only_TNNI3

Past versions of "Pull Out Some Cardiac Genes-5.png"

Version	Author	Date
be23fa9	emmapfort	2025-04-15

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

Past versions of "Pull Out Some Cardiac Genes-6.png"

Version	Author	Date
be23fa9	emmapfort	2025-04-15

####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)

              logFC  AveExpr         t      P.Value    adj.P.Val         B
100287102 -1.804419 5.673476 -1.741845 8.886085e-02 1.088296e-01 -4.985757
102466751 -1.386392 6.598993 -2.215141 3.223163e-02 4.236756e-02 -4.208131
100302278  2.117211 4.110796  5.136780 6.832114e-06 1.543790e-05  3.484472
645520    -1.060785 3.557889 -2.870907 6.387858e-03 9.406209e-03 -3.056843
79501     -1.851133 3.191793 -7.289085 5.649161e-09 1.915955e-08 10.231400
102725121 -2.392951 5.717312 -2.447792 1.863753e-02 2.550153e-02 -3.658644

#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)

               logFC  AveExpr          t    P.Value  adj.P.Val         B
100287102  0.2141767 5.673476  0.2255907 0.82261472 0.86440123 -6.218826
102466751 -0.8094950 6.598993 -1.3328291 0.18977853 0.26317888 -5.413117
100302278 -0.8734257 4.110796 -1.7817528 0.08202618 0.12937566 -4.863398
645520    -0.1192432 3.557889 -0.2881042 0.77468499 0.82587957 -6.419091
79501     -0.6825584 3.191793 -2.3475219 0.02368945 0.04379952 -4.150543
102725121  0.3419483 5.717312  0.3858246 0.70157538 0.76548265 -6.184783

#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)

                logFC  AveExpr          t    P.Value adj.P.Val         B
100287102 -0.42467259 5.673476 -0.4139649 0.68100778 0.9656919 -6.176321
102466751 -0.04911403 6.598993 -0.0842465 0.93326102 0.9658168 -6.400185
100302278  0.32459251 4.110796  1.0815817 0.28561401 0.8618346 -6.375234
645520    -0.46815849 3.557889 -1.2874535 0.20499081 0.7713611 -5.861459
79501      0.56678196 3.191793  1.9032026 0.06388777 0.4666442 -5.076972
102725121  0.18759316 5.717312  0.1938705 0.84721256 0.9656919 -6.246426

#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)

     GeneID     logFC  AveExpr         t      P.Value    adj.P.Val        B
1    148753  6.274101 5.578715  22.98007 2.128816e-25 3.016533e-21 47.14980
2    116369  5.789178 6.348094  20.56787 1.542184e-23 1.092637e-19 43.01677
3 101929523 -6.034510 6.305356 -19.08546 2.647316e-22 1.004705e-18 39.91738
4 100996301  5.149384 5.289969  18.98930 3.202808e-22 1.004705e-18 40.23872
5      2899  5.508418 5.862853  18.93819 3.545183e-22 1.004705e-18 40.05644
  Gene_Name
1   FAM163A
2   SLC26A8
3  THBS-AS1
4 FOXD3-AS1
5     GRIK3

#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"))

####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)

  GeneID    logFC  AveExpr        t      P.Value    adj.P.Val        B
1  54207 4.949406 6.530192 15.82299 2.695651e-19 2.698663e-15 33.02274
2   1475 5.603936 5.360183 15.67190 3.808981e-19 2.698663e-15 32.95920
3 353132 4.839166 4.461296 14.34492 8.816170e-18 4.164171e-14 30.06752
4  23440 5.863845 6.216741 13.53171 6.670038e-17 2.362861e-13 27.67891
5 337882 6.367767 5.675415 13.17894 1.644191e-16 4.659637e-13 27.24446
  Gene_Name1
1     KCNK10
2       CSTA
3      LCE1B
4        OTP
5  KRTAP19-1

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"))

####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)

  GeneID    logFC  AveExpr        t      P.Value    adj.P.Val        B
1 440896 4.681589 4.937852 13.65775 4.849711e-17 6.872040e-13 28.36219
2  57282 4.710121 5.295198 12.59160 7.637380e-16 5.411084e-12 25.77519
3   5212 3.923330 4.773412 12.10946 2.782463e-15 1.314250e-11 24.40702
4 143471 3.521809 4.241896 11.71091 8.284121e-15 2.643174e-11 23.33360
5 140469 4.647516 6.057544 11.66805 9.326656e-15 2.643174e-11 23.23254
  Gene_Name2
1  LINC03025
2    SLC4A10
3        VIT
4      PSMA8
5      MYO3B

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"))

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 4
clust1_d <- motif_prob_d %>% 
  as.data.frame() %>% 
  filter(V1>0.57) %>% 
  rownames

#using a filter of >0.57 I get 11130 genes compared to 11156 above

length(clust1_d)

[1] 11130

#11482 > 0.5
#11130 > 0.57
#is this clust1 a non-response?

clust1_d_df <- as.data.frame(clust1_d)

#example gene - UID 4681 - NBL1
NBL1_motif1 <- Cormotif_df_d %>% 
  rownames_to_column(var = "entrezgene_id") %>% 
  dplyr::filter(entrezgene_id == "4681")

NBL1_motif1_long <- melt(NBL1_motif1,
                         id.vars = c("entrezgene_id"),
                         variable.name = "Sample",
                         value.name = "log2cpm")

#now add in my factors like time, tx, tx_time, and ind by breaking up the Sample column
NBL1_motif1_long_df <- 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)))

NBL1_motif1_long_factors <- cbind(NBL1_motif1_long_df, NBL1_motif1_long)

NBL1_motif1_long_factors %>% ggplot(aes(x = txtime, y = log2cpm))+
  geom_boxplot(aes(fill = tx))+
  geom_point(aes(color = ind)) +
  labs(title = "NBL1")+
  theme_bw(base_size = 16)+
  scale_fill_manual(values = c(tx_col))+
  scale_color_manual(values = c(ind_col))+
  xlab("Conditions")+
  ylab("log2cpm")+
  ylim(0,10)+
  theme(plot.title = element_text(face = "italic"))

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

Version	Author	Date
84d5599	emmapfort	2025-04-14

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

clust2_d <- motif_prob_d %>% 
  as.data.frame() %>% 
  filter(V2>0.132) %>% 
  rownames

#using a filter of >0.132 I get the closest - 326 original vs 327 genes here

length(clust2_d)

[1] 327

#0 > 0.5
#326 > 0.132
#is clust2 a dox early response?

clust2_d_df <- as.data.frame(clust2_d)

#example gene - 597 - BCL2A1
BCL2A1_motif1 <- Cormotif_df_d %>% 
  rownames_to_column(var = "entrezgene_id") %>% 
  dplyr::filter(entrezgene_id == "597")

BCL2A1_motif1_long <- melt(BCL2A1_motif1,
                         id.vars = c("entrezgene_id"),
                         variable.name = "Sample",
                         value.name = "log2cpm")

#now add in my factors like time, tx, tx_time, and ind by breaking up the Sample column
BCL2A1_motif1_long_df <- 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)))

BCL2A1_motif1_long_factors <- cbind(BCL2A1_motif1_long_df, BCL2A1_motif1_long)

BCL2A1_motif1_long_factors %>% ggplot(aes(x = txtime, y = log2cpm))+
  geom_boxplot(aes(fill = tx))+
  geom_point(aes(color = ind)) +
  labs(title = "BCL2A1")+
  theme_bw(base_size = 16)+
  scale_fill_manual(values = c(tx_col))+
  scale_color_manual(values = c(ind_col))+
  xlab("Conditions")+
  ylab("log2cpm")+
  ylim(0,10)+
  theme(plot.title = element_text(face = "italic"))

clust3_d <- motif_prob_d %>% 
  as.data.frame() %>% 
  filter(V3>0.3) %>% 
  rownames

#using a filter of >0.3 I get 740 genes vs original 739 genes

length(clust3_d)

[1] 740

#538 > 0.5
#740 > 0.3
#is clust 3 a late response?

clust3_d_df <- as.data.frame(clust3_d)

#example gene - 8856 - NR1I2
NR1I2_motif1 <- Cormotif_df_d %>% 
  rownames_to_column(var = "entrezgene_id") %>% 
  dplyr::filter(entrezgene_id == "8856")

NR1I2_motif1_long <- melt(NR1I2_motif1,
                         id.vars = c("entrezgene_id"),
                         variable.name = "Sample",
                         value.name = "log2cpm")

#now add in my factors like time, tx, tx_time, and ind by breaking up the Sample column
NR1I2_motif1_long_df <- 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)))

NR1I2_motif1_long_factors <- cbind(NR1I2_motif1_long_df, NR1I2_motif1_long)

NR1I2_motif1_long_factors %>% ggplot(aes(x = txtime, y = log2cpm))+
  geom_boxplot(aes(fill = tx))+
  geom_point(aes(color = ind)) +
  labs(title = "NR1I2")+
  theme_bw(base_size = 16)+
  scale_fill_manual(values = c(tx_col))+
  scale_color_manual(values = c(ind_col))+
  xlab("Conditions")+
  ylab("log2cpm")+
  ylim(0,10)+
  theme(plot.title = element_text(face = "italic"))

#cluster 4
clust4_d <- motif_prob_d %>% 
  as.data.frame() %>% 
  filter(V4>0.4) %>% 
  rownames

#using >0.4 as my cutoff, I get 1938 genes as compared to original 1948 genes

length(clust4_d)

[1] 1938

#1576 > 0.5
#1938 > 0.4
#is clust4 a DOX late response?

clust4_d_df <- as.data.frame(clust4_d)

#example gene - 6725 - SRMS 
SRMS_motif1 <- Cormotif_df_d %>% 
  rownames_to_column(var = "entrezgene_id") %>% 
  dplyr::filter(entrezgene_id == "6725")

SRMS_motif1_long <- melt(SRMS_motif1,
                         id.vars = c("entrezgene_id"),
                         variable.name = "Sample",
                         value.name = "log2cpm")

#now add in my factors like time, tx, tx_time, and ind by breaking up the Sample column
SRMS_motif1_long_df <- 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)))

SRMS_motif1_long_factors <- cbind(SRMS_motif1_long_df, SRMS_motif1_long)

SRMS_motif1_long_factors %>% ggplot(aes(x = txtime, y = log2cpm))+
  geom_boxplot(aes(fill = tx))+
  geom_point(aes(color = ind)) +
  labs(title = "SRMS")+
  theme_bw(base_size = 16)+
  scale_fill_manual(values = c(tx_col))+
  scale_color_manual(values = c(ind_col))+
  xlab("Conditions")+
  ylab("log2cpm")+
  ylim(0,10)+
  theme(plot.title = element_text(face = "italic"))

#now let's make a pie chart with the above number of genes for each motif
clusterdata_d_adj <- data.frame(
  Category = c("No Response","Acute Response", "Late Response", "Early Sustained Response"), 
  Value = c(11130, 327, 740, 1938)
)

piecolors <- c("No Response" = "#007896", 
               "Acute Response" = "#079255",
               "Late Response" = "#58508D", 
               "Early Sustained Response" = "#BC5090")

#make a piechart of these distributions
clusterdata_d_adj %>% 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)

#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
#ideally each of these are similar to the number of genes in the above plot

#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 p.prob
prob_motif_1 <- rownames(gene_postprob_motif_df[(gene_postprob_motif_df[,1] < 0.62 
                                              & gene_postprob_motif_df[,2] < 0.62 
                                              & gene_postprob_motif_df[,3] < 0.62),])
length(prob_motif_1)

[1] 11157

#10903 genes post prob

#gene example:  943 - TNFRSF8
TNFRF8_gene <- 

#10903 genes post prob - close to value of 11156 on cormotif pattern graph

#gene example:  11009 - IL24
IL24_gene_motif1 <- 


#motif 2 acute response
prob_motif_2 <- rownames(gene_postprob_motif_df[(gene_postprob_motif_df[,1] > 0.99 
                                              & gene_postprob_motif_df[,2] < 0.5 
                                              & gene_postprob_motif_df[,3] < 0.5),])
length(prob_motif_2)

