- Data Setup
- Import DGElist Data
- KEGG Analysis
- Export Data
KEGG
Ha Tran
22/08/2021
Last updated: 2022-11-05
Checks: 7 0
Knit directory: SRB_2022/1_analysis/
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Data Setup
# working with data
library(dplyr)
library(magrittr)
library(readr)
library(tibble)
library(reshape2)
library(tidyverse)
library(KEGGREST)
# Visualisation:
library(kableExtra)
library(ggplot2)
library(grid)
library(pander)
library(viridis)
library(cowplot)
library(pheatmap)
# Custom ggplot
library(ggplotify)
library(ggpubr)
library(ggbiplot)
library(ggrepel)
# Bioconductor packages:
library(edgeR)
library(limma)
library(Glimma)
library(clusterProfiler)
library(org.Mm.eg.db)
library(enrichplot)
library(pathview)
theme_set(theme_minimal())
pub <- readRDS(here::here("0_data/RDS_objects/pub.rds"))Import DGElist Data
DGElist object containing the raw feature count, sample metadata, and gene metadata, created in the Set Up stage.
# load DGElist previously created in the set up
dge <- readRDS(here::here("0_data/RDS_objects/dge.rds"))
fc <- readRDS(here::here("0_data/RDS_objects/fc.rds"))
lfc <- readRDS(here::here("0_data/RDS_objects/lfc.rds"))
lmTreat <- readRDS(here::here("0_data/RDS_objects/lmTreat.rds"))
lmTreat_sig <- readRDS(here::here("0_data/RDS_objects/lmTreat_sig.rds"))KEGG Analysis
KEGG enrichment analysis is performed with the significant DE genes that have absolute FC > 1.5 ( genes from Limma). Top 30 most significant KEGG are displayed. All enriched KEGG pathways are exported
# chosing the pathways of interest
kegg_id <- c("mmu04670", "mmu04640", "mmu04270", "mmu04151", "mmu04510", "mmu04060")
kegg_pathway <- KEGGREST::keggGet(kegg_id)enrichKEGG <- list()
enrichKEGG_all <- list()
enrichKEGG_sig <- list()
for (i in 1:length(fc)) {
x <- fc[i] %>% as.character()
# find enriched KEGG pathways
enrichKEGG[[x]] <- clusterProfiler::enrichKEGG(
gene = lmTreat_sig[[x]]$entrezid,
keyType = "kegg",
organism = "mmu",
pvalueCutoff = 0.05,
pAdjustMethod = "none"
)
# save to csv
enrichKEGG_all[[x]] <- enrichKEGG[[x]]@result
# filter the significant and print top 30
enrichKEGG_sig[[x]] <- enrichKEGG_all[[x]] %>%
dplyr::filter(pvalue <= 0.05) %>%
separate(col = BgRatio, sep = "/", into = c("Total", "Universe")) %>%
dplyr::mutate(
logPval = -log(pvalue, 10),
GeneRatio = Count / as.numeric(Total)
) %>%
dplyr::select(c("Count", "GeneRatio", "pvalue", "logPval", "p.adjust", "qvalue", "Description", "geneID"))
# at the beginnning of a word (after 35 characters), add a newline. shorten the y axis for dot plot
enrichKEGG_sig[[x]]$Description <- sub(pattern = "(.{1,35})(?:$| )",
replacement = "\\1\n",
x = enrichKEGG_sig[[x]]$Description)
# remove the additional newline at the end of the string
enrichKEGG_sig[[x]]$Description <- sub(pattern = "\n$",
replacement = "",
x = enrichKEGG_sig[[x]]$Description)
}p=1enrichKEGG_sig[[p]][1:20, ] %>%
kable(caption = "Top 20 enriched KEGG pathways") %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Count | GeneRatio | pvalue | logPval | p.adjust | qvalue | Description | geneID | |
|---|---|---|---|---|---|---|---|---|
| mmu04713 | 24 | 0.2448980 | 0.00e+00 | 7.918458 | 0.00e+00 | 0.0000026 | Circadian entrainment | 16519/14802/12288/20190/14677/234889/14812/104111/14710/18795/54195/60596/104110/11513/66066/14702/11517/73086/18796/20192/58226/14697/14708/14696 |
| mmu04514 | 34 | 0.1868132 | 0.00e+00 | 7.668357 | 0.00e+00 | 0.0000026 | Cell adhesion molecules | 16401/241568/19266/192167/12558/16421/272381/15894/83964/54420/386750/19274/12562/225825/16408/69524/14961/245537/269116/15002/20339/18613/14969/18007/12741/14960/80883/241226/20737/12737/12504/13003/216856/67374 |
| mmu04724 | 24 | 0.2123894 | 2.00e-07 | 6.649484 | 2.00e-07 | 0.0000184 | Glutamatergic synapse | 20512/16519/14802/12288/14805/14677/14812/104111/210274/14710/18795/104110/11513/66066/14806/14702/18796/105727/13385/14697/14708/14696/12286/18806 |
| mmu04371 | 26 | 0.1897810 | 7.00e-07 | 6.137567 | 7.00e-07 | 0.0000449 | Apelin signaling pathway | 20190/20541/18127/14677/17260/104111/14710/104709/18795/110893/104110/11513/66066/23796/11607/14702/17897/18796/20192/23797/14219/14697/14708/30878/14696/16890 |
| mmu05414 | 20 | 0.2127660 | 2.20e-06 | 5.653207 | 2.20e-06 | 0.0001095 | Dilated cardiomyopathy | 12288/24052/16401/16000/20541/16421/12293/104111/109700/110893/104110/11513/16773/16404/17897/81904/24051/241226/192897/12298 |
| mmu04340 | 15 | 0.2586207 | 3.20e-06 | 5.489003 | 3.20e-06 | 0.0001190 | Hedgehog signaling pathway | 14632/16147/15245/68525/19207/59056/16576/12444/14634/14725/240888/109689/216869/19206/74239 |
| mmu04015 | 33 | 0.1542056 | 3.40e-06 | 5.470690 | 3.40e-06 | 0.0001190 | Rap1 signaling pathway | 15234/11600/16542/16000/14026/240168/14677/18645/78134/14812/18760/104111/21687/18795/19395/16590/104110/11513/16408/22341/50791/93737/17311/106952/70549/18796/23797/54519/16797/18596/16822/14062/20469 |
| mmu05032 | 19 | 0.2087912 | 5.30e-06 | 5.272311 | 5.30e-06 | 0.0001645 | Morphine addiction | 16519/14677/18574/104111/14710/104110/11513/14397/66066/18573/14702/109689/216869/14697/14708/14696/54393/18584/12286 |
| mmu04022 | 28 | 0.1618497 | 7.30e-06 | 5.134646 | 7.30e-06 | 0.0001863 | cGMP-PKG signaling pathway | 12288/11549/20541/18127/14677/13618/17260/234889/104111/104709/18795/110893/22068/54195/60596/104110/11513/11607/16531/13617/12062/73181/18796/242202/23797/381290/98660/16367 |
| mmu05412 | 17 | 0.2207792 | 7.60e-06 | 5.121322 | 7.60e-06 | 0.0001863 | Arrhythmogenic right ventricular cardiomyopathy | 12288/16842/24052/16401/20541/12558/16421/12293/109700/110893/16773/16404/81904/24051/241226/192897/12298 |
| mmu04512 | 18 | 0.2045455 | 1.27e-05 | 4.895147 | 1.27e-05 | 0.0002851 | ECM-receptor interaction | 16401/94216/21827/114249/12505/23928/16775/16421/14268/109700/12840/329872/16773/16404/75209/241226/192897/12830 |
| mmu04020 | 34 | 0.1416667 | 1.59e-05 | 4.798193 | 1.59e-05 | 0.0003267 | Calcium signaling pathway | 15234/12288/16542/20190/11549/20541/18127/231602/13618/18574/104111/12290/19220/18795/110893/104110/11513/22341/12494/11607/18573/13617/12062/15558/18796/65973/20192/58226/19218/381290/18596/12286/14062/52163 |