[1] 277

#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	391	443	1.264e-213
GO:BP	GO:0035195	miRNA-mediated post-transcriptional gene silencing	472	612	3.524e-208
GO:BP	GO:0050911	detection of chemical stimulus involved in sensory perception of smell	360	397	3.627e-206
GO:BP	GO:0007606	sensory perception of chemical stimulus	414	497	3.627e-206
GO:BP	GO:0035194	regulatory ncRNA-mediated post-transcriptional gene silencing	473	624	2.926e-203
GO:BP	GO:0016441	post-transcriptional gene silencing	474	630	2.423e-201
GO:BP	GO:0009593	detection of chemical stimulus	400	480	2.737e-199
GO:BP	GO:0007608	sensory perception of smell	367	423	4.500e-195
GO:BP	GO:0050906	detection of stimulus involved in sensory perception	414	515	8.464e-195
GO:BP	GO:0031047	regulatory ncRNA-mediated gene silencing	480	686	1.791e-181
GO:BP	GO:0051606	detection of stimulus	451	643	1.107e-170
GO:BP	GO:0007186	G protein-coupled receptor signaling pathway	688	1275	1.722e-169
GO:BP	GO:0007600	sensory perception	546	955	4.494e-147
GO:BP	GO:0010608	post-transcriptional regulation of gene expression	511	1087	9.743e-93
GO:BP	GO:0050877	nervous system process	632	1489	3.079e-92
GO:BP	GO:0010629	negative regulation of gene expression	625	1640	2.152e-68
GO:BP	GO:0003008	system process	784	2266	1.973e-65
GO:BP	GO:0042221	response to chemical	1079	3867	4.895e-38
GO:BP	GO:0065007	biological regulation	2878	12671	2.495e-34
GO:BP	GO:0050789	regulation of biological process	2791	12278	5.075e-32
GO:BP	GO:0042742	defense response to bacterium	163	326	8.829e-32
GO:BP	GO:0006959	humoral immune response	138	254	1.143e-31
GO:BP	GO:0006952	defense response	562	1809	9.256e-30
GO:BP	GO:0050794	regulation of cellular process	2701	11876	9.256e-30
GO:BP	GO:0010558	negative regulation of macromolecule biosynthetic process	787	2772	1.709e-28
GO:BP	GO:0032501	multicellular organismal process	1760	7234	3.177e-28
GO:BP	GO:0009890	negative regulation of biosynthetic process	795	2838	8.308e-27
GO:BP	GO:0009617	response to bacterium	270	721	3.102e-26
GO:BP	GO:0031424	keratinization	62	82	6.445e-25
GO:BP	GO:0019730	antimicrobial humoral response	82	131	4.159e-24
GO:BP	GO:0098542	defense response to other organism	397	1228	6.247e-24
GO:BP	GO:0043207	response to external biotic stimulus	467	1558	1.238e-20
GO:BP	GO:0051707	response to other organism	465	1555	2.567e-20
GO:BP	GO:0009607	response to biotic stimulus	474	1593	2.791e-20
GO:BP	GO:0140546	defense response to symbiont	358	1125	4.440e-20
GO:BP	GO:0007165	signal transduction	1439	5979	9.834e-19
GO:BP	GO:0141060	disruption of anatomical structure in another organism	61	98	1.442e-17
GO:BP	GO:0010605	negative regulation of macromolecule metabolic process	829	3197	3.109e-17
GO:BP	GO:0001906	cell killing	102	219	8.951e-17
GO:BP	GO:0061844	antimicrobial humoral immune response mediated by antimicrobial peptide	54	83	9.352e-17
GO:BP	GO:0031640	killing of cells of another organism	57	91	1.355e-16
GO:BP	GO:0141061	disruption of cell in another organism	57	91	1.355e-16
GO:BP	GO:0009605	response to external stimulus	638	2367	1.659e-16
GO:BP	GO:0006955	immune response	553	2008	5.299e-16
GO:BP	GO:0006954	inflammatory response	272	847	1.527e-15
GO:BP	GO:0045109	intermediate filament organization	48	73	3.954e-15
GO:BP	GO:0044419	biological process involved in interspecies interaction between organisms	482	1724	5.590e-15
GO:BP	GO:0007154	cell communication	1520	6496	6.072e-15
GO:BP	GO:0023052	signaling	1514	6471	7.621e-15
GO:BP	GO:0009892	negative regulation of metabolic process	860	3418	2.574e-14
GO:BP	GO:0045087	innate immune response	300	977	2.609e-14
GO:BP	GO:0030216	keratinocyte differentiation	83	176	5.360e-14
GO:BP	GO:0050830	defense response to Gram-positive bacterium	63	120	3.260e-13
GO:BP	GO:0050829	defense response to Gram-negative bacterium	52	91	8.895e-13
GO:BP	GO:0097530	granulocyte migration	74	156	1.383e-12
GO:BP	GO:0002252	immune effector process	225	703	1.451e-12
GO:BP	GO:1990266	neutrophil migration	65	129	1.483e-12
GO:BP	GO:0050896	response to stimulus	2011	8993	1.588e-12
GO:BP	GO:0050909	sensory perception of taste	42	67	3.801e-12
GO:BP	GO:0030593	neutrophil chemotaxis	56	106	7.292e-12
GO:BP	GO:0071621	granulocyte chemotaxis	63	129	2.269e-11
GO:BP	GO:0009913	epidermal cell differentiation	100	250	2.693e-11
GO:BP	GO:0007586	digestion	65	136	3.273e-11
GO:BP	GO:0050913	sensory perception of bitter taste	30	42	1.067e-10
GO:BP	GO:0002697	regulation of immune effector process	135	381	1.068e-10
GO:BP	GO:0030595	leukocyte chemotaxis	94	237	2.386e-10
GO:BP	GO:0050912	detection of chemical stimulus involved in sensory perception of taste	30	43	2.686e-10
GO:BP	GO:0019731	antibacterial humoral response	40	68	2.686e-10
GO:BP	GO:0045104	intermediate filament cytoskeleton organization	49	94	4.602e-10
GO:BP	GO:0001580	detection of chemical stimulus involved in sensory perception of bitter taste	27	37	6.090e-10
GO:BP	GO:0045103	intermediate filament-based process	49	95	7.457e-10
GO:BP	GO:0002323	natural killer cell activation involved in immune response	26	35	7.504e-10
GO:BP	GO:0002376	immune system process	693	2796	9.320e-10
GO:BP	GO:0050900	leukocyte migration	136	396	1.032e-09
GO:BP	GO:0002237	response to molecule of bacterial origin	125	355	1.062e-09
GO:BP	GO:0097529	myeloid leukocyte migration	92	237	1.473e-09
GO:BP	GO:0051716	cellular response to stimulus	1642	7320	2.062e-09
GO:BP	GO:0070098	chemokine-mediated signaling pathway	46	90	4.511e-09
GO:BP	GO:0071219	cellular response to molecule of bacterial origin	87	224	4.907e-09
GO:BP	GO:0008544	epidermis development	133	394	6.241e-09
GO:BP	GO:0046651	lymphocyte proliferation	110	308	6.493e-09
GO:BP	GO:0042100	B cell proliferation	51	106	6.852e-09
GO:BP	GO:0070661	leukocyte proliferation	121	351	9.824e-09
GO:BP	GO:0007218	neuropeptide signaling pathway	52	110	9.948e-09
GO:BP	GO:0032496	response to lipopolysaccharide	117	337	1.186e-08
GO:BP	GO:0007338	single fertilization	70	169	1.246e-08
GO:BP	GO:0032943	mononuclear cell proliferation	111	315	1.258e-08
GO:BP	GO:0071222	cellular response to lipopolysaccharide	83	214	1.313e-08
GO:BP	GO:0060326	cell chemotaxis	112	319	1.313e-08
GO:BP	GO:0052695	cellular glucuronidation	18	21	1.679e-08
GO:BP	GO:0033141	positive regulation of peptidyl-serine phosphorylation of STAT protein	18	21	1.679e-08
GO:BP	GO:0019221	cytokine-mediated signaling pathway	159	503	2.248e-08
GO:BP	GO:0007283	spermatogenesis	192	637	2.801e-08
GO:BP	GO:0045321	leukocyte activation	267	951	3.624e-08
GO:BP	GO:0001775	cell activation	301	1098	4.438e-08
GO:BP	GO:0009566	fertilization	81	212	4.742e-08
GO:BP	GO:0048232	male gamete generation	195	654	5.249e-08
GO:BP	GO:0002526	acute inflammatory response	50	109	7.298e-08
GO:BP	GO:0002548	monocyte chemotaxis	36	68	1.324e-07
GO:BP	GO:0048245	eosinophil chemotaxis	20	27	1.736e-07
GO:BP	GO:0070663	regulation of leukocyte proliferation	94	265	1.895e-07
GO:BP	GO:1990869	cellular response to chemokine	46	99	1.952e-07
GO:BP	GO:1990868	response to chemokine	46	99	1.952e-07
GO:BP	GO:0002682	regulation of immune system process	395	1526	2.069e-07
GO:BP	GO:0002366	leukocyte activation involved in immune response	104	305	3.139e-07
GO:BP	GO:0002263	cell activation involved in immune response	105	309	3.244e-07
GO:BP	GO:0071216	cellular response to biotic stimulus	89	251	4.844e-07
GO:BP	GO:0071715	icosanoid transport	34	65	5.205e-07
GO:BP	GO:0048609	multicellular organismal reproductive process	267	980	7.291e-07
GO:BP	GO:0033139	regulation of peptidyl-serine phosphorylation of STAT protein	18	24	7.541e-07
GO:BP	GO:0072677	eosinophil migration	21	31	8.249e-07
GO:BP	GO:0006953	acute-phase response	28	49	8.250e-07
GO:BP	GO:0002274	myeloid leukocyte activation	85	240	1.064e-06
GO:BP	GO:0022600	digestive system process	46	105	1.752e-06
GO:BP	GO:0050832	defense response to fungus	31	59	1.977e-06
GO:BP	GO:0042501	serine phosphorylation of STAT protein	18	25	2.076e-06
GO:BP	GO:0060294	cilium movement involved in cell motility	64	167	2.152e-06
GO:BP	GO:0050670	regulation of lymphocyte proliferation	83	236	2.156e-06
GO:BP	GO:0032944	regulation of mononuclear cell proliferation	84	240	2.271e-06
GO:BP	GO:0097722	sperm motility	58	147	2.747e-06
GO:BP	GO:0030317	flagellated sperm motility	58	147	2.747e-06
GO:BP	GO:0022414	reproductive process	394	1556	2.902e-06
GO:BP	GO:0048247	lymphocyte chemotaxis	32	63	3.165e-06
GO:BP	GO:0002699	positive regulation of immune effector process	87	253	3.165e-06
GO:BP	GO:0043588	skin development	105	322	3.203e-06
GO:BP	GO:0050776	regulation of immune response	244	897	3.229e-06
GO:BP	GO:0032649	regulation of type II interferon production	49	117	3.229e-06
GO:BP	GO:0002703	regulation of leukocyte mediated immunity	84	243	3.983e-06
GO:BP	GO:0032609	type II interferon production	49	118	4.392e-06
GO:BP	GO:0002684	positive regulation of immune system process	282	1066	4.680e-06
GO:BP	GO:0006063	uronic acid metabolic process	18	26	4.819e-06
GO:BP	GO:0019585	glucuronate metabolic process	18	26	4.819e-06
GO:BP	GO:0140975	disruption of cellular anatomical structure in another organism	10	10	6.564e-06
GO:BP	GO:0031341	regulation of cell killing	45	106	6.564e-06
GO:BP	GO:0002775	antimicrobial peptide production	10	10	6.564e-06
GO:BP	GO:0001539	cilium or flagellum-dependent cell motility	64	172	6.684e-06
GO:BP	GO:0060285	cilium-dependent cell motility	64	172	6.684e-06
GO:BP	GO:0002922	positive regulation of humoral immune response	16	22	8.534e-06
GO:BP	GO:0042330	taxis	139	465	9.224e-06
GO:BP	GO:0007188	adenylate cyclase-modulating G protein-coupled receptor signaling pathway	84	248	1.005e-05
GO:BP	GO:0030101	natural killer cell activation	41	95	1.337e-05
GO:BP	GO:0002251	organ or tissue specific immune response	24	43	1.355e-05
GO:BP	GO:0022412	cellular process involved in reproduction in multicellular organism	124	408	1.568e-05
GO:BP	GO:0002443	leukocyte mediated immunity	137	461	1.585e-05
GO:BP	GO:0007342	fusion of sperm to egg plasma membrane involved in single fertilization	19	30	1.624e-05
GO:BP	GO:0006935	chemotaxis	137	463	2.051e-05
GO:BP	GO:0007276	gamete generation	222	822	2.055e-05
GO:BP	GO:0019953	sexual reproduction	286	1103	2.287e-05
GO:BP	GO:0072676	lymphocyte migration	49	124	2.346e-05
GO:BP	GO:0001909	leukocyte mediated cytotoxicity	52	135	2.690e-05
GO:BP	GO:0002706	regulation of lymphocyte mediated immunity	65	182	2.751e-05
GO:BP	GO:0015718	monocarboxylic acid transport	64	179	3.148e-05
GO:BP	GO:0007259	cell surface receptor signaling pathway via JAK-STAT	61	168	3.148e-05
GO:BP	GO:0002385	mucosal immune response	22	39	3.148e-05
GO:BP	GO:0050727	regulation of inflammatory response	116	381	3.157e-05
GO:BP	GO:0006690	icosanoid metabolic process	48	122	3.413e-05
GO:BP	GO:0032689	negative regulation of type II interferon production	23	42	3.479e-05
GO:BP	GO:0097696	cell surface receptor signaling pathway via STAT	63	176	3.580e-05
GO:BP	GO:0010468	regulation of gene expression	1223	5515	3.696e-05
GO:BP	GO:0051873	killing by host of symbiont cells	18	29	4.703e-05
GO:BP	GO:0015732	prostaglandin transport	18	29	4.703e-05
GO:BP	GO:0007631	feeding behavior	43	106	4.721e-05
GO:BP	GO:0009620	response to fungus	32	70	5.214e-05
GO:BP	GO:0009584	detection of visible light	19	32	6.033e-05
GO:BP	GO:0001817	regulation of cytokine production	206	765	6.062e-05
GO:BP	GO:0050865	regulation of cell activation	171	616	6.744e-05
GO:BP	GO:0001819	positive regulation of cytokine production	140	486	7.081e-05
GO:BP	GO:0001816	cytokine production	207	772	7.722e-05
GO:BP	GO:0042129	regulation of T cell proliferation	63	180	8.120e-05
GO:BP	GO:0002285	lymphocyte activation involved in immune response	72	214	8.125e-05
GO:BP	GO:0007286	spermatid development	72	214	8.125e-05
GO:BP	GO:0007204	positive regulation of cytosolic calcium ion concentration	60	169	8.216e-05
GO:BP	GO:0036230	granulocyte activation	25	50	9.827e-05
GO:BP	GO:0050778	positive regulation of immune response	197	732	1.026e-04
GO:BP	GO:0048240	sperm capacitation	19	33	1.084e-04
GO:BP	GO:0071674	mononuclear cell migration	77	235	1.105e-04
GO:BP	GO:0002784	regulation of antimicrobial peptide production	8	8	1.253e-04
GO:BP	GO:0002778	antibacterial peptide production	8	8	1.253e-04
GO:BP	GO:0002760	positive regulation of antimicrobial humoral response	8	8	1.253e-04
GO:BP	GO:0046649	lymphocyte activation	209	787	1.311e-04
GO:BP	GO:0042119	neutrophil activation	22	42	1.434e-04
GO:BP	GO:0002920	regulation of humoral immune response	23	45	1.479e-04
GO:BP	GO:0002694	regulation of leukocyte activation	156	561	1.593e-04
GO:BP	GO:0048515	spermatid differentiation	73	222	1.659e-04
GO:BP	GO:0015908	fatty acid transport	45	118	1.732e-04
GO:BP	GO:0045026	plasma membrane fusion	19	34	1.879e-04
GO:BP	GO:0070665	positive regulation of leukocyte proliferation	57	163	2.332e-04
GO:BP	GO:0098586	cellular response to virus	33	78	2.535e-04
GO:BP	GO:0001910	regulation of leukocyte mediated cytotoxicity	37	92	2.921e-04
GO:BP	GO:0032722	positive regulation of chemokine production	31	72	3.105e-04
GO:BP	GO:0032642	regulation of chemokine production	38	96	3.379e-04
GO:BP	GO:0032602	chemokine production	38	96	3.379e-04
GO:BP	GO:0002673	regulation of acute inflammatory response	23	47	3.600e-04
GO:BP	GO:0051249	regulation of lymphocyte activation	139	497	3.677e-04
GO:BP	GO:0002286	T cell activation involved in immune response	46	125	3.901e-04
GO:BP	GO:0006805	xenobiotic metabolic process	46	125	3.901e-04
GO:BP	GO:0042531	positive regulation of tyrosine phosphorylation of STAT protein	28	63	3.982e-04
GO:BP	GO:0051250	negative regulation of lymphocyte activation	55	159	4.619e-04
GO:BP	GO:0030855	epithelial cell differentiation	195	741	4.718e-04
GO:BP	GO:0007602	phototransduction	23	48	5.364e-04
GO:BP	GO:0032309	icosanoid secretion	23	48	5.364e-04
GO:BP	GO:0015670	carbon dioxide transport	11	15	5.364e-04
GO:BP	GO:0007159	leukocyte cell-cell adhesion	116	404	5.371e-04
GO:BP	GO:0052697	xenobiotic glucuronidation	7	7	5.500e-04
GO:BP	GO:0002225	positive regulation of antimicrobial peptide production	7	7	5.500e-04
GO:BP	GO:0010556	regulation of macromolecule biosynthetic process	1231	5633	5.528e-04
GO:BP	GO:0019755	one-carbon compound transport	15	25	5.573e-04
GO:BP	GO:0007200	phospholipase C-activating G protein-coupled receptor signaling pathway	43	116	5.784e-04
GO:BP	GO:0050953	sensory perception of light stimulus	71	222	5.798e-04
GO:BP	GO:0042113	B cell activation	86	282	6.050e-04
GO:BP	GO:0042110	T cell activation	152	558	6.140e-04
GO:BP	GO:0042102	positive regulation of T cell proliferation	39	102	6.140e-04
GO:BP	GO:0002698	negative regulation of immune effector process	44	120	6.204e-04
GO:BP	GO:0002227	innate immune response in mucosa	16	28	6.551e-04
GO:BP	GO:0007601	visual perception	70	219	6.599e-04
GO:BP	GO:0009583	detection of light stimulus	29	68	6.711e-04
GO:BP	GO:1904892	regulation of receptor signaling pathway via STAT	40	106	6.728e-04
GO:BP	GO:0046425	regulation of receptor signaling pathway via JAK-STAT	38	99	6.881e-04
GO:BP	GO:0050671	positive regulation of lymphocyte proliferation	50	143	7.433e-04
GO:BP	GO:0002759	regulation of antimicrobial humoral response	9	11	7.517e-04
GO:BP	GO:0002695	negative regulation of leukocyte activation	61	185	7.716e-04
GO:BP	GO:0034341	response to type II interferon	51	147	7.754e-04
GO:BP	GO:0071346	cellular response to type II interferon	45	125	8.165e-04
GO:BP	GO:0070374	positive regulation of ERK1 and ERK2 cascade	67	210	1.009e-03
GO:BP	GO:0032637	interleukin-8 production	33	83	1.009e-03
GO:BP	GO:0032677	regulation of interleukin-8 production	33	83	1.009e-03
GO:BP	GO:0002685	regulation of leukocyte migration	72	230	1.044e-03
GO:BP	GO:0032757	positive regulation of interleukin-8 production	27	63	1.110e-03
GO:BP	GO:1903037	regulation of leukocyte cell-cell adhesion	105	366	1.252e-03
GO:BP	GO:0032946	positive regulation of mononuclear cell proliferation	50	146	1.331e-03
GO:BP	GO:0050863	regulation of T cell activation	107	375	1.343e-03
GO:BP	GO:0003341	cilium movement	67	212	1.372e-03
GO:BP	GO:0042509	regulation of tyrosine phosphorylation of STAT protein	30	74	1.454e-03
GO:BP	GO:0032945	negative regulation of mononuclear cell proliferation	34	88	1.494e-03
GO:BP	GO:0032612	interleukin-1 production	40	110	1.672e-03
GO:BP	GO:0032652	regulation of interleukin-1 production	40	110	1.672e-03
GO:BP	GO:1903038	negative regulation of leukocyte cell-cell adhesion	47	136	1.691e-03
GO:BP	GO:0050868	negative regulation of T cell activation	44	125	1.762e-03
GO:BP	GO:0009889	regulation of biosynthetic process	1256	5795	1.818e-03
GO:BP	GO:0070664	negative regulation of leukocyte proliferation	36	96	1.846e-03
GO:BP	GO:0007281	germ cell development	105	370	1.929e-03
GO:BP	GO:0006968	cellular defense response	23	52	2.223e-03
GO:BP	GO:0042363	fat-soluble vitamin catabolic process	9	12	2.237e-03
GO:BP	GO:1901317	regulation of flagellated sperm motility	13	22	2.284e-03
GO:BP	GO:0002786	regulation of antibacterial peptide production	6	6	2.295e-03
GO:BP	GO:0051673	disruption of plasma membrane integrity in another organism	6	6	2.295e-03
GO:BP	GO:0051552	flavone metabolic process	6	6	2.295e-03
GO:BP	GO:0002687	positive regulation of leukocyte migration	51	153	2.325e-03
GO:BP	GO:0071345	cellular response to cytokine stimulus	213	843	2.388e-03
GO:BP	GO:0007260	tyrosine phosphorylation of STAT protein	30	76	2.454e-03
GO:BP	GO:0032653	regulation of interleukin-10 production	25	59	2.472e-03
GO:BP	GO:0032613	interleukin-10 production	25	59	2.472e-03
GO:BP	GO:0008228	opsonization	11	17	2.592e-03
GO:BP	GO:0002704	negative regulation of leukocyte mediated immunity	27	66	2.665e-03
GO:BP	GO:0032735	positive regulation of interleukin-12 production	20	43	2.665e-03
GO:BP	GO:0050672	negative regulation of lymphocyte proliferation	33	87	2.704e-03
GO:BP	GO:0042098	T cell proliferation	66	213	2.758e-03
GO:BP	GO:0007189	adenylate cyclase-activating G protein-coupled receptor signaling pathway	52	158	2.776e-03
GO:BP	GO:0060295	regulation of cilium movement involved in cell motility	16	31	2.887e-03
GO:BP	GO:1902019	regulation of cilium-dependent cell motility	16	31	2.887e-03
GO:BP	GO:0071347	cellular response to interleukin-1	38	106	3.287e-03
GO:BP	GO:0030183	B cell differentiation	52	159	3.287e-03
GO:BP	GO:0002544	chronic inflammatory response	12	20	3.343e-03
GO:BP	GO:0050866	negative regulation of cell activation	64	207	3.667e-03
GO:BP	GO:0048519	negative regulation of biological process	1265	5865	3.699e-03
GO:BP	GO:0002444	myeloid leukocyte mediated immunity	40	114	3.699e-03
GO:BP	GO:0003006	developmental process involved in reproduction	251	1022	3.867e-03
GO:BP	GO:0015669	gas transport	13	23	3.897e-03
GO:BP	GO:0030277	maintenance of gastrointestinal epithelium	13	23	3.897e-03
GO:BP	GO:0002449	lymphocyte mediated immunity	101	361	4.256e-03
GO:BP	GO:0042755	eating behavior	18	38	4.256e-03
GO:BP	GO:0060259	regulation of feeding behavior	14	26	4.256e-03
GO:BP	GO:0002275	myeloid cell activation involved in immune response	36	100	4.315e-03
GO:BP	GO:0006691	leukotriene metabolic process	16	32	4.436e-03
GO:BP	GO:1903963	arachidonate transport	16	32	4.436e-03
GO:BP	GO:0050482	arachidonate secretion	16	32	4.436e-03
GO:BP	GO:0009581	detection of external stimulus	47	142	4.779e-03
GO:BP	GO:0031347	regulation of defense response	197	783	5.095e-03
GO:BP	GO:0002707	negative regulation of lymphocyte mediated immunity	23	55	5.477e-03
GO:BP	GO:0002768	immune response-regulating cell surface receptor signaling pathway	94	334	5.515e-03
GO:BP	GO:0001818	negative regulation of cytokine production	83	288	5.529e-03
GO:BP	GO:0002705	positive regulation of leukocyte mediated immunity	48	147	5.710e-03
GO:BP	GO:0032655	regulation of interleukin-12 production	25	62	5.710e-03
GO:BP	GO:0050729	positive regulation of inflammatory response	48	147	5.710e-03
GO:BP	GO:0032615	interleukin-12 production	25	62	5.710e-03
GO:BP	GO:0002228	natural killer cell mediated immunity	29	76	5.710e-03
GO:BP	GO:0032101	regulation of response to external stimulus	260	1071	6.032e-03
GO:BP	GO:0044058	regulation of digestive system process	18	39	6.059e-03
GO:BP	GO:0070555	response to interleukin-1	44	132	6.132e-03
GO:BP	GO:0032760	positive regulation of tumor necrosis factor production	36	102	6.407e-03
GO:BP	GO:0042832	defense response to protozoan	14	27	6.752e-03
GO:BP	GO:1903557	positive regulation of tumor necrosis factor superfamily cytokine production	37	106	6.757e-03
GO:BP	GO:0002709	regulation of T cell mediated immunity	34	95	6.944e-03
GO:BP	GO:1903027	regulation of opsonization	8	11	6.986e-03
GO:BP	GO:0032680	regulation of tumor necrosis factor production	52	164	6.986e-03
GO:BP	GO:0032640	tumor necrosis factor production	52	164	6.986e-03
GO:BP	GO:0002819	regulation of adaptive immune response	62	204	7.018e-03
GO:BP	GO:0015671	oxygen transport	10	16	7.200e-03
GO:BP	GO:0060046	regulation of acrosome reaction	10	16	7.200e-03
GO:BP	GO:0034374	low-density lipoprotein particle remodeling	10	16	7.200e-03
GO:BP	GO:0008037	cell recognition	50	157	7.939e-03
GO:BP	GO:0035036	sperm-egg recognition	22	53	7.939e-03
GO:BP	GO:0071706	tumor necrosis factor superfamily cytokine production	53	169	8.073e-03
GO:BP	GO:1903555	regulation of tumor necrosis factor superfamily cytokine production	53	169	8.073e-03
GO:BP	GO:0002822	regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	58	189	8.083e-03
GO:BP	GO:0002715	regulation of natural killer cell mediated immunity	21	50	8.818e-03
GO:BP	GO:0034097	response to cytokine	229	937	8.945e-03
GO:BP	GO:1903028	positive regulation of opsonization	7	9	8.998e-03
GO:BP	GO:0071466	cellular response to xenobiotic stimulus	59	194	9.181e-03
GO:BP	GO:0052696	flavonoid glucuronidation	5	5	9.181e-03
GO:BP	GO:0002803	positive regulation of antibacterial peptide production	5	5	9.181e-03
GO:BP	GO:0046456	icosanoid biosynthetic process	23	57	9.213e-03
GO:BP	GO:0032103	positive regulation of response to external stimulus	158	619	9.711e-03
GO:BP	GO:0009988	cell-cell recognition	28	75	1.018e-02
GO:BP	GO:0002710	negative regulation of T cell mediated immunity	14	28	1.020e-02
GO:BP	GO:0007198	adenylate cyclase-inhibiting serotonin receptor signaling pathway	6	7	1.042e-02
GO:BP	GO:0070942	neutrophil mediated cytotoxicity	9	14	1.053e-02
GO:BP	GO:0009111	vitamin catabolic process	9	14	1.053e-02
GO:BP	GO:0002820	negative regulation of adaptive immune response	24	61	1.055e-02
GO:BP	GO:0002701	negative regulation of production of molecular mediator of immune response	19	44	1.059e-02
GO:BP	GO:1901652	response to peptide	231	950	1.097e-02
GO:BP	GO:0043330	response to exogenous dsRNA	21	51	1.160e-02
GO:BP	GO:0032733	positive regulation of interleukin-10 production	18	41	1.163e-02
GO:BP	GO:0001523	retinoid metabolic process	30	83	1.181e-02
GO:BP	GO:0050766	positive regulation of phagocytosis	26	69	1.334e-02
GO:BP	GO:0009582	detection of abiotic stimulus	46	145	1.392e-02
GO:BP	GO:0120254	olefinic compound metabolic process	50	161	1.416e-02
GO:BP	GO:0031343	positive regulation of cell killing	27	73	1.464e-02
GO:BP	GO:0002825	regulation of T-helper 1 type immune response	15	32	1.464e-02
GO:BP	GO:0043299	leukocyte degranulation	30	84	1.464e-02
GO:BP	GO:0042445	hormone metabolic process	70	243	1.468e-02
GO:BP	GO:0006910	phagocytosis, recognition	14	29	1.514e-02
GO:BP	GO:0009812	flavonoid metabolic process	8	12	1.514e-02
GO:BP	GO:0016056	G protein-coupled opsin signaling pathway	8	12	1.514e-02
GO:BP	GO:0070943	neutrophil-mediated killing of symbiont cell	8	12	1.514e-02
GO:BP	GO:0018149	peptide cross-linking	14	29	1.514e-02
GO:BP	GO:0032661	regulation of interleukin-18 production	8	12	1.514e-02
GO:BP	GO:0032621	interleukin-18 production	8	12	1.514e-02
GO:BP	GO:0016101	diterpenoid metabolic process	31	88	1.523e-02
GO:BP	GO:0098581	detection of external biotic stimulus	13	26	1.535e-02
GO:BP	GO:0002688	regulation of leukocyte chemotaxis	40	123	1.736e-02
GO:BP	GO:0007187	G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger	22	56	1.739e-02
GO:BP	GO:0002823	negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	22	56	1.739e-02
GO:BP	GO:0072678	T cell migration	27	74	1.786e-02
GO:BP	GO:0032651	regulation of interleukin-1 beta production	32	93	1.956e-02
GO:BP	GO:0032611	interleukin-1 beta production	32	93	1.956e-02
GO:BP	GO:0141005	transposable element silencing by heterochromatin formation	9	15	1.985e-02
GO:BP	GO:0002700	regulation of production of molecular mediator of immune response	56	188	2.010e-02
GO:BP	GO:0002456	T cell mediated immunity	40	124	2.030e-02
GO:BP	GO:0042573	retinoic acid metabolic process	15	33	2.064e-02
GO:BP	GO:0035747	natural killer cell chemotaxis	7	10	2.159e-02
GO:BP	GO:0008343	adult feeding behavior	7	10	2.159e-02
GO:BP	GO:0071947	protein deubiquitination involved in ubiquitin-dependent protein catabolic process	7	10	2.159e-02
GO:BP	GO:0002765	immune response-inhibiting signal transduction	7	10	2.159e-02
GO:BP	GO:0001562	response to protozoan	14	30	2.194e-02
GO:BP	GO:0007603	phototransduction, visible light	10	18	2.238e-02
GO:BP	GO:0002675	positive regulation of acute inflammatory response	13	27	2.308e-02
GO:BP	GO:0002577	regulation of antigen processing and presentation	11	21	2.355e-02
GO:BP	GO:0002523	leukocyte migration involved in inflammatory response	11	21	2.355e-02
GO:BP	GO:0055078	sodium ion homeostasis	19	47	2.522e-02
GO:BP	GO:0022407	regulation of cell-cell adhesion	123	478	2.636e-02
GO:BP	GO:0032729	positive regulation of type II interferon production	27	76	2.716e-02
GO:BP	GO:2000501	regulation of natural killer cell chemotaxis	6	8	2.976e-02
GO:BP	GO:0032741	positive regulation of interleukin-18 production	6	8	2.976e-02
GO:BP	GO:0070268	cornification	6	8	2.976e-02
GO:BP	GO:0060456	positive regulation of digestive system process	8	13	2.976e-02
GO:BP	GO:0031349	positive regulation of defense response	124	484	2.976e-02
GO:BP	GO:0048523	negative regulation of cellular process	1203	5646	2.976e-02
GO:BP	GO:0044706	multi-multicellular organism process	61	212	2.976e-02
GO:BP	GO:0046942	carboxylic acid transport	92	344	2.986e-02
GO:BP	GO:0042116	macrophage activation	35	107	2.986e-02
GO:BP	GO:0002683	negative regulation of immune system process	128	502	2.986e-02
GO:BP	GO:0042267	natural killer cell mediated cytotoxicity	26	73	3.098e-02