| mmu04924 | 16 | 0.2105263 | 2.63e-05 | 4.579335 | 2.63e-05 | 0.0004991 | Renin secretion | 12288/14677/234889/18574/13616/18795/54195/60596/11607/18573/16531/13617/11517/18796/229933/19217 |
| mmu04926 | 22 | 0.1705426 | 3.04e-05 | 4.516919 | 3.04e-05 | 0.0005351 | Relaxin signaling pathway | 94216/18127/14677/13618/17390/20418/104111/14710/18795/104110/11513/66066/22341/14702/109689/18796/216869/23797/14697/14708/14696/12830 |
| mmu04725 | 20 | 0.1785714 | 3.51e-05 | 4.454493 | 3.51e-05 | 0.0005766 | Cholinergic synapse | 16519/12288/14677/226922/104111/14710/104709/18795/104110/11513/66066/14702/18796/14360/23797/14697/14708/14696/60613/12286 |
| mmu04510 | 29 | 0.1442786 | 4.75e-05 | 4.323411 | 4.75e-05 | 0.0006931 | Focal adhesion | 15234/16401/16542/16000/94216/21827/23928/16775/12444/16421/14268/20418/18719/109700/12840/16773/22341/16404/64099/170736/68794/70549/14360/23797/18596/12389/241226/192897/12830 |
| mmu04360 | 27 | 0.1491713 | 4.78e-05 | 4.320237 | 4.78e-05 | 0.0006931 | Axon guidance | 13842/13643/20356/241568/13176/235611/20357/18186/20361/14677/20315/22068/238057/13837/218877/93737/73181/13841/18007/19206/14360/22253/53972/20358/80883/12162/20564 |
| mmu04014 | 32 | 0.1361702 | 6.22e-05 | 4.206315 | 6.22e-05 | 0.0008075 | Ras signaling pathway | 15234/11600/26565/16542/16000/23871/240168/20418/19414/14812/21687/14710/19395/14255/16590/66066/22341/16002/14702/17311/85031/23797/14697/14708/23872/240057/22637/14696/16797/18596/18806/320484 |
| mmu04728 | 22 | 0.1629630 | 6.23e-05 | 4.205596 | 6.23e-05 | 0.0008075 | Dopaminergic synapse | 16519/14802/12288/109731/13491/14677/20265/14812/17161/14710/18795/66066/14702/109689/18796/216869/23797/14697/14708/14696/12286/16572 |
| mmu04974 | 19 | 0.1759259 | 6.78e-05 | 4.169019 | 6.78e-05 | 0.0008345 | Protein digestion and absorption | 12814/140709/12818/94216/20541/58803/107581/234967/110893/12840/12817/17380/12832/12819/98660/20540/237759/12822/12830 |
kegg_dot <- list()
upset=list()
for (i in 1:length(fc)) {
x <- fc[i] %>% as.character()
# dot plot, save
kegg_dot[[x]] <- ggplot(enrichKEGG_sig[[x]][1:15, ]) +
geom_point(aes(x = GeneRatio, y = reorder(Description, GeneRatio), colour = logPval, size = Count)) +
scale_color_gradient(low = "dodgerblue3", high = "firebrick3", limits = c(0, NA)) +
scale_size(range = c(.3,3)) +
ggtitle("KEGG Pathways") +
ylab(label = "") +
xlab(label = "Gene Ratio") +
labs(color = expression("-log"[10] * "Pvalue"), size = "Gene Counts")
ggsave(filename = paste0("kegg_dot_", fc[i], ".svg"), plot = kegg_dot[[x]], path = here::here("2_plots/kegg/"),
width = 88, height = 95, units = "mm")
upset[[x]] <- upsetplot(x = enrichKEGG[[x]], 10)
ggsave(filename = paste0("upset_kegg_", fc[i], ".svg"), plot = upset[[x]], path = here::here("2_plots/kegg/"))
}
kegg_dot[[p]]
upset[[p]]
q=1# create df with normalised read counts with an additional entrezid column for binding
logCPM <- cpm(dge, prior.count = 3, log = TRUE)
logCPM <- logCPM[,1:7]
logCPM <- cbind(logCPM, dge$genes$entrezid)
rownames(logCPM) <- dge$genes$gene_name
colnames(logCPM) <- c("Control 1", "Control 2", "Control 4", "Intact 1", "Intact 2", "Intact 3", "Intact 4", "entrezid")
### full pathway method
# complete_pathway <- kegg_pathway[[1]]$GENE %>% as.data.frame()
# complete_pathway <- focal_adhesion[seq(1, nrow(focal_adhesion), 2),]
# match_complete_pathway <- logCPM[,"entrezid"] %in% complete_pathway
# my_palette <- colorRampPalette(c("dodgerblue3", "white", "firebrick3"))(n = 201)
my_palette <- viridis_pal(option = "viridis")(300)
# df for heatmap annotation of sample group
anno <- as.factor(dge$samples$group) %>% as.data.frame()
anno <- anno[1:7,] %>% as.data.frame()
colnames(anno) <- "Sample Groups"
anno$`Sample Groups` <- gsub("CONT", "Control", anno$`Sample Groups`)
anno$`Sample Groups` <- gsub("INT", "Intact", anno$`Sample Groups`)
rownames(anno) <- colnames(logCPM[, 1:7])
# setting colour of sample group annotation
# original sample colours
# anno_colours <- c("#66C2A5", "#FC8D62")
# new sample colours
anno_colours <- c("#f8766d", "#00bdc4")
names(anno_colours) <- c("Control", "Intact")matrix <- list()
display_matrix <- list()
kegg_heat=list()
for (i in 1:length(fc)) {
x <- fc[i] %>% as.character()
for (j in 1:length(kegg_id)) {
y <- kegg_pathway[[j]]$PATHWAY_MAP
partial <- enrichKEGG_all[[x]][, c("ID", "geneID")]
partial <- partial[kegg_id[j], "geneID"] %>% as.data.frame()
partial <- separate_rows(partial, ., sep = "/")
colnames(partial) <- "entrezid"
# heatmap matrix
match <- logCPM[, "entrezid"] %in% partial$entrezid
matrix[[x]][[y]] <- logCPM[match, c("Control 1", "Control 2", "Control 4", "Intact 1", "Intact 2", "Intact 3", "Intact 4")] %>%
as.data.frame()
# changing the colname to numeric for some reason, cant remember
matrix[[x]][[y]][, c("Control 1", "Control 2", "Control 4", "Intact 1", "Intact 2", "Intact 3", "Intact 4")] <- as.numeric(as.character(unlist(matrix[[x]][[y]][, c("Control 1", "Control 2", "Control 4", "Intact 1", "Intact 2", "Intact 3", "Intact 4")])))
# display matrix
match2 <- lmTreat_sig[[x]][, "entrezid"] %in% partial$entrezid
display_matrix[[x]][[y]] <- lmTreat_sig[[x]][match2, c("gene_name", "logFC", "P.Value", "adj.P.Val", "description")] %>%
as.data.frame()
colnames(display_matrix[[x]][[y]]) <- c("Gene Name", "logFC", "P Value", "Adjusted P Value", "Description")
## Heatmap
kegg_heat[[x]][[y]] <- pheatmap(
mat = matrix[[x]][[y]],
### Publish
show_colnames = T,
main = paste0(y, "\n"),
legend = F,
annotation_legend = F,
fontsize = 8,
fontsize_col = 9,
fontsize_number = 7,
fontsize_row = 8,
treeheight_row = 25,
treeheight_col = 10,
cluster_cols = T,
clustering_distance_rows = "euclidean",
legend_breaks = c(seq(-3, 11, by = .5), 1.4),
legend_labels = c(seq(-3, 11, by = .5), "Z-Score"),
angle_col = 90,
cutree_cols = 2,
cutree_rows = 2,
color = my_palette,
scale = "row",
border_color = NA,
annotation_col = anno,
annotation_colors = list("Sample Groups" = anno_colours),
annotation_names_col = F,
annotation = T,
silent = T,
labels_row = as.expression(lapply(rownames(matrix[[x]][[y]]), function(a) bquote(italic(.(a)))))
) %>% as.ggplot()
# save
ggsave(filename = paste0("heat_", x, "_", y, ".svg"),