GO:BP	GO:0009072	aromatic amino acid metabolic process	17	41	3.163e-02
GO:BP	GO:0006775	fat-soluble vitamin metabolic process	19	48	3.258e-02
GO:BP	GO:0015849	organic acid transport	92	345	3.258e-02
GO:BP	GO:0010817	regulation of hormone levels	138	548	3.277e-02
GO:BP	GO:0030888	regulation of B cell proliferation	24	66	3.324e-02
GO:BP	GO:1902221	erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process	13	28	3.324e-02
GO:BP	GO:0051607	defense response to virus	84	311	3.403e-02
GO:BP	GO:0035821	modulation of process of another organism	9	16	3.403e-02
GO:BP	GO:0050867	positive regulation of cell activation	98	372	3.480e-02
GO:BP	GO:0019370	leukotriene biosynthetic process	10	19	3.571e-02
GO:BP	GO:0030431	sleep	11	22	3.571e-02
GO:BP	GO:0009253	peptidoglycan catabolic process	5	6	3.571e-02
GO:BP	GO:0002325	natural killer cell differentiation involved in immune response	4	4	3.571e-02
GO:BP	GO:0032635	interleukin-6 production	46	152	3.571e-02
GO:BP	GO:0032675	regulation of interleukin-6 production	46	152	3.571e-02
GO:BP	GO:0098543	detection of other organism	10	19	3.571e-02
GO:BP	GO:0000270	peptidoglycan metabolic process	5	6	3.571e-02
GO:BP	GO:0044278	disruption of cell wall in another organism	4	4	3.571e-02
GO:BP	GO:0034382	chylomicron remnant clearance	5	6	3.571e-02
GO:BP	GO:0035743	CD4-positive, alpha-beta T cell cytokine production	10	19	3.571e-02
GO:BP	GO:0097272	ammonium homeostasis	5	6	3.571e-02
GO:BP	GO:0060480	lung goblet cell differentiation	4	4	3.571e-02
GO:BP	GO:2000503	positive regulation of natural killer cell chemotaxis	5	6	3.571e-02
GO:BP	GO:2000851	positive regulation of glucocorticoid secretion	4	4	3.571e-02
GO:BP	GO:0042320	regulation of circadian sleep/wake cycle, REM sleep	4	4	3.571e-02
GO:BP	GO:0051464	positive regulation of cortisol secretion	4	4	3.571e-02
GO:BP	GO:0032826	regulation of natural killer cell differentiation involved in immune response	4	4	3.571e-02
GO:BP	GO:0042747	circadian sleep/wake cycle, REM sleep	4	4	3.571e-02
GO:BP	GO:0006869	lipid transport	111	431	3.906e-02
GO:BP	GO:0044703	multi-organism reproductive process	58	203	4.221e-02
GO:BP	GO:0032732	positive regulation of interleukin-1 production	25	71	4.221e-02
GO:BP	GO:0032372	negative regulation of sterol transport	7	11	4.274e-02
GO:BP	GO:0032375	negative regulation of cholesterol transport	7	11	4.274e-02
GO:BP	GO:0070944	neutrophil-mediated killing of bacterium	7	11	4.274e-02
GO:BP	GO:0002440	production of molecular mediator of immune response	62	220	4.285e-02
GO:BP	GO:0007340	acrosome reaction	16	39	4.545e-02
GO:BP	GO:0015721	bile acid and bile salt transport	13	29	4.563e-02
GO:BP	GO:0042269	regulation of natural killer cell mediated cytotoxicity	18	46	4.607e-02
GO:BP	GO:0030098	lymphocyte differentiation	112	438	4.710e-02
GO:BP	GO:0019369	arachidonate metabolic process	21	57	4.919e-02
KEGG	KEGG:04740	Olfactory transduction	367	428	1.117e-182
KEGG	KEGG:04060	Cytokine-cytokine receptor interaction	152	291	3.555e-28
KEGG	KEGG:04080	Neuroactive ligand-receptor interaction	169	365	9.506e-24
KEGG	KEGG:05206	MicroRNAs in cancer	147	310	7.052e-22
KEGG	KEGG:05150	Staphylococcus aureus infection	58	86	1.316e-17
KEGG	KEGG:04061	Viral protein interaction with cytokine and cytokine receptor	62	98	8.388e-17
KEGG	KEGG:00830	Retinol metabolism	40	68	2.581e-09
KEGG	KEGG:05320	Autoimmune thyroid disease	32	49	4.064e-09
KEGG	KEGG:04742	Taste transduction	45	85	1.597e-08
KEGG	KEGG:00980	Metabolism of xenobiotics by cytochrome P450	40	74	5.987e-08
KEGG	KEGG:05310	Asthma	20	27	3.423e-07
KEGG	KEGG:04640	Hematopoietic cell lineage	45	92	3.423e-07
KEGG	KEGG:05204	Chemical carcinogenesis - DNA adducts	36	67	3.698e-07
KEGG	KEGG:04672	Intestinal immune network for IgA production	26	44	2.759e-06
KEGG	KEGG:00982	Drug metabolism - cytochrome P450	34	68	8.022e-06
KEGG	KEGG:04630	JAK-STAT signaling pathway	63	162	1.691e-05
KEGG	KEGG:05323	Rheumatoid arthritis	40	88	1.700e-05
KEGG	KEGG:00053	Ascorbate and aldarate metabolism	19	30	2.543e-05
KEGG	KEGG:05322	Systemic lupus erythematosus	52	132	7.983e-05
KEGG	KEGG:05332	Graft-versus-host disease	21	37	7.983e-05
KEGG	KEGG:00140	Steroid hormone biosynthesis	29	62	2.206e-04
KEGG	KEGG:04976	Bile secretion	37	89	4.124e-04
KEGG	KEGG:05144	Malaria	24	49	4.179e-04
KEGG	KEGG:00590	Arachidonic acid metabolism	28	61	4.179e-04
KEGG	KEGG:00591	Linoleic acid metabolism	17	30	5.363e-04
KEGG	KEGG:05321	Inflammatory bowel disease	28	62	5.568e-04
KEGG	KEGG:00040	Pentose and glucuronate interconversions	19	36	6.668e-04
KEGG	KEGG:00592	alpha-Linolenic acid metabolism	15	26	1.038e-03
KEGG	KEGG:05330	Allograft rejection	17	34	3.520e-03
KEGG	KEGG:00860	Porphyrin metabolism	20	43	3.520e-03
KEGG	KEGG:04975	Fat digestion and absorption	20	43	3.520e-03
KEGG	KEGG:04650	Natural killer cell mediated cytotoxicity	44	124	4.374e-03
KEGG	KEGG:05152	Tuberculosis	57	175	8.150e-03
KEGG	KEGG:00983	Drug metabolism - other enzymes	30	79	9.433e-03
KEGG	KEGG:04940	Type I diabetes mellitus	18	40	9.990e-03
KEGG	KEGG:05340	Primary immunodeficiency	17	37	9.995e-03
KEGG	KEGG:04610	Complement and coagulation cascades	31	86	1.923e-02
KEGG	KEGG:05164	Influenza A	53	167	1.925e-02
KEGG	KEGG:00350	Tyrosine metabolism	16	36	1.925e-02
KEGG	KEGG:05143	African trypanosomiasis	16	36	1.925e-02
KEGG	KEGG:04620	Toll-like receptor signaling pathway	36	106	2.611e-02
KEGG	KEGG:04613	Neutrophil extracellular trap formation	57	188	3.938e-02
KEGG	KEGG:04744	Phototransduction	13	29	4.150e-02
KEGG	KEGG:04950	Maturity onset diabetes of the young	12	26	4.202e-02
KEGG	KEGG:04972	Pancreatic secretion	34	102	4.245e-02
KEGG	KEGG:04657	IL-17 signaling pathway	31	92	4.935e-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	390	443	1.287e-211
GO:BP	GO:0050911	detection of chemical stimulus involved in sensory perception of smell	361	397	3.880e-207
GO:BP	GO:0035195	miRNA-mediated post-transcriptional gene silencing	470	612	1.992e-205
GO:BP	GO:0007606	sensory perception of chemical stimulus	413	497	2.606e-204
GO:BP	GO:0035194	regulatory ncRNA-mediated post-transcriptional gene silencing	471	624	2.134e-200
GO:BP	GO:0016441	post-transcriptional gene silencing	472	630	1.663e-198
GO:BP	GO:0009593	detection of chemical stimulus	399	480	1.882e-197
GO:BP	GO:0007608	sensory perception of smell	368	423	4.525e-196
GO:BP	GO:0050906	detection of stimulus involved in sensory perception	412	515	8.753e-192
GO:BP	GO:0031047	regulatory ncRNA-mediated gene silencing	478	686	7.125e-179
GO:BP	GO:0007186	G protein-coupled receptor signaling pathway	691	1275	6.531e-171
GO:BP	GO:0051606	detection of stimulus	450	643	3.612e-169
GO:BP	GO:0007600	sensory perception	550	955	1.330e-149
GO:BP	GO:0050877	nervous system process	640	1489	7.974e-96
GO:BP	GO:0010608	post-transcriptional regulation of gene expression	507	1087	6.512e-90
GO:BP	GO:0003008	system process	792	2266	7.511e-68
GO:BP	GO:0010629	negative regulation of gene expression	623	1640	4.964e-67
GO:BP	GO:0042221	response to chemical	1081	3867	6.538e-38
GO:BP	GO:0065007	biological regulation	2890	12671	3.299e-35
GO:BP	GO:0050789	regulation of biological process	2803	12278	6.612e-33
GO:BP	GO:0042742	defense response to bacterium	163	326	1.270e-31
GO:BP	GO:0006952	defense response	567	1809	7.997e-31
GO:BP	GO:0032501	multicellular organismal process	1775	7234	4.261e-30
GO:BP	GO:0050794	regulation of cellular process	2710	11876	4.261e-30
GO:BP	GO:0006959	humoral immune response	135	254	1.532e-29
GO:BP	GO:0010558	negative regulation of macromolecule biosynthetic process	784	2772	2.288e-27
GO:BP	GO:0009617	response to bacterium	270	721	5.192e-26
GO:BP	GO:0009890	negative regulation of biosynthetic process	792	2838	1.031e-25
GO:BP	GO:0098542	defense response to other organism	401	1228	7.042e-25
GO:BP	GO:0031424	keratinization	62	82	7.370e-25
GO:BP	GO:0019730	antimicrobial humoral response	81	131	3.323e-23
GO:BP	GO:0043207	response to external biotic stimulus	472	1558	1.127e-21
GO:BP	GO:0051707	response to other organism	470	1555	2.367e-21
GO:BP	GO:0140546	defense response to symbiont	363	1125	2.502e-21
GO:BP	GO:0009607	response to biotic stimulus	479	1593	2.604e-21
GO:BP	GO:0007165	signal transduction	1438	5979	5.050e-18
GO:BP	GO:0009605	response to external stimulus	645	2367	1.527e-17
GO:BP	GO:0141060	disruption of anatomical structure in another organism	60	98	1.074e-16
GO:BP	GO:0001906	cell killing	102	219	1.111e-16
GO:BP	GO:0010605	negative regulation of macromolecule metabolic process	826	3197	2.318e-16
GO:BP	GO:0006954	inflammatory response	275	847	3.167e-16
GO:BP	GO:0044419	biological process involved in interspecies interaction between organisms	489	1724	3.212e-16
GO:BP	GO:0061844	antimicrobial humoral immune response mediated by antimicrobial peptide	53	83	7.347e-16
GO:BP	GO:0031640	killing of cells of another organism	56	91	9.719e-16
GO:BP	GO:0141061	disruption of cell in another organism	56	91	9.719e-16
GO:BP	GO:0045087	innate immune response	305	977	1.891e-15
GO:BP	GO:0045109	intermediate filament organization	48	73	4.381e-15
GO:BP	GO:0006955	immune response	549	2008	5.955e-15
GO:BP	GO:0030216	keratinocyte differentiation	84	176	1.835e-14
GO:BP	GO:0007154	cell communication	1520	6496	1.967e-14
GO:BP	GO:0023052	signaling	1513	6471	3.321e-14
GO:BP	GO:0009892	negative regulation of metabolic process	859	3418	7.863e-14
GO:BP	GO:0097530	granulocyte migration	74	156	1.684e-12
GO:BP	GO:1990266	neutrophil migration	65	129	1.812e-12
GO:BP	GO:0050896	response to stimulus	2016	8993	1.856e-12
GO:BP	GO:0050829	defense response to Gram-negative bacterium	51	91	5.170e-12
GO:BP	GO:0050830	defense response to Gram-positive bacterium	61	120	6.701e-12
GO:BP	GO:0030593	neutrophil chemotaxis	56	106	8.589e-12
GO:BP	GO:0009913	epidermal cell differentiation	101	250	1.235e-11
GO:BP	GO:0002252	immune effector process	221	703	2.576e-11
GO:BP	GO:0071621	granulocyte chemotaxis	63	129	2.607e-11
GO:BP	GO:0007586	digestion	65	136	3.831e-11
GO:BP	GO:0030595	leukocyte chemotaxis	95	237	1.092e-10
GO:BP	GO:0050900	leukocyte migration	139	396	1.402e-10
GO:BP	GO:0050909	sensory perception of taste	40	67	1.572e-10
GO:BP	GO:0002237	response to molecule of bacterial origin	127	355	2.877e-10
GO:BP	GO:0002697	regulation of immune effector process	134	381	2.911e-10
GO:BP	GO:0045104	intermediate filament cytoskeleton organization	49	94	5.229e-10
GO:BP	GO:0002376	immune system process	696	2796	6.460e-10
GO:BP	GO:0097529	myeloid leukocyte migration	93	237	7.182e-10
GO:BP	GO:0002323	natural killer cell activation involved in immune response	26	35	8.175e-10
GO:BP	GO:0045103	intermediate filament-based process	49	95	8.229e-10
GO:BP	GO:0007218	neuropeptide signaling pathway	54	110	8.825e-10
GO:BP	GO:0019731	antibacterial humoral response	39	68	1.527e-09
GO:BP	GO:0071219	cellular response to molecule of bacterial origin	88	224	2.298e-09
GO:BP	GO:0032496	response to lipopolysaccharide	119	337	3.248e-09
GO:BP	GO:0008544	epidermis development	134	394	3.770e-09
GO:BP	GO:0070661	leukocyte proliferation	122	351	5.808e-09
GO:BP	GO:0071222	cellular response to lipopolysaccharide	84	214	6.541e-09
GO:BP	GO:0050913	sensory perception of bitter taste	28	42	7.382e-09
GO:BP	GO:0046651	lymphocyte proliferation	110	308	7.797e-09
GO:BP	GO:0051716	cellular response to stimulus	1639	7320	1.120e-08
GO:BP	GO:0007283	spermatogenesis	194	637	1.246e-08
GO:BP	GO:0007338	single fertilization	70	169	1.462e-08
GO:BP	GO:0032943	mononuclear cell proliferation	111	315	1.544e-08
GO:BP	GO:0050912	detection of chemical stimulus involved in sensory perception of taste	28	43	1.592e-08
GO:BP	GO:0052695	cellular glucuronidation	18	21	1.831e-08
GO:BP	GO:0033141	positive regulation of peptidyl-serine phosphorylation of STAT protein	18	21	1.831e-08
GO:BP	GO:0070098	chemokine-mediated signaling pathway	45	90	1.838e-08
GO:BP	GO:0048232	male gamete generation	197	654	2.315e-08
GO:BP	GO:0042100	B cell proliferation	50	106	2.576e-08
GO:BP	GO:0071715	icosanoid transport	36	65	2.911e-08
GO:BP	GO:0060326	cell chemotaxis	111	319	3.324e-08
GO:BP	GO:0001580	detection of chemical stimulus involved in sensory perception of bitter taste	25	37	4.338e-08
GO:BP	GO:0009566	fertilization	81	212	5.545e-08
GO:BP	GO:0002682	regulation of immune system process	399	1526	7.018e-08
GO:BP	GO:0045321	leukocyte activation	265	951	1.229e-07
GO:BP	GO:0002548	monocyte chemotaxis	36	68	1.442e-07
GO:BP	GO:0001775	cell activation	299	1098	1.442e-07
GO:BP	GO:0019221	cytokine-mediated signaling pathway	156	503	1.723e-07
GO:BP	GO:0048245	eosinophil chemotaxis	20	27	1.818e-07
GO:BP	GO:0070663	regulation of leukocyte proliferation	94	265	2.192e-07
GO:BP	GO:0071216	cellular response to biotic stimulus	90	251	2.555e-07
GO:BP	GO:0002526	acute inflammatory response	49	109	2.614e-07
GO:BP	GO:0022414	reproductive process	401	1556	3.920e-07
GO:BP	GO:0048609	multicellular organismal reproductive process	269	980	4.080e-07
GO:BP	GO:0022600	digestive system process	47	105	6.278e-07
GO:BP	GO:1990869	cellular response to chemokine	45	99	7.116e-07
GO:BP	GO:1990868	response to chemokine	45	99	7.116e-07
GO:BP	GO:0002366	leukocyte activation involved in immune response	103	305	7.469e-07