plot = kegg_heat[[x]][[y]],
path = here::here("2_plots/kegg/"),
width = 58,
height = 110,
units = "mm")}
}kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000027009 | Itga4 | 2.074185 | 0.0000155 | 0.0025120 | integrin alpha 4 [Source:MGI Symbol;Acc:MGI:96603] |
| ENSMUSG00000057614 | Gnai1 | 2.405667 | 0.0001011 | 0.0055045 | guanine nucleotide binding protein (G protein), alpha inhibiting 1 [Source:MGI Symbol;Acc:MGI:95771] |
| ENSMUSG00000031740 | Mmp2 | 2.270956 | 0.0001333 | 0.0062896 | matrix metallopeptidase 2 [Source:MGI Symbol;Acc:MGI:97009] |
| ENSMUSG00000037405 | Icam1 | 1.989282 | 0.0001592 | 0.0068723 | intercellular adhesion molecule 1 [Source:MGI Symbol;Acc:MGI:96392] |
| ENSMUSG00000020395 | Itk | 2.082706 | 0.0001896 | 0.0074705 | IL2 inducible T cell kinase [Source:MGI Symbol;Acc:MGI:96621] |
| ENSMUSG00000031990 | Jam3 | 1.932372 | 0.0001934 | 0.0075172 | junction adhesion molecule 3 [Source:MGI Symbol;Acc:MGI:1933825] |
| ENSMUSG00000061353 | Cxcl12 | 2.574792 | 0.0002010 | 0.0076920 | chemokine (C-X-C motif) ligand 12 [Source:MGI Symbol;Acc:MGI:103556] |
| ENSMUSG00000050520 | Cldn8 | 1.948402 | 0.0002705 | 0.0093445 | claudin 8 [Source:MGI Symbol;Acc:MGI:1859286] |
| ENSMUSG00000031871 | Cdh5 | 2.498728 | 0.0004002 | 0.0116843 | cadherin 5 [Source:MGI Symbol;Acc:MGI:105057] |
| ENSMUSG00000032011 | Thy1 | 1.783613 | 0.0004132 | 0.0118214 | thymus cell antigen 1, theta [Source:MGI Symbol;Acc:MGI:98747] |
| ENSMUSG00000031207 | Msn | 1.375211 | 0.0004493 | 0.0121659 | moesin [Source:MGI Symbol;Acc:MGI:97167] |
| ENSMUSG00000030830 | Itgal | 1.816463 | 0.0006482 | 0.0150234 | integrin alpha L [Source:MGI Symbol;Acc:MGI:96606] |
| ENSMUSG00000001946 | Esam | 1.936624 | 0.0006493 | 0.0150234 | endothelial cell-specific adhesion molecule [Source:MGI Symbol;Acc:MGI:1916774] |
| ENSMUSG00000020717 | Pecam1 | 1.731782 | 0.0009000 | 0.0178528 | platelet/endothelial cell adhesion molecule 1 [Source:MGI Symbol;Acc:MGI:97537] |
| ENSMUSG00000041378 | Cldn5 | 1.919823 | 0.0018784 | 0.0281045 | claudin 5 [Source:MGI Symbol;Acc:MGI:1276112] |
| ENSMUSG00000022512 | Cldn1 | 1.838024 | 0.0037807 | 0.0435854 | claudin 1 [Source:MGI Symbol;Acc:MGI:1276109] |
| ENSMUSG00000056917 | Sipa1 | 1.252646 | 0.0042264 | 0.0465693 | signal-induced proliferation associated gene 1 [Source:MGI Symbol;Acc:MGI:107576] |
| ENSMUSG00000053062 | Jam2 | 3.164427 | 0.0046329 | 0.0493355 | junction adhesion molecule 2 [Source:MGI Symbol;Acc:MGI:1933820] |
# adjusting the kegg id to suit the parameters of the pathview funtion
adj.keggID <- gsub("mmu", "", kegg_id)
for (i in 1:length(fc)) {
x <- fc[i] %>% as.character()
# extract the logFC from the DE gene list
pathview_table <- dplyr::select(.data = lmTreat_sig[[x]], c("logFC")) %>% as.matrix()
# run pathview with Ensembl ID instead of entrezID
pathview <- pathview(
gene.data = pathview_table[, 1],
gene.idtype = "ENSEMBL",
pathway.id = adj.keggID,
species = "mmu",
out.suffix = "pv",
kegg.dir = here::here("2_plots/kegg/"),
kegg.native = T
)
# move the result file to the plot directory
file.rename(
from = paste0("mmu", adj.keggID, ".pv.png"),
to = here::here(paste0("2_plots/kegg/pv_", x, "_", kegg_id, ".png"))
)
}[1] "Note: 166 of 1629 unique input IDs unmapped."[1] "Note: 151 of 1447 unique input IDs unmapped."[1] "Note: 63 of 388 unique input IDs unmapped."# display the pathview graph. doesnt work when knitting!!!!
# knitr::include_graphics(here::here(paste0("2_plots/kegg/pv_", fc[p], "_", kegg_id[q], ".png")))q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000027009 | Itga4 | 2.074185 | 0.0000155 | 0.0025120 | integrin alpha 4 [Source:MGI Symbol;Acc:MGI:96603] |
| ENSMUSG00000005087 | Cd44 | 2.271713 | 0.0000724 | 0.0046732 | CD44 antigen [Source:MGI Symbol;Acc:MGI:88338] |
| ENSMUSG00000073889 | Il11ra1 | 1.542982 | 0.0001081 | 0.0056640 | interleukin 11 receptor, alpha chain 1 [Source:MGI Symbol;Acc:MGI:107426] |
| ENSMUSG00000002033 | Cd3g | 3.645674 | 0.0002123 | 0.0079664 | CD3 antigen, gamma polypeptide [Source:MGI Symbol;Acc:MGI:88333] |
| ENSMUSG00000042284 | Itga1 | 1.938967 | 0.0003108 | 0.0102149 | integrin alpha 1 [Source:MGI Symbol;Acc:MGI:96599] |
| ENSMUSG00000042817 | Flt3 | 2.075768 | 0.0004099 | 0.0118214 | FMS-like tyrosine kinase 3 [Source:MGI Symbol;Acc:MGI:95559] |
| ENSMUSG00000028076 | Cd1d1 | 2.344493 | 0.0005063 | 0.0130930 | CD1d1 antigen [Source:MGI Symbol;Acc:MGI:107674] |
| ENSMUSG00000005672 | Kit | 1.518478 | 0.0005311 | 0.0134106 | KIT proto-oncogene receptor tyrosine kinase [Source:MGI Symbol;Acc:MGI:96677] |
| ENSMUSG00000027820 | Mme | 3.737788 | 0.0005351 | 0.0134543 | membrane metallo endopeptidase [Source:MGI Symbol;Acc:MGI:97004] |
| ENSMUSG00000073421 | H2-Ab1 | 1.742382 | 0.0006499 | 0.0150234 | histocompatibility 2, class II antigen A, beta 1 [Source:MGI Symbol;Acc:MGI:103070] |
| ENSMUSG00000029084 | Cd38 | 1.711230 | 0.0007558 | 0.0163113 | CD38 antigen [Source:MGI Symbol;Acc:MGI:107474] |
| ENSMUSG00000041538 | H2-Ob | 1.716311 | 0.0008312 | 0.0170615 | histocompatibility 2, O region beta locus [Source:MGI Symbol;Acc:MGI:95925] |
| ENSMUSG00000019966 | Kitl | 1.310648 | 0.0010693 | 0.0200607 | kit ligand [Source:MGI Symbol;Acc:MGI:96974] |
| ENSMUSG00000060586 | H2-Eb1 | 1.690764 | 0.0013795 | 0.0231779 | histocompatibility 2, class II antigen E beta [Source:MGI Symbol;Acc:MGI:95901] |
| ENSMUSG00000036594 | H2-Aa | 1.672690 | 0.0021648 | 0.0308677 | histocompatibility 2, class II antigen A, alpha [Source:MGI Symbol;Acc:MGI:95895] |
| ENSMUSG00000003882 | Il7r | 2.257016 | 0.0040536 | 0.0454821 | interleukin 7 receptor [Source:MGI Symbol;Acc:MGI:96562] |
| ENSMUSG00000023274 | Cd4 | 2.413573 | 0.0040842 | 0.0457300 | CD4 antigen [Source:MGI Symbol;Acc:MGI:88335] |
q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000051331 | Cacna1c | 1.120969 | 0.0000094 | 0.0019883 | calcium channel, voltage-dependent, L type, alpha 1C subunit [Source:MGI Symbol;Acc:MGI:103013] |
| ENSMUSG00000022683 | Pla2g10 | 5.773220 | 0.0000180 | 0.0025584 | phospholipase A2, group X [Source:MGI Symbol;Acc:MGI:1347522] |
| ENSMUSG00000045875 | Adra1a | 4.131590 | 0.0000560 | 0.0042689 | adrenergic receptor, alpha 1a [Source:MGI Symbol;Acc:MGI:104773] |