GO:BP	GO:0002263	cell activation involved in immune response	104	309	7.689e-07
GO:BP	GO:0033139	regulation of peptidyl-serine phosphorylation of STAT protein	18	24	7.793e-07
GO:BP	GO:0002699	positive regulation of immune effector process	89	253	8.236e-07
GO:BP	GO:0072677	eosinophil migration	21	31	8.501e-07
GO:BP	GO:0006953	acute-phase response	28	49	8.612e-07
GO:BP	GO:0002274	myeloid leukocyte activation	85	240	1.193e-06
GO:BP	GO:0050832	defense response to fungus	31	59	2.090e-06
GO:BP	GO:0042501	serine phosphorylation of STAT protein	18	25	2.145e-06
GO:BP	GO:0060294	cilium movement involved in cell motility	64	167	2.377e-06
GO:BP	GO:0050670	regulation of lymphocyte proliferation	83	236	2.430e-06
GO:BP	GO:0032944	regulation of mononuclear cell proliferation	84	240	2.562e-06
GO:BP	GO:0031341	regulation of cell killing	46	106	2.568e-06
GO:BP	GO:0002684	positive regulation of immune system process	284	1066	2.902e-06
GO:BP	GO:0030317	flagellated sperm motility	58	147	2.965e-06
GO:BP	GO:0097722	sperm motility	58	147	2.965e-06
GO:BP	GO:0048247	lymphocyte chemotaxis	32	63	3.354e-06
GO:BP	GO:0032649	regulation of type II interferon production	49	117	3.559e-06
GO:BP	GO:0043588	skin development	105	322	3.654e-06
GO:BP	GO:0032609	type II interferon production	49	118	4.838e-06
GO:BP	GO:0019585	glucuronate metabolic process	18	26	5.102e-06
GO:BP	GO:0006063	uronic acid metabolic process	18	26	5.102e-06
GO:BP	GO:0007188	adenylate cyclase-modulating G protein-coupled receptor signaling pathway	85	248	5.705e-06
GO:BP	GO:0050776	regulation of immune response	243	897	6.122e-06
GO:BP	GO:0002775	antimicrobial peptide production	10	10	6.776e-06
GO:BP	GO:0140975	disruption of cellular anatomical structure in another organism	10	10	6.776e-06
GO:BP	GO:0019953	sexual reproduction	290	1103	7.052e-06
GO:BP	GO:0007631	feeding behavior	45	106	7.082e-06
GO:BP	GO:0001539	cilium or flagellum-dependent cell motility	64	172	7.376e-06
GO:BP	GO:0060285	cilium-dependent cell motility	64	172	7.376e-06
GO:BP	GO:0002922	positive regulation of humoral immune response	16	22	8.801e-06
GO:BP	GO:0002703	regulation of leukocyte mediated immunity	83	243	8.934e-06
GO:BP	GO:0072676	lymphocyte migration	50	124	9.854e-06
GO:BP	GO:0030101	natural killer cell activation	41	95	1.434e-05
GO:BP	GO:0007259	cell surface receptor signaling pathway via JAK-STAT	62	168	1.566e-05
GO:BP	GO:0010468	regulation of gene expression	1231	5515	1.601e-05
GO:BP	GO:0007342	fusion of sperm to egg plasma membrane involved in single fertilization	19	30	1.685e-05
GO:BP	GO:0007276	gamete generation	223	822	1.685e-05
GO:BP	GO:0022412	cellular process involved in reproduction in multicellular organism	124	408	1.784e-05
GO:BP	GO:0097696	cell surface receptor signaling pathway via STAT	64	176	1.813e-05
GO:BP	GO:0050727	regulation of inflammatory response	117	381	2.093e-05
GO:BP	GO:0048240	sperm capacitation	20	33	2.241e-05
GO:BP	GO:0001909	leukocyte mediated cytotoxicity	52	135	2.922e-05
GO:BP	GO:0042330	taxis	137	465	3.037e-05
GO:BP	GO:0001819	positive regulation of cytokine production	142	486	3.187e-05
GO:BP	GO:0015908	fatty acid transport	47	118	3.220e-05
GO:BP	GO:0071674	mononuclear cell migration	79	235	3.327e-05
GO:BP	GO:0015718	monocarboxylic acid transport	64	179	3.440e-05
GO:BP	GO:0006690	icosanoid metabolic process	48	122	3.689e-05
GO:BP	GO:0032309	icosanoid secretion	25	48	4.224e-05
GO:BP	GO:0042129	regulation of T cell proliferation	64	180	4.227e-05
GO:BP	GO:0007286	spermatid development	73	214	4.564e-05
GO:BP	GO:0007200	phospholipase C-activating G protein-coupled receptor signaling pathway	46	116	4.695e-05
GO:BP	GO:0015732	prostaglandin transport	18	29	4.842e-05
GO:BP	GO:0051873	killing by host of symbiont cells	18	29	4.842e-05
GO:BP	GO:0001817	regulation of cytokine production	207	765	4.892e-05
GO:BP	GO:0007159	leukocyte cell-cell adhesion	121	404	5.096e-05
GO:BP	GO:0009620	response to fungus	32	70	5.455e-05
GO:BP	GO:0002251	organ or tissue specific immune response	23	43	5.998e-05
GO:BP	GO:0001816	cytokine production	208	772	6.150e-05
GO:BP	GO:0006935	chemotaxis	135	463	6.150e-05
GO:BP	GO:0002706	regulation of lymphocyte mediated immunity	64	182	6.150e-05
GO:BP	GO:0050865	regulation of cell activation	171	616	7.851e-05
GO:BP	GO:0050778	positive regulation of immune response	198	732	8.254e-05
GO:BP	GO:0034341	response to type II interferon	54	147	8.849e-05
GO:BP	GO:0002285	lymphocyte activation involved in immune response	72	214	8.885e-05
GO:BP	GO:0098586	cellular response to virus	34	78	9.303e-05
GO:BP	GO:0050953	sensory perception of light stimulus	74	222	9.367e-05
GO:BP	GO:0048515	spermatid differentiation	74	222	9.367e-05
GO:BP	GO:0036230	granulocyte activation	25	50	1.007e-04
GO:BP	GO:0007601	visual perception	73	219	1.084e-04
GO:BP	GO:0051250	negative regulation of lymphocyte activation	57	159	1.093e-04
GO:BP	GO:0001910	regulation of leukocyte mediated cytotoxicity	38	92	1.145e-04
GO:BP	GO:0002694	regulation of leukocyte activation	157	561	1.184e-04
GO:BP	GO:0002760	positive regulation of antimicrobial humoral response	8	8	1.237e-04
GO:BP	GO:0002778	antibacterial peptide production	8	8	1.237e-04
GO:BP	GO:0002784	regulation of antimicrobial peptide production	8	8	1.237e-04
GO:BP	GO:0002443	leukocyte mediated immunity	133	461	1.239e-04
GO:BP	GO:0042531	positive regulation of tyrosine phosphorylation of STAT protein	29	63	1.296e-04
GO:BP	GO:0002385	mucosal immune response	21	39	1.355e-04
GO:BP	GO:0042119	neutrophil activation	22	42	1.433e-04
GO:BP	GO:0032689	negative regulation of type II interferon production	22	42	1.433e-04
GO:BP	GO:0002920	regulation of humoral immune response	23	45	1.480e-04
GO:BP	GO:0051249	regulation of lymphocyte activation	141	497	1.646e-04
GO:BP	GO:0071346	cellular response to type II interferon	47	125	1.725e-04
GO:BP	GO:0002286	T cell activation involved in immune response	47	125	1.725e-04
GO:BP	GO:0006805	xenobiotic metabolic process	47	125	1.725e-04
GO:BP	GO:0007204	positive regulation of cytosolic calcium ion concentration	59	169	1.783e-04
GO:BP	GO:0045026	plasma membrane fusion	19	34	1.852e-04
GO:BP	GO:1903037	regulation of leukocyte cell-cell adhesion	109	366	1.921e-04
GO:BP	GO:0042363	fat-soluble vitamin catabolic process	10	12	2.025e-04
GO:BP	GO:0046649	lymphocyte activation	208	787	2.146e-04
GO:BP	GO:0070665	positive regulation of leukocyte proliferation	57	163	2.373e-04
GO:BP	GO:0009584	detection of visible light	18	32	2.865e-04
GO:BP	GO:0010556	regulation of macromolecule biosynthetic process	1238	5633	2.971e-04
GO:BP	GO:0032722	positive regulation of chemokine production	31	72	3.070e-04
GO:BP	GO:0070374	positive regulation of ERK1 and ERK2 cascade	69	210	3.102e-04
GO:BP	GO:0032642	regulation of chemokine production	38	96	3.356e-04
GO:BP	GO:0032602	chemokine production	38	96	3.356e-04
GO:BP	GO:0002685	regulation of leukocyte migration	74	230	3.391e-04
GO:BP	GO:0050863	regulation of T cell activation	110	375	3.516e-04
GO:BP	GO:0050868	negative regulation of T cell activation	46	125	3.931e-04
GO:BP	GO:1903038	negative regulation of leukocyte cell-cell adhesion	49	136	3.991e-04
GO:BP	GO:0002695	negative regulation of leukocyte activation	62	185	4.263e-04
GO:BP	GO:0003341	cilium movement	69	212	4.284e-04
GO:BP	GO:0042110	T cell activation	153	558	4.571e-04
GO:BP	GO:0015670	carbon dioxide transport	11	15	5.153e-04
GO:BP	GO:0030855	epithelial cell differentiation	195	741	5.213e-04
GO:BP	GO:0002225	positive regulation of antimicrobial peptide production	7	7	5.269e-04
GO:BP	GO:0052697	xenobiotic glucuronidation	7	7	5.269e-04
GO:BP	GO:0019755	one-carbon compound transport	15	25	5.456e-04
GO:BP	GO:0042509	regulation of tyrosine phosphorylation of STAT protein	31	74	5.586e-04
GO:BP	GO:0032945	negative regulation of mononuclear cell proliferation	35	88	6.260e-04
GO:BP	GO:0042102	positive regulation of T cell proliferation	39	102	6.260e-04
GO:BP	GO:1904892	regulation of receptor signaling pathway via STAT	40	106	7.014e-04
GO:BP	GO:0046425	regulation of receptor signaling pathway via JAK-STAT	38	99	7.157e-04
GO:BP	GO:0002759	regulation of antimicrobial humoral response	9	11	7.523e-04
GO:BP	GO:0007189	adenylate cyclase-activating G protein-coupled receptor signaling pathway	54	158	7.761e-04
GO:BP	GO:0050671	positive regulation of lymphocyte proliferation	50	143	7.761e-04
GO:BP	GO:0070664	negative regulation of leukocyte proliferation	37	96	8.104e-04
GO:BP	GO:0030277	maintenance of gastrointestinal epithelium	14	23	8.118e-04
GO:BP	GO:0003006	developmental process involved in reproduction	257	1022	8.286e-04
GO:BP	GO:0032613	interleukin-10 production	26	59	8.894e-04
GO:BP	GO:0032653	regulation of interleukin-10 production	26	59	8.894e-04
GO:BP	GO:0007260	tyrosine phosphorylation of STAT protein	31	76	9.966e-04
GO:BP	GO:0032637	interleukin-8 production	33	83	1.030e-03
GO:BP	GO:0032677	regulation of interleukin-8 production	33	83	1.030e-03
GO:BP	GO:0032757	positive regulation of interleukin-8 production	27	63	1.130e-03
GO:BP	GO:0002673	regulation of acute inflammatory response	22	47	1.171e-03
GO:BP	GO:0050672	negative regulation of lymphocyte proliferation	34	87	1.182e-03
GO:BP	GO:0050482	arachidonate secretion	17	32	1.192e-03
GO:BP	GO:0006691	leukotriene metabolic process	17	32	1.192e-03
GO:BP	GO:1903963	arachidonate transport	17	32	1.192e-03
GO:BP	GO:0002687	positive regulation of leukocyte migration	52	153	1.220e-03
GO:BP	GO:0032946	positive regulation of mononuclear cell proliferation	50	146	1.361e-03
GO:BP	GO:0009889	regulation of biosynthetic process	1261	5795	1.384e-03
GO:BP	GO:0002705	positive regulation of leukocyte mediated immunity	50	147	1.653e-03
GO:BP	GO:0042098	T cell proliferation	67	213	1.665e-03
GO:BP	GO:0009111	vitamin catabolic process	10	14	1.665e-03
GO:BP	GO:0007602	phototransduction	22	48	1.679e-03
GO:BP	GO:0009583	detection of light stimulus	28	68	1.847e-03
GO:BP	GO:0071466	cellular response to xenobiotic stimulus	62	194	1.847e-03
GO:BP	GO:0048519	negative regulation of biological process	1273	5865	1.948e-03
GO:BP	GO:0007281	germ cell development	105	370	2.077e-03
GO:BP	GO:0051552	flavone metabolic process	6	6	2.251e-03
GO:BP	GO:1901317	regulation of flagellated sperm motility	13	22	2.251e-03
GO:BP	GO:0002786	regulation of antibacterial peptide production	6	6	2.251e-03
GO:BP	GO:0051673	disruption of plasma membrane integrity in another organism	6	6	2.251e-03
GO:BP	GO:0032655	regulation of interleukin-12 production	26	62	2.262e-03
GO:BP	GO:0032615	interleukin-12 production	26	62	2.262e-03
GO:BP	GO:0032735	positive regulation of interleukin-12 production	20	43	2.735e-03
GO:BP	GO:0002227	innate immune response in mucosa	15	28	2.833e-03
GO:BP	GO:0031343	positive regulation of cell killing	29	73	2.833e-03
GO:BP	GO:1902221	erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process	15	28	2.833e-03
GO:BP	GO:0060295	regulation of cilium movement involved in cell motility	16	31	2.946e-03
GO:BP	GO:1902019	regulation of cilium-dependent cell motility	16	31	2.946e-03
GO:BP	GO:0042113	B cell activation	83	282	2.979e-03
GO:BP	GO:0035036	sperm-egg recognition	23	53	3.039e-03
GO:BP	GO:0032760	positive regulation of tumor necrosis factor production	37	102	3.171e-03
GO:BP	GO:0031347	regulation of defense response	199	783	3.171e-03
GO:BP	GO:0050729	positive regulation of inflammatory response	49	147	3.178e-03
GO:BP	GO:0032101	regulation of response to external stimulus	263	1071	3.242e-03
GO:BP	GO:0002715	regulation of natural killer cell mediated immunity	22	50	3.287e-03
GO:BP	GO:0002544	chronic inflammatory response	12	20	3.327e-03
GO:BP	GO:0071347	cellular response to interleukin-1	38	106	3.346e-03
GO:BP	GO:1903557	positive regulation of tumor necrosis factor superfamily cytokine production	38	106	3.346e-03
GO:BP	GO:0032652	regulation of interleukin-1 production	39	110	3.566e-03
GO:BP	GO:0032612	interleukin-1 production	39	110	3.566e-03
GO:BP	GO:0001818	negative regulation of cytokine production	84	288	3.652e-03
GO:BP	GO:0050866	negative regulation of cell activation	64	207	3.794e-03
GO:BP	GO:0015669	gas transport	13	23	3.873e-03
GO:BP	GO:0032680	regulation of tumor necrosis factor production	53	164	4.006e-03
GO:BP	GO:0032733	positive regulation of interleukin-10 production	19	41	4.006e-03
GO:BP	GO:0032640	tumor necrosis factor production	53	164	4.006e-03
GO:BP	GO:0009072	aromatic amino acid metabolic process	19	41	4.006e-03
GO:BP	GO:0060259	regulation of feeding behavior	14	26	4.204e-03
GO:BP	GO:0042755	eating behavior	18	38	4.204e-03
GO:BP	GO:0002825	regulation of T-helper 1 type immune response	16	32	4.434e-03
GO:BP	GO:0009988	cell-cell recognition	29	75	4.561e-03
GO:BP	GO:0071345	cellular response to cytokine stimulus	211	843	4.722e-03
GO:BP	GO:0071706	tumor necrosis factor superfamily cytokine production	54	169	4.722e-03
GO:BP	GO:1903555	regulation of tumor necrosis factor superfamily cytokine production	54	169	4.722e-03
GO:BP	GO:0002698	negative regulation of immune effector process	41	120	5.800e-03
GO:BP	GO:0032103	positive regulation of response to external stimulus	160	619	5.831e-03
GO:BP	GO:0002228	natural killer cell mediated immunity	29	76	5.859e-03