| ENSMUSG00000041624 | Gucy1a2 | 2.199471 | 0.0001654 | 0.0070122 | guanylate cyclase 1, soluble, alpha 2 [Source:MGI Symbol;Acc:MGI:2660877] |
| ENSMUSG00000020654 | Adcy3 | 1.648297 | 0.0001903 | 0.0074705 | adenylate cyclase 3 [Source:MGI Symbol;Acc:MGI:99675] |
| ENSMUSG00000027524 | Edn3 | 3.849271 | 0.0003001 | 0.0100411 | endothelin 3 [Source:MGI Symbol;Acc:MGI:95285] |
| ENSMUSG00000051177 | Plcb1 | 1.960299 | 0.0003205 | 0.0104215 | phospholipase C, beta 1 [Source:MGI Symbol;Acc:MGI:97613] |
| ENSMUSG00000030669 | Calca | 5.762174 | 0.0003662 | 0.0111446 | calcitonin/calcitonin-related polypeptide, alpha [Source:MGI Symbol;Acc:MGI:2151253] |
| ENSMUSG00000028005 | Gucy1b1 | 1.861114 | 0.0004126 | 0.0118214 | guanylate cyclase 1, soluble, beta 1 [Source:MGI Symbol;Acc:MGI:1860604] |
| ENSMUSG00000033910 | Gucy1a1 | 1.985306 | 0.0005168 | 0.0132227 | guanylate cyclase 1, soluble, alpha 1 [Source:MGI Symbol;Acc:MGI:1926562] |
| ENSMUSG00000022220 | Adcy4 | 1.867108 | 0.0005490 | 0.0136242 | adenylate cyclase 4 [Source:MGI Symbol;Acc:MGI:99674] |
| ENSMUSG00000031659 | Adcy7 | 1.309423 | 0.0005572 | 0.0137479 | adenylate cyclase 7 [Source:MGI Symbol;Acc:MGI:102891] |
| ENSMUSG00000049115 | Agtr1a | 1.761758 | 0.0007646 | 0.0164599 | angiotensin II receptor, type 1a [Source:MGI Symbol;Acc:MGI:87964] |
| ENSMUSG00000063142 | Kcnma1 | 2.434426 | 0.0008434 | 0.0171847 | potassium large conductance calcium-activated channel, subfamily M, alpha member 1 [Source:MGI Symbol;Acc:MGI:99923] |
| ENSMUSG00000031616 | Ednra | 1.779614 | 0.0008698 | 0.0175204 | endothelin receptor type A [Source:MGI Symbol;Acc:MGI:105923] |
| ENSMUSG00000040061 | Plcb2 | 1.498256 | 0.0015357 | 0.0249268 | phospholipase C, beta 2 [Source:MGI Symbol;Acc:MGI:107465] |
| ENSMUSG00000059588 | Calcrl | 1.494208 | 0.0018856 | 0.0281484 | calcitonin receptor-like [Source:MGI Symbol;Acc:MGI:1926944] |
q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000028864 | Hgf | 4.1253117 | 0.0000044 | 0.0015028 | hepatocyte growth factor [Source:MGI Symbol;Acc:MGI:96079] |
| ENSMUSG00000022309 | Angpt1 | 3.3885860 | 0.0000102 | 0.0021117 | angiopoietin 1 [Source:MGI Symbol;Acc:MGI:108448] |
| ENSMUSG00000027009 | Itga4 | 2.0741848 | 0.0000155 | 0.0025120 | integrin alpha 4 [Source:MGI Symbol;Acc:MGI:96603] |
| ENSMUSG00000062960 | Kdr | 2.0456427 | 0.0000226 | 0.0028011 | kinase insert domain protein receptor [Source:MGI Symbol;Acc:MGI:96683] |
| ENSMUSG00000020053 | Igf1 | 2.7804446 | 0.0000309 | 0.0032608 | insulin-like growth factor 1 [Source:MGI Symbol;Acc:MGI:96432] |
| ENSMUSG00000031273 | Col4a6 | 3.4668103 | 0.0000409 | 0.0037259 | collagen, type IV, alpha 6 [Source:MGI Symbol;Acc:MGI:2152695] |
| ENSMUSG00000028047 | Thbs3 | 1.6738088 | 0.0000461 | 0.0039924 | thrombospondin 3 [Source:MGI Symbol;Acc:MGI:98739] |
| ENSMUSG00000028978 | Nos3 | 2.1486818 | 0.0000581 | 0.0043512 | nitric oxide synthase 3, endothelial cell [Source:MGI Symbol;Acc:MGI:97362] |
| ENSMUSG00000026840 | Lamc3 | 3.8038416 | 0.0000783 | 0.0048313 | laminin gamma 3 [Source:MGI Symbol;Acc:MGI:1344394] |
| ENSMUSG00000019846 | Lama4 | 1.9402802 | 0.0000823 | 0.0049752 | laminin, alpha 4 [Source:MGI Symbol;Acc:MGI:109321] |
| ENSMUSG00000000184 | Ccnd2 | 1.7053911 | 0.0001079 | 0.0056640 | cyclin D2 [Source:MGI Symbol;Acc:MGI:88314] |
| ENSMUSG00000001281 | Itgb7 | 1.8062915 | 0.0001092 | 0.0056640 | integrin beta 7 [Source:MGI Symbol;Acc:MGI:96616] |
| ENSMUSG00000026193 | Fn1 | 1.9696894 | 0.0001143 | 0.0057552 | fibronectin 1 [Source:MGI Symbol;Acc:MGI:95566] |
| ENSMUSG00000029378 | Areg | 5.2465226 | 0.0001304 | 0.0062202 | amphiregulin [Source:MGI Symbol;Acc:MGI:88068] |
| ENSMUSG00000049929 | Lpar4 | 2.1460743 | 0.0001661 | 0.0070122 | lysophosphatidic acid receptor 4 [Source:MGI Symbol;Acc:MGI:1925384] |
| ENSMUSG00000006386 | Tek | 2.3390336 | 0.0001955 | 0.0075310 | TEK receptor tyrosine kinase [Source:MGI Symbol;Acc:MGI:98664] |
| ENSMUSG00000038811 | Gngt2 | 1.8196583 | 0.0002207 | 0.0081751 | guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2 [Source:MGI Symbol;Acc:MGI:893584] |
| ENSMUSG00000046207 | Pik3r6 | 1.6924253 | 0.0002696 | 0.0093445 | phosphoinositide-3-kinase regulatory subunit 5 [Source:MGI Symbol;Acc:MGI:2144613] |
| ENSMUSG00000042284 | Itga1 | 1.9389666 | 0.0003108 | 0.0102149 | integrin alpha 1 [Source:MGI Symbol;Acc:MGI:96599] |
| ENSMUSG00000028626 | Col9a2 | 4.1297594 | 0.0003600 | 0.0110798 | collagen, type IX, alpha 2 [Source:MGI Symbol;Acc:MGI:88466] |
| ENSMUSG00000042817 | Flt3 | 2.0757680 | 0.0004099 | 0.0118214 | FMS-like tyrosine kinase 3 [Source:MGI Symbol;Acc:MGI:95559] |
| ENSMUSG00000005672 | Kit | 1.5184784 | 0.0005311 | 0.0134106 | KIT proto-oncogene receptor tyrosine kinase [Source:MGI Symbol;Acc:MGI:96677] |
| ENSMUSG00000032766 | Gng11 | 2.0192291 | 0.0005737 | 0.0139360 | guanine nucleotide binding protein (G protein), gamma 11 [Source:MGI Symbol;Acc:MGI:1913316] |
| ENSMUSG00000019899 | Lama2 | 1.8339350 | 0.0005773 | 0.0140035 | laminin, alpha 2 [Source:MGI Symbol;Acc:MGI:99912] |
| ENSMUSG00000031520 | Vegfc | 2.1245474 | 0.0007514 | 0.0162972 | vascular endothelial growth factor C [Source:MGI Symbol;Acc:MGI:109124] |
| ENSMUSG00000040003 | Magi2 | 1.5230701 | 0.0007976 | 0.0166697 | membrane associated guanylate kinase, WW and PDZ domain containing 2 [Source:MGI Symbol;Acc:MGI:1354953] |
| ENSMUSG00000048583 | Igf2 | 2.4269395 | 0.0009328 | 0.0183389 | insulin-like growth factor 2 [Source:MGI Symbol;Acc:MGI:96434] |
| ENSMUSG00000043004 | Gng2 | 1.2390569 | 0.0009402 | 0.0184405 | guanine nucleotide binding protein (G protein), gamma 2 [Source:MGI Symbol;Acc:MGI:102705] |
| ENSMUSG00000025348 | Itga7 | 1.5797819 | 0.0009870 | 0.0189401 | integrin alpha 7 [Source:MGI Symbol;Acc:MGI:102700] |
| ENSMUSG00000019966 | Kitl | 1.3106480 | 0.0010693 | 0.0200607 | kit ligand [Source:MGI Symbol;Acc:MGI:96974] |
| ENSMUSG00000019699 | Akt3 | 1.2001093 | 0.0020912 | 0.0301880 | thymoma viral proto-oncogene 3 [Source:MGI Symbol;Acc:MGI:1345147] |
| ENSMUSG00000032192 | Gnb5 | 1.0340057 | 0.0021925 | 0.0310772 | guanine nucleotide binding protein (G protein), beta 5 [Source:MGI Symbol;Acc:MGI:101848] |