GO:BP	GO:0006968	cellular defense response	22	52	6.103e-03
GO:BP	GO:0044058	regulation of digestive system process	18	39	6.143e-03
GO:BP	GO:0030183	B cell differentiation	51	159	6.256e-03
GO:BP	GO:0070555	response to interleukin-1	44	132	6.378e-03
GO:BP	GO:0050891	multicellular organismal-level water homeostasis	16	33	6.736e-03
GO:BP	GO:0042832	defense response to protozoan	14	27	6.782e-03
GO:BP	GO:0015671	oxygen transport	10	16	7.332e-03
GO:BP	GO:0007187	G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger	23	56	7.332e-03
GO:BP	GO:0034374	low-density lipoprotein particle remodeling	10	16	7.332e-03
GO:BP	GO:0022407	regulation of cell-cell adhesion	127	478	7.559e-03
GO:BP	GO:0002444	myeloid leukocyte mediated immunity	39	114	7.636e-03
GO:BP	GO:0008037	cell recognition	50	157	8.438e-03
GO:BP	GO:0072678	T cell migration	28	74	8.473e-03
GO:BP	GO:0120254	olefinic compound metabolic process	51	161	8.473e-03
GO:BP	GO:0042436	indole-containing compound catabolic process	7	9	9.139e-03
GO:BP	GO:0006569	tryptophan catabolic process	7	9	9.139e-03
GO:BP	GO:0002275	myeloid cell activation involved in immune response	35	100	9.235e-03
GO:BP	GO:0002803	positive regulation of antibacterial peptide production	5	5	9.235e-03
GO:BP	GO:0009581	detection of external stimulus	46	142	9.235e-03
GO:BP	GO:0052696	flavonoid glucuronidation	5	5	9.235e-03
GO:BP	GO:0019369	arachidonate metabolic process	23	57	9.561e-03
GO:BP	GO:0002688	regulation of leukocyte chemotaxis	41	123	9.712e-03
GO:BP	GO:0030431	sleep	12	22	9.851e-03
GO:BP	GO:0032651	regulation of interleukin-1 beta production	33	93	9.917e-03
GO:BP	GO:0055078	sodium ion homeostasis	20	47	9.917e-03
GO:BP	GO:0032611	interleukin-1 beta production	33	93	9.917e-03
GO:BP	GO:0007198	adenylate cyclase-inhibiting serotonin receptor signaling pathway	6	7	1.046e-02
GO:BP	GO:0050795	regulation of behavior	28	75	1.046e-02
GO:BP	GO:0010273	detoxification of copper ion	9	14	1.054e-02
GO:BP	GO:0070942	neutrophil mediated cytotoxicity	9	14	1.054e-02
GO:BP	GO:0034116	positive regulation of heterotypic cell-cell adhesion	9	14	1.054e-02
GO:BP	GO:1990169	stress response to copper ion	9	14	1.054e-02
GO:BP	GO:0043330	response to exogenous dsRNA	21	51	1.193e-02
GO:BP	GO:0044706	multi-multicellular organism process	63	212	1.215e-02
GO:BP	GO:0001523	retinoid metabolic process	30	83	1.228e-02
GO:BP	GO:0032729	positive regulation of type II interferon production	28	76	1.312e-02
GO:BP	GO:0034097	response to cytokine	228	937	1.314e-02
GO:BP	GO:0006775	fat-soluble vitamin metabolic process	20	48	1.330e-02
GO:BP	GO:0008228	opsonization	10	17	1.330e-02
GO:BP	GO:0050766	positive regulation of phagocytosis	26	69	1.364e-02
GO:BP	GO:0002709	regulation of T cell mediated immunity	33	95	1.470e-02
GO:BP	GO:0002449	lymphocyte mediated immunity	98	361	1.513e-02
GO:BP	GO:0032661	regulation of interleukin-18 production	8	12	1.545e-02
GO:BP	GO:0018149	peptide cross-linking	14	29	1.545e-02
GO:BP	GO:0070943	neutrophil-mediated killing of symbiont cell	8	12	1.545e-02
GO:BP	GO:0032621	interleukin-18 production	8	12	1.545e-02
GO:BP	GO:0001912	positive regulation of leukocyte mediated cytotoxicity	25	66	1.549e-02
GO:BP	GO:0042445	hormone metabolic process	70	243	1.549e-02
GO:BP	GO:0098581	detection of external biotic stimulus	13	26	1.571e-02
GO:BP	GO:0016101	diterpenoid metabolic process	31	88	1.584e-02
GO:BP	GO:1901652	response to peptide	230	950	1.603e-02
GO:BP	GO:0042116	macrophage activation	36	107	1.629e-02
GO:BP	GO:0051607	defense response to virus	86	311	1.666e-02
GO:BP	GO:0031349	positive regulation of defense response	126	484	1.670e-02
GO:BP	GO:0044703	multi-organism reproductive process	60	203	1.791e-02
GO:BP	GO:0050867	positive regulation of cell activation	100	372	1.845e-02
GO:BP	GO:0042269	regulation of natural killer cell mediated cytotoxicity	19	46	1.967e-02
GO:BP	GO:0141005	transposable element silencing by heterochromatin formation	9	15	2.007e-02
GO:BP	GO:0002819	regulation of adaptive immune response	60	204	2.027e-02
GO:BP	GO:0010669	epithelial structure maintenance	15	33	2.106e-02
GO:BP	GO:0042573	retinoic acid metabolic process	15	33	2.106e-02
GO:BP	GO:0002700	regulation of production of molecular mediator of immune response	56	188	2.117e-02
GO:BP	GO:0008343	adult feeding behavior	7	10	2.169e-02
GO:BP	GO:0071947	protein deubiquitination involved in ubiquitin-dependent protein catabolic process	7	10	2.169e-02
GO:BP	GO:0035747	natural killer cell chemotaxis	7	10	2.169e-02
GO:BP	GO:0048523	negative regulation of cellular process	1209	5646	2.169e-02
GO:BP	GO:0001562	response to protozoan	14	30	2.230e-02
GO:BP	GO:0006869	lipid transport	113	431	2.256e-02
GO:BP	GO:0019373	epoxygenase P450 pathway	10	18	2.256e-02
GO:BP	GO:0046456	icosanoid biosynthetic process	22	57	2.269e-02
GO:BP	GO:0002675	positive regulation of acute inflammatory response	13	27	2.330e-02
GO:BP	GO:0002577	regulation of antigen processing and presentation	11	21	2.357e-02
GO:BP	GO:0002822	regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	56	189	2.357e-02
GO:BP	GO:0002523	leukocyte migration involved in inflammatory response	11	21	2.357e-02
GO:BP	GO:0022408	negative regulation of cell-cell adhesion	56	189	2.357e-02
GO:BP	GO:0009074	aromatic amino acid family catabolic process	12	24	2.367e-02
GO:BP	GO:0002708	positive regulation of lymphocyte mediated immunity	40	125	2.419e-02
GO:BP	GO:0009582	detection of abiotic stimulus	45	145	2.498e-02
GO:BP	GO:0042130	negative regulation of T cell proliferation	26	72	2.572e-02
GO:BP	GO:0010817	regulation of hormone levels	139	548	2.650e-02
GO:BP	GO:0002768	immune response-regulating cell surface receptor signaling pathway	90	334	2.845e-02
GO:BP	GO:0002690	positive regulation of leukocyte chemotaxis	32	95	2.859e-02
GO:BP	GO:0002701	negative regulation of production of molecular mediator of immune response	18	44	2.861e-02
GO:BP	GO:0032741	positive regulation of interleukin-18 production	6	8	2.932e-02
GO:BP	GO:0070268	cornification	6	8	2.932e-02
GO:BP	GO:2000501	regulation of natural killer cell chemotaxis	6	8	2.932e-02
GO:BP	GO:0060456	positive regulation of digestive system process	8	13	2.948e-02
GO:BP	GO:1900015	regulation of cytokine production involved in inflammatory response	23	62	3.141e-02
GO:BP	GO:0002534	cytokine production involved in inflammatory response	23	62	3.141e-02
GO:BP	GO:0042267	natural killer cell mediated cytotoxicity	26	73	3.153e-02
GO:BP	GO:0002683	negative regulation of immune system process	128	502	3.217e-02
GO:BP	GO:0060046	regulation of acrosome reaction	9	16	3.408e-02
GO:BP	GO:0002704	negative regulation of leukocyte mediated immunity	24	66	3.408e-02
GO:BP	GO:0035821	modulation of process of another organism	9	16	3.408e-02
GO:BP	GO:0072378	blood coagulation, fibrin clot formation	9	16	3.408e-02
GO:BP	GO:0051969	regulation of transmission of nerve impulse	9	16	3.408e-02
GO:BP	GO:0050878	regulation of body fluid levels	98	371	3.419e-02
GO:BP	GO:0042320	regulation of circadian sleep/wake cycle, REM sleep	4	4	3.485e-02
GO:BP	GO:0002325	natural killer cell differentiation involved in immune response	4	4	3.485e-02
GO:BP	GO:0048520	positive regulation of behavior	12	25	3.485e-02
GO:BP	GO:0042747	circadian sleep/wake cycle, REM sleep	4	4	3.485e-02
GO:BP	GO:0036101	leukotriene B4 catabolic process	4	4	3.485e-02
GO:BP	GO:0042430	indole-containing compound metabolic process	12	25	3.485e-02
GO:BP	GO:0042377	vitamin K catabolic process	4	4	3.485e-02
GO:BP	GO:0042376	phylloquinone catabolic process	4	4	3.485e-02
GO:BP	GO:0045938	positive regulation of circadian sleep/wake cycle, sleep	4	4	3.485e-02
GO:BP	GO:0042374	phylloquinone metabolic process	4	4	3.485e-02
GO:BP	GO:0036100	leukotriene catabolic process	5	6	3.485e-02
GO:BP	GO:0044278	disruption of cell wall in another organism	4	4	3.485e-02
GO:BP	GO:0097272	ammonium homeostasis	5	6	3.485e-02
GO:BP	GO:0034382	chylomicron remnant clearance	5	6	3.485e-02
GO:BP	GO:0097501	stress response to metal ion	10	19	3.485e-02
GO:BP	GO:0072376	protein activation cascade	10	19	3.485e-02
GO:BP	GO:0019370	leukotriene biosynthetic process	10	19	3.485e-02
GO:BP	GO:0098543	detection of other organism	10	19	3.485e-02
GO:BP	GO:0019805	quinolinate biosynthetic process	4	4	3.485e-02
GO:BP	GO:0035743	CD4-positive, alpha-beta T cell cytokine production	10	19	3.485e-02
GO:BP	GO:0060480	lung goblet cell differentiation	4	4	3.485e-02
GO:BP	GO:0032826	regulation of natural killer cell differentiation involved in immune response	4	4	3.485e-02
GO:BP	GO:0051464	positive regulation of cortisol secretion	4	4	3.485e-02
GO:BP	GO:0002827	positive regulation of T-helper 1 type immune response	10	19	3.485e-02
GO:BP	GO:2000851	positive regulation of glucocorticoid secretion	4	4	3.485e-02
GO:BP	GO:2000503	positive regulation of natural killer cell chemotaxis	5	6	3.485e-02
GO:BP	GO:0002456	T cell mediated immunity	39	124	3.533e-02
GO:BP	GO:0030098	lymphocyte differentiation	113	438	3.570e-02
GO:BP	GO:0140962	multicellular organismal-level chemical homeostasis	26	74	3.612e-02
GO:BP	GO:0002696	positive regulation of leukocyte activation	94	355	3.613e-02
GO:BP	GO:0034105	positive regulation of tissue remodeling	7	11	4.159e-02
GO:BP	GO:0021562	vestibulocochlear nerve development	7	11	4.159e-02
GO:BP	GO:0032372	negative regulation of sterol transport	7	11	4.159e-02
GO:BP	GO:0032375	negative regulation of cholesterol transport	7	11	4.159e-02
GO:BP	GO:1903027	regulation of opsonization	7	11	4.159e-02
GO:BP	GO:0070944	neutrophil-mediated killing of bacterium	7	11	4.159e-02
GO:BP	GO:0032732	positive regulation of interleukin-1 production	25	71	4.166e-02
GO:BP	GO:0032731	positive regulation of interleukin-1 beta production	22	60	4.209e-02
GO:BP	GO:0046942	carboxylic acid transport	91	344	4.277e-02
GO:BP	GO:0002440	production of molecular mediator of immune response	62	220	4.368e-02
GO:BP	GO:1903039	positive regulation of leukocyte cell-cell adhesion	74	271	4.404e-02
GO:BP	GO:0032814	regulation of natural killer cell activation	16	39	4.443e-02
GO:BP	GO:0006910	phagocytosis, recognition	13	29	4.443e-02
GO:BP	GO:0015849	organic acid transport	91	345	4.636e-02
GO:BP	GO:0022409	positive regulation of cell-cell adhesion	85	319	4.654e-02
GO:BP	GO:0002430	complement receptor mediated signaling pathway	8	14	4.950e-02
KEGG	KEGG:04740	Olfactory transduction	368	428	7.954e-184
KEGG	KEGG:04060	Cytokine-cytokine receptor interaction	148	291	9.354e-26
KEGG	KEGG:04080	Neuroactive ligand-receptor interaction	173	365	9.354e-26
KEGG	KEGG:05206	MicroRNAs in cancer	146	310	2.799e-21
KEGG	KEGG:05150	Staphylococcus aureus infection	58	86	1.424e-17
KEGG	KEGG:04061	Viral protein interaction with cytokine and cytokine receptor	59	98	1.828e-14
KEGG	KEGG:04742	Taste transduction	46	85	4.526e-09
KEGG	KEGG:05320	Autoimmune thyroid disease	32	49	4.526e-09
KEGG	KEGG:00830	Retinol metabolism	39	68	1.056e-08
KEGG	KEGG:00980	Metabolism of xenobiotics by cytochrome P450	38	74	1.027e-06
KEGG	KEGG:04640	Hematopoietic cell lineage	44	92	1.236e-06
KEGG	KEGG:05204	Chemical carcinogenesis - DNA adducts	35	67	1.708e-06
KEGG	KEGG:05310	Asthma	19	27	2.846e-06
KEGG	KEGG:04672	Intestinal immune network for IgA production	26	44	2.846e-06
KEGG	KEGG:00982	Drug metabolism - cytochrome P450	34	68	8.326e-06
KEGG	KEGG:05323	Rheumatoid arthritis	40	88	1.881e-05
KEGG	KEGG:00053	Ascorbate and aldarate metabolism	19	30	2.755e-05
KEGG	KEGG:04630	JAK-STAT signaling pathway	62	162	3.659e-05
KEGG	KEGG:05332	Graft-versus-host disease	21	37	8.608e-05
KEGG	KEGG:00591	Linoleic acid metabolism	18	30	1.351e-04
KEGG	KEGG:00590	Arachidonic acid metabolism	29	61	1.530e-04
KEGG	KEGG:04976	Bile secretion	38	89	1.598e-04
KEGG	KEGG:05322	Systemic lupus erythematosus	51	132	1.676e-04
KEGG	KEGG:00140	Steroid hormone biosynthesis	29	62	1.909e-04
KEGG	KEGG:05321	Inflammatory bowel disease	29	62	1.909e-04
KEGG	KEGG:05144	Malaria	24	49	3.872e-04
KEGG	KEGG:00040	Pentose and glucuronate interconversions	19	36	6.806e-04
KEGG	KEGG:05330	Allograft rejection	18	34	9.773e-04
KEGG	KEGG:00592	alpha-Linolenic acid metabolism	15	26	1.019e-03
KEGG	KEGG:04650	Natural killer cell mediated cytotoxicity	45	124	2.337e-03
KEGG	KEGG:04975	Fat digestion and absorption	20	43	3.383e-03
KEGG	KEGG:04940	Type I diabetes mellitus	19	40	3.383e-03
KEGG	KEGG:05340	Primary immunodeficiency	18	37	3.383e-03
KEGG	KEGG:05164	Influenza A	56	167	4.074e-03
KEGG	KEGG:04610	Complement and coagulation cascades	33	86	4.297e-03
KEGG	KEGG:05152	Tuberculosis	58	175	4.297e-03
KEGG	KEGG:05143	African trypanosomiasis	17	36	6.533e-03
KEGG	KEGG:00350	Tyrosine metabolism	17	36	6.533e-03
KEGG	KEGG:04514	Cell adhesion molecules	51	153	7.350e-03
KEGG	KEGG:00983	Drug metabolism - other enzymes	30	79	8.217e-03
KEGG	KEGG:00860	Porphyrin metabolism	19	43	8.340e-03
KEGG	KEGG:04620	Toll-like receptor signaling pathway	37	106	1.339e-02
KEGG	KEGG:04972	Pancreatic secretion	35	102	2.385e-02
KEGG	KEGG:04950	Maturity onset diabetes of the young	12	26	4.247e-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) This one doesn’t seem to work, most likely since it’s not really picking up a motif