| ENSMUSG00000048240 | Gng7 | 2.3093807 | 0.0022679 | 0.0316071 | guanine nucleotide binding protein (G protein), gamma 7 [Source:MGI Symbol;Acc:MGI:95787] |
| ENSMUSG00000027669 | Gnb4 | 1.1575446 | 0.0027290 | 0.0356047 | guanine nucleotide binding protein (G protein), beta 4 [Source:MGI Symbol;Acc:MGI:104581] |
| ENSMUSG00000024620 | Pdgfrb | 0.9572539 | 0.0029764 | 0.0376073 | platelet derived growth factor receptor, beta polypeptide [Source:MGI Symbol;Acc:MGI:97531] |
| ENSMUSG00000031304 | Il2rg | 1.8830596 | 0.0033557 | 0.0405276 | interleukin 2 receptor, gamma chain [Source:MGI Symbol;Acc:MGI:96551] |
| ENSMUSG00000026768 | Itga8 | 1.5873015 | 0.0033743 | 0.0407238 | integrin alpha 8 [Source:MGI Symbol;Acc:MGI:109442] |
| ENSMUSG00000020758 | Itgb4 | -1.4990466 | 0.0035398 | 0.0419565 | integrin beta 4 [Source:MGI Symbol;Acc:MGI:96613] |
| ENSMUSG00000048376 | F2r | 2.1925090 | 0.0040492 | 0.0454821 | coagulation factor II (thrombin) receptor [Source:MGI Symbol;Acc:MGI:101802] |
| ENSMUSG00000003882 | Il7r | 2.2570158 | 0.0040536 | 0.0454821 | interleukin 7 receptor [Source:MGI Symbol;Acc:MGI:96562] |
| ENSMUSG00000022346 | Myc | 1.8123908 | 0.0043062 | 0.0470865 | myelocytomatosis oncogene [Source:MGI Symbol;Acc:MGI:97250] |
| ENSMUSG00000031274 | Col4a5 | 1.6976014 | 0.0047060 | 0.0498134 | collagen, type IV, alpha 5 [Source:MGI Symbol;Acc:MGI:88456] |
| ENSMUSG00000055980 | Irs1 | 0.9503609 | 0.0047208 | 0.0499093 | insulin receptor substrate 1 [Source:MGI Symbol;Acc:MGI:99454] |
q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000028864 | Hgf | 4.1253117 | 0.0000044 | 0.0015028 | hepatocyte growth factor [Source:MGI Symbol;Acc:MGI:96079] |
| ENSMUSG00000027009 | Itga4 | 2.0741848 | 0.0000155 | 0.0025120 | integrin alpha 4 [Source:MGI Symbol;Acc:MGI:96603] |
| ENSMUSG00000062960 | Kdr | 2.0456427 | 0.0000226 | 0.0028011 | kinase insert domain protein receptor [Source:MGI Symbol;Acc:MGI:96683] |
| ENSMUSG00000020053 | Igf1 | 2.7804446 | 0.0000309 | 0.0032608 | insulin-like growth factor 1 [Source:MGI Symbol;Acc:MGI:96432] |
| ENSMUSG00000031273 | Col4a6 | 3.4668103 | 0.0000409 | 0.0037259 | collagen, type IV, alpha 6 [Source:MGI Symbol;Acc:MGI:2152695] |
| ENSMUSG00000028047 | Thbs3 | 1.6738088 | 0.0000461 | 0.0039924 | thrombospondin 3 [Source:MGI Symbol;Acc:MGI:98739] |
| ENSMUSG00000026840 | Lamc3 | 3.8038416 | 0.0000783 | 0.0048313 | laminin gamma 3 [Source:MGI Symbol;Acc:MGI:1344394] |
| ENSMUSG00000019846 | Lama4 | 1.9402802 | 0.0000823 | 0.0049752 | laminin, alpha 4 [Source:MGI Symbol;Acc:MGI:109321] |
| ENSMUSG00000000184 | Ccnd2 | 1.7053911 | 0.0001079 | 0.0056640 | cyclin D2 [Source:MGI Symbol;Acc:MGI:88314] |
| ENSMUSG00000001281 | Itgb7 | 1.8062915 | 0.0001092 | 0.0056640 | integrin beta 7 [Source:MGI Symbol;Acc:MGI:96616] |
| ENSMUSG00000026193 | Fn1 | 1.9696894 | 0.0001143 | 0.0057552 | fibronectin 1 [Source:MGI Symbol;Acc:MGI:95566] |
| ENSMUSG00000021448 | Shc3 | 2.1490360 | 0.0001372 | 0.0063240 | src homology 2 domain-containing transforming protein C3 [Source:MGI Symbol;Acc:MGI:106179] |
| ENSMUSG00000024867 | Pip5k1b | 1.5003642 | 0.0001491 | 0.0066795 | phosphatidylinositol-4-phosphate 5-kinase, type 1 beta [Source:MGI Symbol;Acc:MGI:107930] |
| ENSMUSG00000042284 | Itga1 | 1.9389666 | 0.0003108 | 0.0102149 | integrin alpha 1 [Source:MGI Symbol;Acc:MGI:96599] |
| ENSMUSG00000028626 | Col9a2 | 4.1297594 | 0.0003600 | 0.0110798 | collagen, type IX, alpha 2 [Source:MGI Symbol;Acc:MGI:88466] |
| ENSMUSG00000019899 | Lama2 | 1.8339350 | 0.0005773 | 0.0140035 | laminin, alpha 2 [Source:MGI Symbol;Acc:MGI:99912] |
| ENSMUSG00000031520 | Vegfc | 2.1245474 | 0.0007514 | 0.0162972 | vascular endothelial growth factor C [Source:MGI Symbol;Acc:MGI:109124] |
| ENSMUSG00000025348 | Itga7 | 1.5797819 | 0.0009870 | 0.0189401 | integrin alpha 7 [Source:MGI Symbol;Acc:MGI:102700] |
| ENSMUSG00000022439 | Parvg | 1.7706088 | 0.0010067 | 0.0191779 | parvin, gamma [Source:MGI Symbol;Acc:MGI:2158329] |
| ENSMUSG00000022438 | Parvb | 1.6425559 | 0.0012361 | 0.0215474 | parvin, beta [Source:MGI Symbol;Acc:MGI:2153063] |
| ENSMUSG00000068699 | Flnc | 1.1797740 | 0.0013967 | 0.0234216 | filamin C, gamma [Source:MGI Symbol;Acc:MGI:95557] |
| ENSMUSG00000052698 | Tln2 | 1.2448359 | 0.0014789 | 0.0243963 | talin 2 [Source:MGI Symbol;Acc:MGI:1917799] |
| ENSMUSG00000019843 | Fyn | 1.1786653 | 0.0017407 | 0.0266942 | Fyn proto-oncogene [Source:MGI Symbol;Acc:MGI:95602] |
| ENSMUSG00000019699 | Akt3 | 1.2001093 | 0.0020912 | 0.0301880 | thymoma viral proto-oncogene 3 [Source:MGI Symbol;Acc:MGI:1345147] |
| ENSMUSG00000024620 | Pdgfrb | 0.9572539 | 0.0029764 | 0.0376073 | platelet derived growth factor receptor, beta polypeptide [Source:MGI Symbol;Acc:MGI:97531] |
| ENSMUSG00000007655 | Cav1 | 1.6011191 | 0.0031814 | 0.0392979 | caveolin 1, caveolae protein [Source:MGI Symbol;Acc:MGI:102709] |
| ENSMUSG00000026768 | Itga8 | 1.5873015 | 0.0033743 | 0.0407238 | integrin alpha 8 [Source:MGI Symbol;Acc:MGI:109442] |
| ENSMUSG00000020758 | Itgb4 | -1.4990466 | 0.0035398 | 0.0419565 | integrin beta 4 [Source:MGI Symbol;Acc:MGI:96613] |
| ENSMUSG00000031274 | Col4a5 | 1.6976014 | 0.0047060 | 0.0498134 | collagen, type IV, alpha 5 [Source:MGI Symbol;Acc:MGI:88456] |
q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000029375 | Cxcl15 | 6.916834 | 0.0000000 | 0.0001479 | chemokine (C-X-C motif) ligand 15 [Source:MGI Symbol;Acc:MGI:1339941] |
| ENSMUSG00000034457 | Eda2r | 3.524309 | 0.0000387 | 0.0036589 | ectodysplasin A2 receptor [Source:MGI Symbol;Acc:MGI:2442860] |
| ENSMUSG00000073889 | Il11ra1 | 1.542982 | 0.0001081 | 0.0056640 | interleukin 11 receptor, alpha chain 1 [Source:MGI Symbol;Acc:MGI:107426] |
| ENSMUSG00000050232 | Cxcr3 | 2.280257 | 0.0001954 | 0.0075310 | chemokine (C-X-C motif) receptor 3 [Source:MGI Symbol;Acc:MGI:1277207] |
| ENSMUSG00000061353 | Cxcl12 | 2.574792 | 0.0002010 | 0.0076920 | chemokine (C-X-C motif) ligand 12 [Source:MGI Symbol;Acc:MGI:103556] |
| ENSMUSG00000025352 | Gdf11 | 2.251448 | 0.0002430 | 0.0087564 | growth differentiation factor 11 [Source:MGI Symbol;Acc:MGI:1338027] |