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	90	1256	4.956e-16
GO:BP	GO:0034220	monoatomic ion transmembrane transport	75	1017	9.212e-14
GO:BP	GO:0055085	transmembrane transport	95	1538	2.667e-13
GO:BP	GO:0098660	inorganic ion transmembrane transport	68	903	5.761e-13
GO:BP	GO:0015698	inorganic anion transport	26	165	7.506e-11
GO:BP	GO:0006820	monoatomic anion transport	26	167	8.385e-11
GO:BP	GO:0006812	monoatomic cation transport	68	1032	2.164e-10
GO:BP	GO:0030001	metal ion transport	61	875	3.272e-10
GO:BP	GO:0030154	cell differentiation	178	4381	1.062e-09
GO:BP	GO:0048869	cellular developmental process	178	4382	1.062e-09
GO:BP	GO:0006821	chloride transport	21	122	1.495e-09
GO:BP	GO:0032502	developmental process	237	6478	1.495e-09
GO:BP	GO:0098661	inorganic anion transmembrane transport	21	127	2.871e-09
GO:BP	GO:0006810	transport	174	4341	5.023e-09
GO:BP	GO:0098655	monoatomic cation transmembrane transport	55	832	2.061e-08
GO:BP	GO:0098656	monoatomic anion transmembrane transport	21	142	2.086e-08
GO:BP	GO:0048468	cell development	125	2833	2.754e-08
GO:BP	GO:0032501	multicellular organismal process	252	7234	2.772e-08
GO:BP	GO:1902476	chloride transmembrane transport	18	107	4.673e-08
GO:BP	GO:0048856	anatomical structure development	215	5924	5.365e-08
GO:BP	GO:0098662	inorganic cation transmembrane transport	52	811	1.500e-07
GO:BP	GO:0050896	response to stimulus	293	8993	3.487e-07
GO:BP	GO:0007188	adenylate cyclase-modulating G protein-coupled receptor signaling pathway	25	248	9.241e-07
GO:BP	GO:0007155	cell adhesion	75	1511	2.123e-06
GO:BP	GO:0002521	leukocyte differentiation	42	632	2.228e-06
GO:BP	GO:0051234	establishment of localization	178	4869	2.720e-06
GO:BP	GO:0006813	potassium ion transport	23	238	7.285e-06
GO:BP	GO:0006968	cellular defense response	11	52	9.549e-06
GO:BP	GO:0065008	regulation of biological quality	116	2847	9.549e-06
GO:BP	GO:0009605	response to external stimulus	100	2367	1.757e-05
GO:BP	GO:0098609	cell-cell adhesion	52	948	1.829e-05
GO:BP	GO:0006814	sodium ion transport	22	235	2.133e-05
GO:BP	GO:1903131	mononuclear cell differentiation	35	529	3.275e-05
GO:BP	GO:0007200	phospholipase C-activating G protein-coupled receptor signaling pathway	15	116	3.305e-05
GO:BP	GO:0042110	T cell activation	36	558	3.809e-05
GO:BP	GO:0035725	sodium ion transmembrane transport	18	169	3.911e-05
GO:BP	GO:0045321	leukocyte activation	51	951	4.086e-05
GO:BP	GO:0051179	localization	190	5521	4.814e-05
GO:BP	GO:0030003	intracellular monoatomic cation homeostasis	34	521	5.698e-05
GO:BP	GO:0055082	intracellular chemical homeostasis	42	723	5.704e-05
GO:BP	GO:0050957	equilibrioception	5	8	6.531e-05
GO:BP	GO:0050877	nervous system process	69	1489	6.786e-05
GO:BP	GO:0007267	cell-cell signaling	63	1316	7.215e-05
GO:BP	GO:0007193	adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway	12	79	7.215e-05
GO:BP	GO:0006873	intracellular monoatomic ion homeostasis	34	530	7.306e-05
GO:BP	GO:0001775	cell activation	55	1098	9.547e-05
GO:BP	GO:0015711	organic anion transport	30	442	1.018e-04
GO:BP	GO:0060004	reflex	7	23	1.129e-04
GO:BP	GO:0055080	monoatomic cation homeostasis	36	598	1.402e-04
GO:BP	GO:0065007	biological regulation	369	12671	1.668e-04
GO:BP	GO:0046649	lymphocyte activation	43	787	1.668e-04
GO:BP	GO:0050851	antigen receptor-mediated signaling pathway	18	192	1.777e-04
GO:BP	GO:0050801	monoatomic ion homeostasis	36	608	1.876e-04
GO:BP	GO:0071805	potassium ion transmembrane transport	19	213	1.876e-04
GO:BP	GO:0030098	lymphocyte differentiation	29	438	2.167e-04
GO:BP	GO:0019725	cellular homeostasis	44	826	2.191e-04
GO:BP	GO:0002429	immune response-activating cell surface receptor signaling pathway	23	306	2.958e-04
GO:BP	GO:0048232	male gamete generation	37	654	3.582e-04
GO:BP	GO:0002768	immune response-regulating cell surface receptor signaling pathway	24	334	3.751e-04
GO:BP	GO:0007154	cell communication	211	6496	3.751e-04
GO:BP	GO:0030217	T cell differentiation	23	312	3.821e-04
GO:BP	GO:0023052	signaling	210	6471	4.153e-04
GO:BP	GO:0098771	inorganic ion homeostasis	32	531	4.166e-04
GO:BP	GO:0048878	chemical homeostasis	50	1026	4.787e-04
GO:BP	GO:0099536	synaptic signaling	41	783	6.366e-04
GO:BP	GO:1902105	regulation of leukocyte differentiation	23	325	6.808e-04
GO:BP	GO:0006874	intracellular calcium ion homeostasis	22	302	6.808e-04
GO:BP	GO:0050778	positive regulation of immune response	39	732	6.847e-04
GO:BP	GO:0055074	calcium ion homeostasis	23	326	6.950e-04
GO:BP	GO:0010817	regulation of hormone levels	32	548	7.129e-04
GO:BP	GO:0007283	spermatogenesis	35	637	9.995e-04
GO:BP	GO:0046631	alpha-beta T cell activation	16	181	1.010e-03
GO:BP	GO:0007275	multicellular organism development	158	4658	1.033e-03
GO:BP	GO:0002694	regulation of leukocyte activation	32	561	1.078e-03
GO:BP	GO:0007186	G protein-coupled receptor signaling pathway	57	1275	1.156e-03
GO:BP	GO:0009410	response to xenobiotic stimulus	27	436	1.172e-03
GO:BP	GO:0050870	positive regulation of T cell activation	19	248	1.189e-03
GO:BP	GO:0042592	homeostatic process	71	1711	1.191e-03
GO:BP	GO:1903037	regulation of leukocyte cell-cell adhesion	24	366	1.314e-03
GO:BP	GO:0099537	trans-synaptic signaling	39	759	1.322e-03
GO:BP	GO:0003006	developmental process involved in reproduction	48	1022	1.520e-03
GO:BP	GO:0050867	positive regulation of cell activation	24	372	1.648e-03
GO:BP	GO:0030097	hemopoiesis	46	971	1.787e-03
GO:BP	GO:0050863	regulation of T cell activation	24	375	1.830e-03
GO:BP	GO:0002366	leukocyte activation involved in immune response	21	305	1.967e-03
GO:BP	GO:0022414	reproductive process	65	1556	2.075e-03
GO:BP	GO:0002696	positive regulation of leukocyte activation	23	355	2.110e-03
GO:BP	GO:0007159	leukocyte cell-cell adhesion	25	404	2.110e-03
GO:BP	GO:0098916	anterograde trans-synaptic signaling	38	753	2.217e-03
GO:BP	GO:0007268	chemical synaptic transmission	38	753	2.217e-03
GO:BP	GO:0002263	cell activation involved in immune response	21	309	2.223e-03
GO:BP	GO:0050776	regulation of immune response	43	897	2.229e-03
GO:BP	GO:0050865	regulation of cell activation	33	616	2.229e-03
GO:BP	GO:0140013	meiotic nuclear division	16	198	2.339e-03
GO:BP	GO:1901700	response to oxygen-containing compound	67	1632	2.405e-03
GO:BP	GO:0042445	hormone metabolic process	18	243	2.449e-03
GO:BP	GO:0045582	positive regulation of T cell differentiation	12	119	2.449e-03
GO:BP	GO:0050953	sensory perception of light stimulus	17	222	2.577e-03
GO:BP	GO:0050852	T cell receptor signaling pathway	13	139	2.588e-03
GO:BP	GO:0002253	activation of immune response	30	543	2.646e-03
GO:BP	GO:0007276	gamete generation	40	822	2.766e-03
GO:BP	GO:0003008	system process	86	2266	2.995e-03
GO:BP	GO:1903039	positive regulation of leukocyte cell-cell adhesion	19	271	3.000e-03
GO:BP	GO:0050805	negative regulation of synaptic transmission	8	55	3.073e-03
GO:BP	GO:0006955	immune response	78	2008	3.073e-03
GO:BP	GO:0045580	regulation of T cell differentiation	15	183	3.073e-03
GO:BP	GO:0032604	granulocyte macrophage colony-stimulating factor production	5	18	3.073e-03
GO:BP	GO:0032645	regulation of granulocyte macrophage colony-stimulating factor production	5	18	3.073e-03
GO:BP	GO:0046942	carboxylic acid transport	22	344	3.073e-03
GO:BP	GO:0015849	organic acid transport	22	345	3.142e-03
GO:BP	GO:0002684	positive regulation of immune system process	48	1066	3.154e-03
GO:BP	GO:0050853	B cell receptor signaling pathway	9	71	3.199e-03
GO:BP	GO:0048609	multicellular organismal reproductive process	45	980	3.354e-03
GO:BP	GO:0007610	behavior	34	665	3.479e-03
GO:BP	GO:0019953	sexual reproduction	49	1103	3.554e-03
GO:BP	GO:0002757	immune response-activating signaling pathway	27	477	3.601e-03
GO:BP	GO:0002764	immune response-regulating signaling pathway	28	504	3.646e-03
GO:BP	GO:0022407	regulation of cell-cell adhesion	27	478	3.666e-03
GO:BP	GO:0070661	leukocyte proliferation	22	351	3.739e-03
GO:BP	GO:1903708	positive regulation of hemopoiesis	15	189	3.842e-03
GO:BP	GO:1902107	positive regulation of leukocyte differentiation	15	189	3.842e-03
GO:BP	GO:0098742	cell-cell adhesion via plasma-membrane adhesion molecules	19	280	3.912e-03
GO:BP	GO:0003341	cilium movement	16	212	4.037e-03
GO:BP	GO:0051240	positive regulation of multicellular organismal process	66	1644	4.094e-03
GO:BP	GO:0010951	negative regulation of endopeptidase activity	6	31	4.366e-03
GO:BP	GO:0051480	regulation of cytosolic calcium ion concentration	8	59	4.435e-03
GO:BP	GO:0045619	regulation of lymphocyte differentiation	16	215	4.583e-03
GO:BP	GO:0015747	urate transport	4	11	4.583e-03
GO:BP	GO:0042221	response to chemical	131	3867	4.631e-03
GO:BP	GO:0051932	synaptic transmission, GABAergic	8	60	4.852e-03
GO:BP	GO:0043266	regulation of potassium ion transport	10	94	4.942e-03
GO:BP	GO:0009653	anatomical structure morphogenesis	97	2692	5.112e-03
GO:BP	GO:0001818	negative regulation of cytokine production	19	288	5.112e-03
GO:BP	GO:0019722	calcium-mediated signaling	16	218	5.112e-03
GO:BP	GO:0051716	cellular response to stimulus	224	7320	5.112e-03
GO:BP	GO:0002376	immune system process	100	2796	5.137e-03
GO:BP	GO:0021879	forebrain neuron differentiation	7	46	5.179e-03
GO:BP	GO:0070663	regulation of leukocyte proliferation	18	265	5.179e-03
GO:BP	GO:0007601	visual perception	16	219	5.179e-03
GO:BP	GO:0001816	cytokine production	37	772	5.179e-03
GO:BP	GO:0045621	positive regulation of lymphocyte differentiation	12	134	5.333e-03
GO:BP	GO:1903046	meiotic cell cycle process	16	220	5.382e-03
GO:BP	GO:0051249	regulation of lymphocyte activation	27	497	5.739e-03
GO:BP	GO:1903706	regulation of hemopoiesis	24	420	6.200e-03
GO:BP	GO:0048485	sympathetic nervous system development	5	22	6.481e-03
GO:BP	GO:0007189	adenylate cyclase-activating G protein-coupled receptor signaling pathway	13	158	6.481e-03
GO:BP	GO:0002683	negative regulation of immune system process	27	502	6.562e-03
GO:BP	GO:0042129	regulation of T cell proliferation	14	180	6.614e-03
GO:BP	GO:0048731	system development	133	3985	6.784e-03
GO:BP	GO:0051239	regulation of multicellular organismal process	103	2928	6.784e-03
GO:BP	GO:0002706	regulation of lymphocyte mediated immunity	14	182	7.273e-03
GO:BP	GO:0051251	positive regulation of lymphocyte activation	20	324	7.429e-03
GO:BP	GO:0044419	biological process involved in interspecies interaction between organisms	67	1724	7.478e-03
GO:BP	GO:0060284	regulation of cell development	39	851	7.774e-03
GO:BP	GO:0048513	animal organ development	106	3047	7.901e-03
GO:BP	GO:0001817	regulation of cytokine production	36	765	8.085e-03
GO:BP	GO:0042102	positive regulation of T cell proliferation	10	102	8.130e-03
GO:BP	GO:0006869	lipid transport	24	431	8.289e-03
GO:BP	GO:0006816	calcium ion transport	24	433	8.816e-03
GO:BP	GO:0002407	dendritic cell chemotaxis	5	24	9.108e-03
GO:BP	GO:0009582	detection of abiotic stimulus	12	145	9.774e-03
GO:BP	GO:0015850	organic hydroxy compound transport	18	283	9.921e-03
GO:BP	GO:0042127	regulation of cell population proliferation	65	1682	1.023e-02
GO:BP	GO:0050670	regulation of lymphocyte proliferation	16	236	1.033e-02
GO:BP	GO:0042098	T cell proliferation	15	213	1.046e-02
GO:BP	GO:0031341	regulation of cell killing	10	106	1.052e-02
GO:BP	GO:0050789	regulation of biological process	346	12278	1.059e-02
GO:BP	GO:0043207	response to external biotic stimulus	61	1558	1.096e-02
GO:BP	GO:0002682	regulation of immune system process	60	1526	1.096e-02
GO:BP	GO:0051241	negative regulation of multicellular organismal process	46	1088	1.196e-02
GO:BP	GO:0032944	regulation of mononuclear cell proliferation	16	240	1.196e-02
GO:BP	GO:0090660	cerebrospinal fluid circulation	4	15	1.297e-02
GO:BP	GO:0007140	male meiotic nuclear division	7	55	1.297e-02
GO:BP	GO:0001906	cell killing	15	219	1.332e-02
GO:BP	GO:0002703	regulation of leukocyte mediated immunity	16	243	1.338e-02
GO:BP	GO:0050900	leukocyte migration	22	396	1.373e-02
GO:BP	GO:0022409	positive regulation of cell-cell adhesion	19	319	1.408e-02
GO:BP	GO:0021872	forebrain generation of neurons	7	56	1.408e-02
GO:BP	GO:0042472	inner ear morphogenesis	10	111	1.408e-02
GO:BP	GO:0051321	meiotic cell cycle	18	294	1.408e-02
GO:BP	GO:0006952	defense response	68	1809	1.432e-02
GO:BP	GO:0070372	regulation of ERK1 and ERK2 cascade	18	295	1.449e-02
GO:BP	GO:0045588	positive regulation of gamma-delta T cell differentiation	3	7	1.455e-02
GO:BP	GO:0035249	synaptic transmission, glutamatergic	10	112	1.476e-02
GO:BP	GO:0007420	brain development	34	739	1.505e-02
GO:BP	GO:0045058	T cell selection	7	57	1.505e-02
GO:BP	GO:0006957	complement activation, alternative pathway	4	16	1.566e-02
GO:BP	GO:0051707	response to other organism	60	1555	1.586e-02
GO:BP	GO:0015913	short-chain fatty acid transmembrane transport	2	2	1.610e-02
GO:BP	GO:0021630	olfactory nerve maturation	2	2	1.610e-02
GO:BP	GO:0015741	fumarate transport	2	2	1.610e-02
GO:BP	GO:0015718	monocarboxylic acid transport	13	179	1.610e-02
GO:BP	GO:0038112	interleukin-8-mediated signaling pathway	2	2	1.610e-02
GO:BP	GO:0007600	sensory perception	41	955	1.610e-02
GO:BP	GO:0030573	bile acid catabolic process	2	2	1.610e-02
GO:BP	GO:0006817	phosphate ion transport	5	28	1.610e-02
GO:BP	GO:2000471	regulation of hematopoietic stem cell migration	2	2	1.610e-02
GO:BP	GO:2000473	positive regulation of hematopoietic stem cell migration	2	2	1.610e-02
GO:BP	GO:0001762	beta-alanine transport	2	2	1.610e-02
GO:BP	GO:0050883	musculoskeletal movement, spinal reflex action	2	2	1.610e-02
GO:BP	GO:0032102	negative regulation of response to external stimulus	22	403	1.610e-02
GO:BP	GO:0009607	response to biotic stimulus	61	1593	1.610e-02
GO:BP	GO:0036368	cone photoresponse recovery	2	2	1.610e-02
GO:BP	GO:0033626	positive regulation of integrin activation by cell surface receptor linked signal transduction	2	2	1.610e-02
GO:BP	GO:0046634	regulation of alpha-beta T cell activation	10	115	1.632e-02
GO:BP	GO:0042391	regulation of membrane potential	23	433	1.634e-02
GO:BP	GO:0050912	detection of chemical stimulus involved in sensory perception of taste	6	43	1.693e-02
GO:BP	GO:0007043	cell-cell junction assembly	12	159	1.741e-02
GO:BP	GO:0036037	CD8-positive, alpha-beta T cell activation	5	29	1.757e-02
GO:BP	GO:0048562	embryonic organ morphogenesis	18	305	1.853e-02
GO:BP	GO:0045494	photoreceptor cell maintenance	6	44	1.883e-02
GO:BP	GO:0008283	cell population proliferation	73	2009	1.945e-02
GO:BP	GO:0046645	positive regulation of gamma-delta T cell activation	3	8	1.945e-02
GO:BP	GO:0120197	mucociliary clearance	3	8	1.945e-02
GO:BP	GO:0051967	negative regulation of synaptic transmission, glutamatergic	3	8	1.945e-02
GO:BP	GO:0014070	response to organic cyclic compound	39	909	1.987e-02
GO:BP	GO:0046651	lymphocyte proliferation	18	308	2.006e-02
GO:BP	GO:0010466	negative regulation of peptidase activity	6	45	2.059e-02
GO:BP	GO:0070665	positive regulation of leukocyte proliferation	12	163	2.059e-02
GO:BP	GO:0007165	signal transduction	183	5979	2.067e-02
GO:BP	GO:0032663	regulation of interleukin-2 production	7	62	2.107e-02
GO:BP	GO:0032623	interleukin-2 production	7	62	2.107e-02
GO:BP	GO:0007417	central nervous system development	43	1038	2.119e-02
GO:BP	GO:0002923	regulation of humoral immune response mediated by circulating immunoglobulin	4	18	2.119e-02
GO:BP	GO:0009581	detection of external stimulus	11	142	2.136e-02
GO:BP	GO:0002252	immune effector process	32	703	2.136e-02
GO:BP	GO:0036336	dendritic cell migration	5	31	2.221e-02
GO:BP	GO:0050671	positive regulation of lymphocyte proliferation	11	143	2.243e-02
GO:BP	GO:0070588	calcium ion transmembrane transport	19	339	2.270e-02
GO:BP	GO:0098657	import into cell	39	921	2.379e-02
GO:BP	GO:0007626	locomotory behavior	14	214	2.404e-02
GO:BP	GO:0032943	mononuclear cell proliferation	18	315	2.424e-02
GO:BP	GO:0048518	positive regulation of biological process	189	6235	2.499e-02
GO:BP	GO:0010876	lipid localization	24	480	2.535e-02
GO:BP	GO:0010720	positive regulation of cell development	23	452	2.535e-02
GO:BP	GO:0002274	myeloid leukocyte activation	15	240	2.535e-02
GO:BP	GO:0045216	cell-cell junction organization	14	216	2.551e-02
GO:BP	GO:0032946	positive regulation of mononuclear cell proliferation	11	146	2.551e-02
GO:BP	GO:0007204	positive regulation of cytosolic calcium ion concentration	12	169	2.562e-02
GO:BP	GO:0030450	regulation of complement activation, classical pathway	3	9	2.562e-02
GO:BP	GO:0045586	regulation of gamma-delta T cell differentiation	3	9	2.562e-02
GO:BP	GO:0045597	positive regulation of cell differentiation	37	866	2.575e-02
GO:BP	GO:0070371	ERK1 and ERK2 cascade	18	318	2.575e-02
GO:BP	GO:0045471	response to ethanol	10	125	2.615e-02
GO:BP	GO:0021543	pallium development	13	194	2.720e-02
GO:BP	GO:0060078	regulation of postsynaptic membrane potential	11	148	2.752e-02
GO:BP	GO:0002704	negative regulation of leukocyte mediated immunity	7	66	2.752e-02
GO:BP	GO:0001819	positive regulation of cytokine production	24	486	2.851e-02
GO:BP	GO:0060348	bone development	14	220	2.903e-02
GO:BP	GO:0048522	positive regulation of cellular process	179	5886	2.949e-02
GO:BP	GO:0050909	sensory perception of taste	7	67	2.960e-02
GO:BP	GO:0046632	alpha-beta T cell differentiation	10	128	3.030e-02
GO:BP	GO:0045745	positive regulation of G protein-coupled receptor signaling pathway	5	34	3.068e-02
GO:BP	GO:0008277	regulation of G protein-coupled receptor signaling pathway	11	151	3.133e-02
GO:BP	GO:0071695	anatomical structure maturation	16	274	3.268e-02
GO:BP	GO:0009887	animal organ morphogenesis	42	1037	3.268e-02
GO:BP	GO:0060322	head development	34	789	3.304e-02
GO:BP	GO:0023061	signal release	24	493	3.314e-02
GO:BP	GO:2001204	regulation of osteoclast development	3	10	3.319e-02
GO:BP	GO:0046643	regulation of gamma-delta T cell activation	3	10	3.319e-02
GO:BP	GO:0030449	regulation of complement activation	4	21	3.340e-02
GO:BP	GO:0033563	dorsal/ventral axon guidance	2	3	3.423e-02
GO:BP	GO:0021605	cranial nerve maturation	2	3	3.423e-02
GO:BP	GO:0072249	metanephric podocyte development	2	3	3.423e-02
GO:BP	GO:0072312	metanephric glomerular epithelial cell differentiation	2	3	3.423e-02
GO:BP	GO:0071486	cellular response to high light intensity	2	3	3.423e-02
GO:BP	GO:0045957	negative regulation of complement activation, alternative pathway	2	3	3.423e-02
GO:BP	GO:0015912	short-chain fatty acid transport	2	3	3.423e-02
GO:BP	GO:0007166	cell surface receptor signaling pathway	94	2803	3.423e-02
GO:BP	GO:0072313	metanephric glomerular epithelial cell development	2	3	3.423e-02
GO:BP	GO:0070543	response to linoleic acid	2	3	3.423e-02
GO:BP	GO:0097195	pilomotor reflex	2	3	3.423e-02
GO:BP	GO:0007127	meiosis I	10	132	3.423e-02
GO:BP	GO:0010482	regulation of epidermal cell division	2	3	3.423e-02
GO:BP	GO:0072248	metanephric podocyte differentiation	2	3	3.423e-02
GO:BP	GO:0072244	metanephric glomerular epithelium development	2	3	3.423e-02
GO:BP	GO:0010481	epidermal cell division	2	3	3.423e-02
GO:BP	GO:0098758	response to interleukin-8	2	3	3.423e-02
GO:BP	GO:0098759	cellular response to interleukin-8	2	3	3.423e-02
GO:BP	GO:0006311	meiotic gene conversion	2	3	3.423e-02
GO:BP	GO:0002277	myeloid dendritic cell activation involved in immune response	2	3	3.423e-02
GO:BP	GO:0042471	ear morphogenesis	10	132	3.423e-02
GO:BP	GO:0007218	neuropeptide signaling pathway	9	110	3.423e-02
GO:BP	GO:0021953	central nervous system neuron differentiation	13	203	3.521e-02
GO:BP	GO:0040020	regulation of meiotic nuclear division	5	36	3.541e-02
GO:BP	GO:0006959	humoral immune response	15	254	3.625e-02
GO:BP	GO:0070166	enamel mineralization	4	22	3.627e-02
GO:BP	GO:0046629	gamma-delta T cell activation	4	22	3.627e-02
GO:BP	GO:0070887	cellular response to chemical stimulus	76	2186	3.756e-02
GO:BP	GO:0030900	forebrain development	21	417	3.765e-02
GO:BP	GO:0045595	regulation of cell differentiation	58	1577	3.856e-02
GO:BP	GO:0001910	regulation of leukocyte mediated cytotoxicity	8	92	3.902e-02
GO:BP	GO:0001580	detection of chemical stimulus involved in sensory perception of bitter taste	5	37	3.902e-02
GO:BP	GO:1990918	double-strand break repair involved in meiotic recombination	3	11	3.921e-02
GO:BP	GO:0033625	positive regulation of integrin activation	3	11	3.921e-02
GO:BP	GO:1903977	positive regulation of glial cell migration	3	11	3.921e-02
GO:BP	GO:0072015	podocyte development	3	11	3.921e-02
GO:BP	GO:0051898	negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	6	54	3.943e-02
GO:BP	GO:0050866	negative regulation of cell activation	13	207	3.943e-02
GO:BP	GO:0048839	inner ear development	13	207	3.943e-02
GO:BP	GO:0007399	nervous system development	86	2541	3.943e-02
GO:BP	GO:0048870	cell motility	62	1716	3.968e-02
GO:BP	GO:0031343	positive regulation of cell killing	7	73	4.027e-02
GO:BP	GO:0046635	positive regulation of alpha-beta T cell activation	7	73	4.027e-02
GO:BP	GO:0016338	calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules	4	23	4.064e-02
GO:BP	GO:0048871	multicellular organismal-level homeostasis	34	809	4.157e-02
GO:BP	GO:0006909	phagocytosis	14	234	4.161e-02
GO:BP	GO:0046164	alcohol catabolic process	5	38	4.161e-02
GO:BP	GO:0050982	detection of mechanical stimulus	6	55	4.161e-02
GO:BP	GO:0050885	neuromuscular process controlling balance	6	55	4.161e-02
GO:BP	GO:0043270	positive regulation of monoatomic ion transport	13	209	4.161e-02
GO:BP	GO:0046903	secretion	39	968	4.242e-02
GO:BP	GO:0002695	negative regulation of leukocyte activation	12	185	4.242e-02
GO:BP	GO:0071674	mononuclear cell migration	14	235	4.247e-02
GO:BP	GO:0070374	positive regulation of ERK1 and ERK2 cascade	13	210	4.271e-02
GO:BP	GO:0042475	odontogenesis of dentin-containing tooth	8	95	4.426e-02
GO:BP	GO:0007281	germ cell development	19	370	4.442e-02
GO:BP	GO:0002823	negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	6	56	4.463e-02
GO:BP	GO:0006706	steroid catabolic process	4	24	4.507e-02
GO:BP	GO:0032649	regulation of type II interferon production	9	117	4.507e-02
GO:BP	GO:1903306	negative regulation of regulated secretory pathway	4	24	4.507e-02
GO:BP	GO:0009566	fertilization	13	212	4.507e-02
GO:BP	GO:0009074	aromatic amino acid family catabolic process	4	24	4.507e-02
GO:BP	GO:0050728	negative regulation of inflammatory response	11	163	4.507e-02
GO:BP	GO:1903818	positive regulation of voltage-gated potassium channel activity	3	12	4.660e-02
GO:BP	GO:0072310	glomerular epithelial cell development	3	12	4.660e-02
GO:BP	GO:0044341	sodium-dependent phosphate transport	3	12	4.660e-02
GO:BP	GO:0032609	type II interferon production	9	118	4.662e-02
GO:BP	GO:0001895	retina homeostasis	6	57	4.708e-02
GO:BP	GO:0002573	myeloid leukocyte differentiation	14	239	4.708e-02
GO:BP	GO:0061982	meiosis I cell cycle process	10	141	4.713e-02
GO:BP	GO:0002285	lymphocyte activation involved in immune response	13	214	4.769e-02
GO:BP	GO:0009888	tissue development	70	2012	4.842e-02
GO:BP	GO:0090066	regulation of anatomical structure size	24	518	4.848e-02
GO:BP	GO:0035270	endocrine system development	10	142	4.900e-02
GO:BP	GO:0050954	sensory perception of mechanical stimulus	12	190	4.901e-02
GO:BP	GO:0007605	sensory perception of sound	11	166	4.963e-02
KEGG	KEGG:04080	Neuroactive ligand-receptor interaction	37	365	9.137e-09
KEGG	KEGG:00430	Taurine and hypotaurine metabolism	5	16	9.906e-03
KEGG	KEGG:00982	Drug metabolism - cytochrome P450	9	68	1.110e-02
KEGG	KEGG:05033	Nicotine addiction	7	40	1.110e-02

#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	426	6478	6.312e-15
GO:BP	GO:0048856	anatomical structure development	398	5924	6.312e-15
GO:BP	GO:0032501	multicellular organismal process	453	7234	1.746e-12
GO:BP	GO:0030154	cell differentiation	296	4381	4.863e-10
GO:BP	GO:0048869	cellular developmental process	296	4382	4.863e-10
GO:BP	GO:0045165	cell fate commitment	45	291	1.087e-09
GO:BP	GO:0007275	multicellular organism development	307	4658	2.268e-09
GO:BP	GO:0048731	system development	270	3985	4.131e-09
GO:BP	GO:0048663	neuron fate commitment	19	73	3.822e-07
GO:BP	GO:0003002	regionalization	51	434	6.431e-07
GO:BP	GO:0007399	nervous system development	181	2541	7.027e-07
GO:BP	GO:0033993	response to lipid	84	921	9.822e-07
GO:BP	GO:0048513	animal organ development	208	3047	9.822e-07
GO:BP	GO:0001708	cell fate specification	22	113	4.095e-06
GO:BP	GO:0007389	pattern specification process	52	478	4.254e-06
GO:BP	GO:0007417	central nervous system development	88	1038	1.055e-05
GO:BP	GO:0034220	monoatomic ion transmembrane transport	86	1017	1.619e-05
GO:BP	GO:0009887	animal organ morphogenesis	87	1037	1.814e-05
GO:BP	GO:0009653	anatomical structure morphogenesis	182	2692	1.819e-05
GO:BP	GO:0060429	epithelium development	98	1229	2.673e-05
GO:BP	GO:0009888	tissue development	143	2012	3.303e-05
GO:BP	GO:0009891	positive regulation of biosynthetic process	181	2707	3.759e-05
GO:BP	GO:0030182	neuron differentiation	109	1434	4.827e-05
GO:BP	GO:0007423	sensory organ development	58	612	5.090e-05
GO:BP	GO:0048665	neuron fate specification	11	35	7.405e-05
GO:BP	GO:0006357	regulation of transcription by RNA polymerase II	171	2572	1.118e-04
GO:BP	GO:0009953	dorsal/ventral pattern formation	17	90	1.595e-04
GO:BP	GO:0048699	generation of neurons	111	1517	1.994e-04
GO:BP	GO:0007204	positive regulation of cytosolic calcium ion concentration	24	169	2.157e-04
GO:BP	GO:0048468	cell development	183	2833	2.404e-04
GO:BP	GO:1901654	response to ketone	28	221	2.767e-04
GO:BP	GO:0006811	monoatomic ion transport	95	1256	2.830e-04
GO:BP	GO:0018958	phenol-containing compound metabolic process	19	116	2.885e-04
GO:BP	GO:0048880	sensory system development	42	414	3.142e-04
GO:BP	GO:0006366	transcription by RNA polymerase II	173	2698	6.837e-04
GO:BP	GO:0002118	aggressive behavior	5	7	7.089e-04
GO:BP	GO:0022008	neurogenesis	121	1746	7.103e-04
GO:BP	GO:0010557	positive regulation of macromolecule biosynthetic process	167	2604	9.557e-04
GO:BP	GO:0150063	visual system development	40	408	1.104e-03
GO:BP	GO:0006954	inflammatory response	68	847	1.111e-03
GO:BP	GO:0050793	regulation of developmental process	158	2453	1.313e-03
GO:BP	GO:0098660	inorganic ion transmembrane transport	71	903	1.320e-03
GO:BP	GO:0045595	regulation of cell differentiation	110	1577	1.320e-03
GO:BP	GO:0001654	eye development	39	404	1.819e-03
GO:BP	GO:0006952	defense response	122	1809	1.884e-03
GO:BP	GO:0042127	regulation of cell population proliferation	115	1682	1.884e-03
GO:BP	GO:0009605	response to external stimulus	152	2367	2.060e-03
GO:BP	GO:0009952	anterior/posterior pattern specification	26	225	2.246e-03
GO:BP	GO:1901615	organic hydroxy compound metabolic process	48	549	2.456e-03
GO:BP	GO:0042759	long-chain fatty acid biosynthetic process	8	27	2.586e-03
GO:BP	GO:0030900	forebrain development	39	417	3.222e-03
GO:BP	GO:0071396	cellular response to lipid	51	609	3.964e-03
GO:BP	GO:0060322	head development	62	789	3.964e-03
GO:BP	GO:0003407	neural retina development	14	85	3.964e-03
GO:BP	GO:0055085	transmembrane transport	105	1538	4.050e-03
GO:BP	GO:1903409	reactive oxygen species biosynthetic process	11	55	4.056e-03
GO:BP	GO:0043010	camera-type eye development	34	352	4.827e-03
GO:BP	GO:0045944	positive regulation of transcription by RNA polymerase II	89	1261	4.827e-03
GO:BP	GO:0098742	cell-cell adhesion via plasma-membrane adhesion molecules	29	280	4.859e-03
GO:BP	GO:0006633	fatty acid biosynthetic process	20	159	4.945e-03
GO:BP	GO:0007420	brain development	58	739	6.473e-03
GO:BP	GO:0014070	response to organic cyclic compound	68	909	6.718e-03
GO:BP	GO:0030855	epithelial cell differentiation	58	741	6.750e-03
GO:BP	GO:1903426	regulation of reactive oxygen species biosynthetic process	9	40	6.858e-03
GO:BP	GO:0022412	cellular process involved in reproduction in multicellular organism	37	408	7.153e-03
GO:BP	GO:0060579	ventral spinal cord interneuron fate commitment	5	11	7.153e-03
GO:BP	GO:0006334	nucleosome assembly	16	115	7.153e-03
GO:BP	GO:0060581	cell fate commitment involved in pattern specification	5	11	7.153e-03
GO:BP	GO:0072330	monocarboxylic acid biosynthetic process	24	218	7.153e-03
GO:BP	GO:0007267	cell-cell signaling	91	1316	7.153e-03
GO:BP	GO:0021515	cell differentiation in spinal cord	10	50	7.202e-03
GO:BP	GO:0021536	diencephalon development	13	81	7.238e-03
GO:BP	GO:0090596	sensory organ morphogenesis	29	290	7.377e-03
GO:BP	GO:0098655	monoatomic cation transmembrane transport	63	832	7.378e-03
GO:BP	GO:0048598	embryonic morphogenesis	50	617	7.654e-03
GO:BP	GO:1901616	organic hydroxy compound catabolic process	11	61	8.104e-03
GO:BP	GO:0007156	homophilic cell adhesion via plasma membrane adhesion molecules	20	168	8.182e-03
GO:BP	GO:0065007	biological regulation	642	12671	8.182e-03
GO:BP	GO:0035115	embryonic forelimb morphogenesis	8	33	8.182e-03
GO:BP	GO:0071542	dopaminergic neuron differentiation	9	42	8.233e-03
GO:BP	GO:0021513	spinal cord dorsal/ventral patterning	6	18	8.579e-03
GO:BP	GO:0008283	cell population proliferation	128	2009	8.587e-03
GO:BP	GO:0048568	embryonic organ development	40	463	8.912e-03
GO:BP	GO:0031960	response to corticosteroid	19	157	8.912e-03
GO:BP	GO:0006812	monoatomic cation transport	74	1032	8.912e-03
GO:BP	GO:0007281	germ cell development	34	370	8.912e-03
GO:BP	GO:0019336	phenol-containing compound catabolic process	5	12	9.104e-03
GO:BP	GO:0098609	cell-cell adhesion	69	948	9.529e-03
GO:BP	GO:0022414	reproductive process	103	1556	9.791e-03
GO:BP	GO:0003008	system process	141	2266	1.008e-02
GO:BP	GO:1901700	response to oxygen-containing compound	107	1632	1.021e-02
GO:BP	GO:2000179	positive regulation of neural precursor cell proliferation	11	64	1.049e-02
GO:BP	GO:0034728	nucleosome organization	17	135	1.135e-02
GO:BP	GO:0051239	regulation of multicellular organismal process	175	2928	1.155e-02
GO:BP	GO:0021953	central nervous system neuron differentiation	22	203	1.261e-02
GO:BP	GO:0021514	ventral spinal cord interneuron differentiation	5	13	1.263e-02
GO:BP	GO:0060732	positive regulation of inositol phosphate biosynthetic process	5	13	1.263e-02
GO:BP	GO:0007501	mesodermal cell fate specification	5	13	1.263e-02
GO:BP	GO:0021511	spinal cord patterning	6	20	1.353e-02
GO:BP	GO:0097305	response to alcohol	26	262	1.383e-02
GO:BP	GO:0045893	positive regulation of DNA-templated transcription	110	1710	1.534e-02
GO:BP	GO:0060041	retina development in camera-type eye	19	166	1.548e-02
GO:BP	GO:0048545	response to steroid hormone	31	339	1.548e-02
GO:BP	GO:1902680	positive regulation of RNA biosynthetic process	110	1713	1.592e-02
GO:BP	GO:0050953	sensory perception of light stimulus	23	222	1.602e-02
GO:BP	GO:0060040	retinal bipolar neuron differentiation	4	8	1.620e-02
GO:BP	GO:0060284	regulation of cell development	62	851	1.643e-02
GO:BP	GO:0042403	thyroid hormone metabolic process	7	29	1.643e-02
GO:BP	GO:0009893	positive regulation of metabolic process	210	3648	1.711e-02
GO:BP	GO:0007154	cell communication	350	6496	1.728e-02
GO:BP	GO:2000177	regulation of neural precursor cell proliferation	14	104	1.728e-02
GO:BP	GO:0010628	positive regulation of gene expression	81	1189	1.728e-02
GO:BP	GO:0032814	regulation of natural killer cell activation	8	39	1.936e-02
GO:BP	GO:2000026	regulation of multicellular organismal development	93	1413	1.973e-02
GO:BP	GO:0061351	neural precursor cell proliferation	19	171	2.026e-02
GO:BP	GO:0098662	inorganic cation transmembrane transport	59	811	2.212e-02
GO:BP	GO:0003006	developmental process involved in reproduction	71	1022	2.233e-02
GO:BP	GO:2001141	regulation of RNA biosynthetic process	199	3454	2.257e-02
GO:BP	GO:0010919	regulation of inositol phosphate biosynthetic process	5	15	2.257e-02
GO:BP	GO:0051094	positive regulation of developmental process	88	1331	2.340e-02
GO:BP	GO:0048562	embryonic organ morphogenesis	28	305	2.406e-02
GO:BP	GO:0042420	dopamine catabolic process	4	9	2.440e-02
GO:BP	GO:0023052	signaling	347	6471	2.464e-02
GO:BP	GO:0035136	forelimb morphogenesis	8	41	2.490e-02
GO:BP	GO:0050789	regulation of biological process	618	12278	2.490e-02
GO:BP	GO:0031343	positive regulation of cell killing	11	73	2.490e-02
GO:BP	GO:0008284	positive regulation of cell population proliferation	67	958	2.490e-02
GO:BP	GO:0006821	chloride transport	15	122	2.509e-02
GO:BP	GO:0051384	response to glucocorticoid	16	135	2.509e-02
GO:BP	GO:0007601	visual perception	22	219	2.621e-02
GO:BP	GO:0007218	neuropeptide signaling pathway	14	110	2.621e-02
GO:BP	GO:0007188	adenylate cyclase-modulating G protein-coupled receptor signaling pathway	24	248	2.621e-02
GO:BP	GO:0048609	multicellular organismal reproductive process	68	980	2.673e-02
GO:BP	GO:0050877	nervous system process	96	1489	2.697e-02
GO:BP	GO:0006355	regulation of DNA-templated transcription	197	3435	2.714e-02
GO:BP	GO:0060563	neuroepithelial cell differentiation	8	42	2.729e-02
GO:BP	GO:0001819	positive regulation of cytokine production	39	486	2.895e-02
GO:BP	GO:0062013	positive regulation of small molecule metabolic process	16	138	2.991e-02
GO:BP	GO:0007186	G protein-coupled receptor signaling pathway	84	1275	3.005e-02
GO:BP	GO:0021545	cranial nerve development	10	64	3.005e-02
GO:BP	GO:0042221	response to chemical	218	3867	3.159e-02
GO:BP	GO:0032729	positive regulation of type II interferon production	11	76	3.160e-02
GO:BP	GO:0062012	regulation of small molecule metabolic process	28	314	3.216e-02
GO:BP	GO:0045597	positive regulation of cell differentiation	61	866	3.240e-02
GO:BP	GO:0048664	neuron fate determination	4	10	3.252e-02
GO:BP	GO:0019614	catechol-containing compound catabolic process	4	10	3.252e-02
GO:BP	GO:0042424	catecholamine catabolic process	4	10	3.252e-02
GO:BP	GO:1902932	positive regulation of alcohol biosynthetic process	6	25	3.392e-02
GO:BP	GO:1903428	positive regulation of reactive oxygen species biosynthetic process	5	17	3.399e-02
GO:BP	GO:0050678	regulation of epithelial cell proliferation	31	363	3.399e-02
GO:BP	GO:0051254	positive regulation of RNA metabolic process	114	1844	3.465e-02
GO:BP	GO:0019953	sexual reproduction	74	1103	3.505e-02
GO:BP	GO:0001912	positive regulation of leukocyte mediated cytotoxicity	10	66	3.518e-02
GO:BP	GO:0050727	regulation of inflammatory response	32	381	3.621e-02
GO:BP	GO:0035270	endocrine system development	16	142	3.638e-02
GO:BP	GO:0046069	cGMP catabolic process	3	5	3.688e-02
GO:BP	GO:0032101	regulation of response to external stimulus	72	1071	3.761e-02
GO:BP	GO:0042391	regulation of membrane potential	35	433	4.100e-02
GO:BP	GO:1905962	glutamatergic neuron differentiation	5	18	4.245e-02
GO:BP	GO:0001710	mesodermal cell fate commitment	5	18	4.245e-02
GO:BP	GO:2000049	positive regulation of cell-cell adhesion mediated by cadherin	4	11	4.413e-02
GO:BP	GO:0010455	positive regulation of cell fate commitment	4	11	4.413e-02
GO:BP	GO:0014049	positive regulation of glutamate secretion	4	11	4.413e-02
GO:BP	GO:0010752	regulation of cGMP-mediated signaling	4	11	4.413e-02
GO:BP	GO:0042471	ear morphogenesis	15	132	4.475e-02
GO:BP	GO:0009725	response to hormone	62	902	4.657e-02
GO:BP	GO:0010604	positive regulation of macromolecule metabolic process	190	3349	4.740e-02
GO:BP	GO:0046189	phenol-containing compound biosynthetic process	8	47	4.799e-02
GO:BP	GO:1902476	chloride transmembrane transport	13	107	4.928e-02
KEGG	KEGG:04080	Neuroactive ligand-receptor interaction	49	365	1.734e-09
KEGG	KEGG:05322	Systemic lupus erythematosus	24	132	7.521e-07
KEGG	KEGG:05034	Alcoholism	25	187	1.212e-04
KEGG	KEGG:05032	Morphine addiction	15	89	7.783e-04
KEGG	KEGG:04613	Neutrophil extracellular trap formation	22	188	2.676e-03
KEGG	KEGG:04060	Cytokine-cytokine receptor interaction	29	291	3.029e-03
KEGG	KEGG:04950	Maturity onset diabetes of the young	7	26	4.479e-03
KEGG	KEGG:04742	Taste transduction	13	85	4.479e-03
KEGG	KEGG:05033	Nicotine addiction	8	40	1.228e-02
KEGG	KEGG:05202	Transcriptional misregulation in cancer	20	192	1.417e-02
KEGG	KEGG:05321	Inflammatory bowel disease	9	62	4.904e-02
KEGG	KEGG:04658	Th1 and Th2 cell differentiation	11	89	4.904e-02
KEGG	KEGG:04670	Leukocyte transendothelial migration	13	114	4.904e-02
KEGG	KEGG:04727	GABAergic synapse	11	89	4.904e-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