| ENSMUSG00000037660 | Gdf7 | 3.410398 | 0.0004003 | 0.0116843 | growth differentiation factor 7 [Source:MGI Symbol;Acc:MGI:95690] |
| ENSMUSG00000031497 | Tnfsf13b | 2.218370 | 0.0004343 | 0.0120034 | tumor necrosis factor (ligand) superfamily, member 13b [Source:MGI Symbol;Acc:MGI:1344376] |
| ENSMUSG00000021943 | Gdf10 | 2.741543 | 0.0005206 | 0.0132671 | growth differentiation factor 10 [Source:MGI Symbol;Acc:MGI:95684] |
| ENSMUSG00000005465 | Il27ra | 1.937581 | 0.0006697 | 0.0153371 | interleukin 27 receptor, alpha [Source:MGI Symbol;Acc:MGI:1355318] |
| ENSMUSG00000063727 | Tnfrsf11b | 2.131252 | 0.0007401 | 0.0161954 | tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin) [Source:MGI Symbol;Acc:MGI:109587] |
| ENSMUSG00000026573 | Xcl1 | 2.671247 | 0.0011054 | 0.0204395 | chemokine (C motif) ligand 1 [Source:MGI Symbol;Acc:MGI:104593] |
| ENSMUSG00000060509 | Xcr1 | 2.001440 | 0.0017559 | 0.0268808 | chemokine (C motif) receptor 1 [Source:MGI Symbol;Acc:MGI:1346338] |
| ENSMUSG00000071713 | Csf2rb | 2.031328 | 0.0017896 | 0.0271305 | colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage) [Source:MGI Symbol;Acc:MGI:1339759] |
| ENSMUSG00000000791 | Il12rb1 | 2.130604 | 0.0031159 | 0.0386619 | interleukin 12 receptor, beta 1 [Source:MGI Symbol;Acc:MGI:104579] |
| ENSMUSG00000031304 | Il2rg | 1.883060 | 0.0033557 | 0.0405276 | interleukin 2 receptor, gamma chain [Source:MGI Symbol;Acc:MGI:96551] |
| ENSMUSG00000003227 | Edar | 2.573653 | 0.0038496 | 0.0439969 | ectodysplasin-A receptor [Source:MGI Symbol;Acc:MGI:1343498] |
| ENSMUSG00000008999 | Bmp7 | 1.585592 | 0.0040494 | 0.0454821 | bone morphogenetic protein 7 [Source:MGI Symbol;Acc:MGI:103302] |
| ENSMUSG00000003882 | Il7r | 2.257016 | 0.0040536 | 0.0454821 | interleukin 7 receptor [Source:MGI Symbol;Acc:MGI:96562] |
| ENSMUSG00000023274 | Cd4 | 2.413573 | 0.0040842 | 0.0457300 | CD4 antigen [Source:MGI Symbol;Acc:MGI:88335] |
p=p+1enrichKEGG_sig[[p]][1:20, ] %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Count | GeneRatio | pvalue | logPval | p.adjust | qvalue | Description | geneID | |
|---|---|---|---|---|---|---|---|---|
| mmu04713 | 24 | 0.2448980 | 0.00e+00 | 9.071978 | 0.00e+00 | 0.0000002 | Circadian entrainment | 16519/14802/12288/20190/14677/234889/14812/104111/14710/18795/54195/60596/104110/66066/11513/11517/14702/73086/18796/20192/58226/14708/14697/14696 |
| mmu04371 | 26 | 0.1897810 | 1.00e-07 | 7.277696 | 1.00e-07 | 0.0000064 | Apelin signaling pathway | 20190/18127/20541/14677/17260/104111/14710/104709/110893/18795/104110/66066/23796/11513/11607/17897/14702/18796/20192/14219/30878/14708/23797/14697/14696/16890 |
| mmu04724 | 23 | 0.2035398 | 1.00e-07 | 7.087147 | 1.00e-07 | 0.0000066 | Glutamatergic synapse | 16519/20512/14802/14805/12288/14677/14812/104111/210274/14710/18795/104110/66066/11513/14806/14702/18796/105727/13385/14708/14697/14696/12286 |
| mmu05414 | 20 | 0.2127660 | 3.00e-07 | 6.568740 | 3.00e-07 | 0.0000164 | Dilated cardiomyopathy | 24052/12288/16401/16000/20541/16421/12293/104111/110893/109700/104110/16773/11513/16404/17897/81904/24051/241226/192897/12298 |
| mmu04514 | 29 | 0.1593407 | 5.00e-07 | 6.328504 | 5.00e-07 | 0.0000228 | Cell adhesion molecules | 16401/241568/19266/192167/12558/272381/16421/15894/83964/54420/386750/12562/19274/225825/245537/69524/16408/14961/269116/20339/15002/18613/14969/12741/18007/14960/80883/241226/12737 |
| mmu05412 | 17 | 0.2207792 | 1.20e-06 | 5.909386 | 1.20e-06 | 0.0000499 | Arrhythmogenic right ventricular cardiomyopathy | 16842/24052/12288/16401/20541/12558/16421/12293/110893/109700/16773/16404/81904/24051/241226/192897/12298 |
| mmu04022 | 27 | 0.1560694 | 1.80e-06 | 5.751113 | 1.80e-06 | 0.0000616 | cGMP-PKG signaling pathway | 12288/11549/18127/20541/14677/13618/17260/234889/104111/104709/110893/18795/54195/22068/60596/104110/11513/11607/16531/13617/12062/18796/242202/73181/381290/23797/98660 |
| mmu05032 | 18 | 0.1978022 | 3.30e-06 | 5.486280 | 3.30e-06 | 0.0000949 | Morphine addiction | 16519/14677/18574/104111/14710/14397/104110/66066/11513/18573/14702/109689/216869/14708/14697/14696/54393/12286 |
| mmu04340 | 14 | 0.2413793 | 3.50e-06 | 5.454437 | 3.50e-06 | 0.0000949 | Hedgehog signaling pathway | 14632/16147/15245/68525/19207/59056/16576/12444/14634/14725/240888/109689/19206/216869 |
| mmu04725 | 20 | 0.1785714 | 4.90e-06 | 5.306682 | 4.90e-06 | 0.0001200 | Cholinergic synapse | 16519/12288/14677/226922/104111/14710/104709/18795/104110/66066/11513/14702/18796/14360/14708/23797/14697/14696/60613/12286 |
| mmu04512 | 17 | 0.1931818 | 8.50e-06 | 5.068903 | 8.50e-06 | 0.0001886 | ECM-receptor interaction | 16401/94216/114249/21827/23928/12505/16775/16421/14268/109700/12840/329872/16773/16404/75209/241226/192897 |
| mmu04926 | 21 | 0.1627907 | 1.29e-05 | 4.888815 | 1.29e-05 | 0.0002207 | Relaxin signaling pathway | 94216/18127/14677/13618/17390/20418/104111/14710/18795/104110/66066/11513/22341/14702/109689/18796/216869/14708/23797/14697/14696 |
| mmu04015 | 29 | 0.1355140 | 1.31e-05 | 4.881899 | 1.31e-05 | 0.0002207 | Rap1 signaling pathway | 15234/11600/16542/16000/14026/240168/14677/18645/14812/78134/18760/21687/104111/18795/19395/104110/16590/11513/16408/22341/50791/106952/93737/17311/18796/70549/23797/16797/54519 |
| mmu04062 | 27 | 0.1406250 | 1.32e-05 | 4.879785 | 1.32e-05 | 0.0002207 | Chemokine signaling pathway | 20309/14677/20418/16428/12766/20315/104111/14710/104709/18795/19395/94176/104110/66066/11513/16963/14702/109689/18796/23832/216869/14708/14191/20851/23797/14697/14696 |
| mmu05410 | 17 | 0.1868132 | 1.36e-05 | 4.865970 | 1.36e-05 | 0.0002207 | Hypertrophic cardiomyopathy | 24052/12288/16401/16000/20541/16421/12293/110893/109700/16773/16404/17897/81904/24051/241226/192897/12298 |
| mmu04020 | 31 | 0.1291667 | 1.76e-05 | 4.753641 | 1.76e-05 | 0.0002680 | Calcium signaling pathway | 15234/12288/20190/16542/11549/18127/20541/231602/13618/18574/104111/12290/19220/110893/18795/104110/11513/22341/18573/12494/11607/13617/12062/15558/18796/65973/20192/58226/19218/381290/12286 |
| mmu04970 | 16 | 0.1882353 | 2.20e-05 | 4.656709 | 2.20e-05 | 0.0002979 | Salivary secretion | 11549/234889/104111/18795/54195/60596/104110/11513/12494/17105/16531/18796/20192/17110/381290/98660 |
| mmu04924 | 15 | 0.1973684 | 2.20e-05 | 4.656604 | 2.20e-05 | 0.0002979 | Renin secretion | 12288/14677/234889/18574/13616/18795/54195/60596/18573/11607/16531/13617/11517/18796/229933 |
| mmu04728 | 21 | 0.1555556 | 2.63e-05 | 4.579580 | 2.63e-05 | 0.0003369 | Dopaminergic synapse | 16519/14802/109731/12288/13491/14677/20265/14812/17161/14710/18795/66066/14702/109689/18796/216869/14708/23797/14697/14696/12286 |
| mmu04510 | 27 | 0.1343284 | 3.05e-05 | 4.515260 | 3.05e-05 | 0.0003712 | Focal adhesion | 15234/16401/16542/16000/94216/21827/23928/16775/16421/12444/14268/20418/18719/109700/12840/16773/22341/64099/16404/170736/68794/70549/14360/23797/12389/241226/192897 |
kegg_dot[[p]]
upset[[p]]
q=1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000027009 | Itga4 | 2.074185 | 0.0000191 | 0.0028514 | integrin alpha 4 [Source:MGI Symbol;Acc:MGI:96603] |
| ENSMUSG00000057614 | Gnai1 | 2.405667 | 0.0001147 | 0.0063953 | guanine nucleotide binding protein (G protein), alpha inhibiting 1 [Source:MGI Symbol;Acc:MGI:95771] |
| ENSMUSG00000031740 | Mmp2 | 2.270956 | 0.0001526 | 0.0071629 | matrix metallopeptidase 2 [Source:MGI Symbol;Acc:MGI:97009] |
| ENSMUSG00000037405 | Icam1 | 1.989282 | 0.0001885 | 0.0082607 | intercellular adhesion molecule 1 [Source:MGI Symbol;Acc:MGI:96392] |
| ENSMUSG00000020395 | Itk | 2.082706 | 0.0002206 | 0.0087952 | IL2 inducible T cell kinase [Source:MGI Symbol;Acc:MGI:96621] |
| ENSMUSG00000061353 | Cxcl12 | 2.574792 | 0.0002222 | 0.0088088 | chemokine (C-X-C motif) ligand 12 [Source:MGI Symbol;Acc:MGI:103556] |
| ENSMUSG00000031990 | Jam3 | 1.932372 | 0.0002299 | 0.0089179 | junction adhesion molecule 3 [Source:MGI Symbol;Acc:MGI:1933825] |
| ENSMUSG00000050520 | Cldn8 | 1.948402 | 0.0003180 | 0.0110875 | claudin 8 [Source:MGI Symbol;Acc:MGI:1859286] |
| ENSMUSG00000031871 | Cdh5 | 2.498728 | 0.0004399 | 0.0132230 | cadherin 5 [Source:MGI Symbol;Acc:MGI:105057] |
| ENSMUSG00000032011 | Thy1 | 1.783613 | 0.0004934 | 0.0139533 | thymus cell antigen 1, theta [Source:MGI Symbol;Acc:MGI:98747] |
| ENSMUSG00000031207 | Msn | 1.375211 | 0.0005939 | 0.0153674 | moesin [Source:MGI Symbol;Acc:MGI:97167] |
| ENSMUSG00000001946 | Esam | 1.936624 | 0.0007470 | 0.0176708 | endothelial cell-specific adhesion molecule [Source:MGI Symbol;Acc:MGI:1916774] |
| ENSMUSG00000030830 | Itgal | 1.816463 | 0.0007591 | 0.0178553 | integrin alpha L [Source:MGI Symbol;Acc:MGI:96606] |
| ENSMUSG00000020717 | Pecam1 | 1.731782 | 0.0010578 | 0.0211587 | platelet/endothelial cell adhesion molecule 1 [Source:MGI Symbol;Acc:MGI:97537] |
| ENSMUSG00000041378 | Cldn5 | 1.919823 | 0.0021023 | 0.0324715 | claudin 5 [Source:MGI Symbol;Acc:MGI:1276112] |
| ENSMUSG00000022512 | Cldn1 | 1.838024 | 0.0041828 | 0.0498233 | claudin 1 [Source:MGI Symbol;Acc:MGI:1276109] |
q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000027009 | Itga4 | 2.074185 | 0.0000191 | 0.0028514 | integrin alpha 4 [Source:MGI Symbol;Acc:MGI:96603] |
| ENSMUSG00000005087 | Cd44 | 2.271713 | 0.0000838 | 0.0053858 | CD44 antigen [Source:MGI Symbol;Acc:MGI:88338] |
| ENSMUSG00000073889 | Il11ra1 | 1.542982 | 0.0001432 | 0.0068940 | interleukin 11 receptor, alpha chain 1 [Source:MGI Symbol;Acc:MGI:107426] |
| ENSMUSG00000002033 | Cd3g | 3.645674 | 0.0002234 | 0.0088088 | CD3 antigen, gamma polypeptide [Source:MGI Symbol;Acc:MGI:88333] |
| ENSMUSG00000042284 | Itga1 | 1.938967 | 0.0003646 | 0.0117800 | integrin alpha 1 [Source:MGI Symbol;Acc:MGI:96599] |
| ENSMUSG00000042817 | Flt3 | 2.075768 | 0.0004687 | 0.0137336 | FMS-like tyrosine kinase 3 [Source:MGI Symbol;Acc:MGI:95559] |
| ENSMUSG00000027820 | Mme | 3.737788 | 0.0005576 | 0.0148797 | membrane metallo endopeptidase [Source:MGI Symbol;Acc:MGI:97004] |
| ENSMUSG00000028076 | Cd1d1 | 2.344493 | 0.0005609 | 0.0148797 | CD1d1 antigen [Source:MGI Symbol;Acc:MGI:107674] |
| ENSMUSG00000005672 | Kit | 1.518478 | 0.0006666 | 0.0164221 | KIT proto-oncogene receptor tyrosine kinase [Source:MGI Symbol;Acc:MGI:96677] |
| ENSMUSG00000073421 | H2-Ab1 | 1.742382 | 0.0007707 | 0.0178553 | histocompatibility 2, class II antigen A, beta 1 [Source:MGI Symbol;Acc:MGI:103070] |
| ENSMUSG00000029084 | Cd38 | 1.711230 | 0.0008968 | 0.0193746 | CD38 antigen [Source:MGI Symbol;Acc:MGI:107474] |
| ENSMUSG00000041538 | H2-Ob | 1.716311 | 0.0009822 | 0.0203799 | histocompatibility 2, O region beta locus [Source:MGI Symbol;Acc:MGI:95925] |
| ENSMUSG00000019966 | Kitl | 1.310648 | 0.0013846 | 0.0249431 | kit ligand [Source:MGI Symbol;Acc:MGI:96974] |
| ENSMUSG00000060586 | H2-Eb1 | 1.690764 | 0.0016090 | 0.0274087 | histocompatibility 2, class II antigen E beta [Source:MGI Symbol;Acc:MGI:95901] |
| ENSMUSG00000036594 | H2-Aa | 1.672690 | 0.0024922 | 0.0360270 | histocompatibility 2, class II antigen A, alpha [Source:MGI Symbol;Acc:MGI:95895] |
q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000051331 | Cacna1c | 1.120969 | 0.0000172 | 0.0028514 | calcium channel, voltage-dependent, L type, alpha 1C subunit [Source:MGI Symbol;Acc:MGI:103013] |
| ENSMUSG00000022683 | Pla2g10 | 5.773220 | 0.0000185 | 0.0028514 | phospholipase A2, group X [Source:MGI Symbol;Acc:MGI:1347522] |
| ENSMUSG00000045875 | Adra1a | 4.131590 | 0.0000588 | 0.0047985 | adrenergic receptor, alpha 1a [Source:MGI Symbol;Acc:MGI:104773] |
| ENSMUSG00000041624 | Gucy1a2 | 2.199471 | 0.0001902 | 0.0082833 | guanylate cyclase 1, soluble, alpha 2 [Source:MGI Symbol;Acc:MGI:2660877] |
| ENSMUSG00000020654 | Adcy3 | 1.648297 | 0.0002399 | 0.0092013 | adenylate cyclase 3 [Source:MGI Symbol;Acc:MGI:99675] |
| ENSMUSG00000027524 | Edn3 | 3.849271 | 0.0003134 | 0.0110143 | endothelin 3 [Source:MGI Symbol;Acc:MGI:95285] |
| ENSMUSG00000030669 | Calca | 5.762174 | 0.0003731 | 0.0119508 | calcitonin/calcitonin-related polypeptide, alpha [Source:MGI Symbol;Acc:MGI:2151253] |
| ENSMUSG00000051177 | Plcb1 | 1.960299 | 0.0003744 | 0.0119561 | phospholipase C, beta 1 [Source:MGI Symbol;Acc:MGI:97613] |
| ENSMUSG00000028005 | Gucy1b1 | 1.861114 | 0.0004861 | 0.0139237 | guanylate cyclase 1, soluble, beta 1 [Source:MGI Symbol;Acc:MGI:1860604] |
| ENSMUSG00000033910 | Gucy1a1 | 1.985306 | 0.0005943 | 0.0153674 | guanylate cyclase 1, soluble, alpha 1 [Source:MGI Symbol;Acc:MGI:1926562] |
| ENSMUSG00000022220 | Adcy4 | 1.867108 | 0.0006410 | 0.0161149 | adenylate cyclase 4 [Source:MGI Symbol;Acc:MGI:99674] |
| ENSMUSG00000031659 | Adcy7 | 1.309423 | 0.0007469 | 0.0176708 | adenylate cyclase 7 [Source:MGI Symbol;Acc:MGI:102891] |
| ENSMUSG00000049115 | Agtr1a | 1.761758 | 0.0008988 | 0.0193746 | angiotensin II receptor, type 1a [Source:MGI Symbol;Acc:MGI:87964] |
| ENSMUSG00000063142 | Kcnma1 | 2.434426 | 0.0009192 | 0.0195760 | potassium large conductance calcium-activated channel, subfamily M, alpha member 1 [Source:MGI Symbol;Acc:MGI:99923] |
| ENSMUSG00000031616 | Ednra | 1.779614 | 0.0010153 | 0.0206446 | endothelin receptor type A [Source:MGI Symbol;Acc:MGI:105923] |
| ENSMUSG00000040061 | Plcb2 | 1.498256 | 0.0018527 | 0.0299595 | phospholipase C, beta 2 [Source:MGI Symbol;Acc:MGI:107465] |
| ENSMUSG00000059588 | Calcrl | 1.494208 | 0.0022567 | 0.0340616 | calcitonin receptor-like [Source:MGI Symbol;Acc:MGI:1926944] |
q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000028864 | Hgf | 4.125312 | 0.0000047 | 0.0015780 | hepatocyte growth factor [Source:MGI Symbol;Acc:MGI:96079] |
| ENSMUSG00000022309 | Angpt1 | 3.388586 | 0.0000111 | 0.0023074 | angiopoietin 1 [Source:MGI Symbol;Acc:MGI:108448] |
| ENSMUSG00000027009 | Itga4 | 2.074185 | 0.0000191 | 0.0028514 | integrin alpha 4 [Source:MGI Symbol;Acc:MGI:96603] |
| ENSMUSG00000062960 | Kdr | 2.045643 | 0.0000277 | 0.0033785 | kinase insert domain protein receptor [Source:MGI Symbol;Acc:MGI:96683] |
| ENSMUSG00000020053 | Igf1 | 2.780445 | 0.0000345 | 0.0036412 | insulin-like growth factor 1 [Source:MGI Symbol;Acc:MGI:96432] |
| ENSMUSG00000031273 | Col4a6 | 3.466810 | 0.0000439 | 0.0041268 | collagen, type IV, alpha 6 [Source:MGI Symbol;Acc:MGI:2152695] |
| ENSMUSG00000028047 | Thbs3 | 1.673809 | 0.0000604 | 0.0048021 | thrombospondin 3 [Source:MGI Symbol;Acc:MGI:98739] |
| ENSMUSG00000028978 | Nos3 | 2.148682 | 0.0000687 | 0.0051480 | nitric oxide synthase 3, endothelial cell [Source:MGI Symbol;Acc:MGI:97362] |
| ENSMUSG00000026840 | Lamc3 | 3.803842 | 0.0000826 | 0.0053543 | laminin gamma 3 [Source:MGI Symbol;Acc:MGI:1344394] |
| ENSMUSG00000019846 | Lama4 | 1.940280 | 0.0000999 | 0.0059120 | laminin, alpha 4 [Source:MGI Symbol;Acc:MGI:109321] |
| ENSMUSG00000029378 | Areg | 5.246523 | 0.0001339 | 0.0067067 | amphiregulin [Source:MGI Symbol;Acc:MGI:88068] |
| ENSMUSG00000001281 | Itgb7 | 1.806291 | 0.0001350 | 0.0067067 | integrin beta 7 [Source:MGI Symbol;Acc:MGI:96616] |
| ENSMUSG00000000184 | Ccnd2 | 1.705391 | 0.0001366 | 0.0067339 | cyclin D2 [Source:MGI Symbol;Acc:MGI:88314] |
| ENSMUSG00000026193 | Fn1 | 1.969689 | 0.0001369 | 0.0067339 | fibronectin 1 [Source:MGI Symbol;Acc:MGI:95566] |
| ENSMUSG00000049929 | Lpar4 | 2.146074 | 0.0001922 | 0.0082958 | lysophosphatidic acid receptor 4 [Source:MGI Symbol;Acc:MGI:1925384] |
| ENSMUSG00000006386 | Tek | 2.339034 | 0.0002206 | 0.0087952 | TEK receptor tyrosine kinase [Source:MGI Symbol;Acc:MGI:98664] |
| ENSMUSG00000038811 | Gngt2 | 1.819658 | 0.0002668 | 0.0098590 | guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2 [Source:MGI Symbol;Acc:MGI:893584] |
| ENSMUSG00000046207 | Pik3r6 | 1.692425 | 0.0003324 | 0.0113962 | phosphoinositide-3-kinase regulatory subunit 5 [Source:MGI Symbol;Acc:MGI:2144613] |
| ENSMUSG00000042284 | Itga1 | 1.938967 | 0.0003646 | 0.0117800 | integrin alpha 1 [Source:MGI Symbol;Acc:MGI:96599] |
| ENSMUSG00000028626 | Col9a2 | 4.129759 | 0.0003733 | 0.0119508 | collagen, type IX, alpha 2 [Source:MGI Symbol;Acc:MGI:88466] |
| ENSMUSG00000042817 | Flt3 | 2.075768 | 0.0004687 | 0.0137336 | FMS-like tyrosine kinase 3 [Source:MGI Symbol;Acc:MGI:95559] |
| ENSMUSG00000032766 | Gng11 | 2.019229 | 0.0006551 | 0.0163107 | guanine nucleotide binding protein (G protein), gamma 11 [Source:MGI Symbol;Acc:MGI:1913316] |
| ENSMUSG00000005672 | Kit | 1.518478 | 0.0006666 | 0.0164221 | KIT proto-oncogene receptor tyrosine kinase [Source:MGI Symbol;Acc:MGI:96677] |
| ENSMUSG00000019899 | Lama2 | 1.833935 | 0.0006765 | 0.0165713 | laminin, alpha 2 [Source:MGI Symbol;Acc:MGI:99912] |
| ENSMUSG00000031520 | Vegfc | 2.124547 | 0.0008424 | 0.0189346 | vascular endothelial growth factor C [Source:MGI Symbol;Acc:MGI:109124] |
| ENSMUSG00000040003 | Magi2 | 1.523070 | 0.0009834 | 0.0203802 | membrane associated guanylate kinase, WW and PDZ domain containing 2 [Source:MGI Symbol;Acc:MGI:1354953] |
| ENSMUSG00000048583 | Igf2 | 2.426940 | 0.0010153 | 0.0206446 | insulin-like growth factor 2 [Source:MGI Symbol;Acc:MGI:96434] |
| ENSMUSG00000025348 | Itga7 | 1.579782 | 0.0011908 | 0.0226598 | integrin alpha 7 [Source:MGI Symbol;Acc:MGI:102700] |
| ENSMUSG00000043004 | Gng2 | 1.239057 | 0.0012599 | 0.0235328 | guanine nucleotide binding protein (G protein), gamma 2 [Source:MGI Symbol;Acc:MGI:102705] |
| ENSMUSG00000019966 | Kitl | 1.310648 | 0.0013846 | 0.0249431 | kit ligand [Source:MGI Symbol;Acc:MGI:96974] |
| ENSMUSG00000048240 | Gng7 | 2.309381 | 0.0024454 | 0.0355698 | guanine nucleotide binding protein (G protein), gamma 7 [Source:MGI Symbol;Acc:MGI:95787] |
| ENSMUSG00000019699 | Akt3 | 1.200109 | 0.0027128 | 0.0380460 | thymoma viral proto-oncogene 3 [Source:MGI Symbol;Acc:MGI:1345147] |
| ENSMUSG00000032192 | Gnb5 | 1.034006 | 0.0030610 | 0.0413459 | guanine nucleotide binding protein (G protein), beta 5 [Source:MGI Symbol;Acc:MGI:101848] |
| ENSMUSG00000027669 | Gnb4 | 1.157545 | 0.0035385 | 0.0449227 | guanine nucleotide binding protein (G protein), beta 4 [Source:MGI Symbol;Acc:MGI:104581] |
| ENSMUSG00000031304 | Il2rg | 1.883060 | 0.0037085 | 0.0462470 | interleukin 2 receptor, gamma chain [Source:MGI Symbol;Acc:MGI:96551] |
| ENSMUSG00000026768 | Itga8 | 1.587301 | 0.0038730 | 0.0475073 | integrin alpha 8 [Source:MGI Symbol;Acc:MGI:109442] |
| ENSMUSG00000020758 | Itgb4 | -1.499047 | 0.0041179 | 0.0494897 | integrin beta 4 [Source:MGI Symbol;Acc:MGI:96613] |
q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000028864 | Hgf | 4.125312 | 0.0000047 | 0.0015780 | hepatocyte growth factor [Source:MGI Symbol;Acc:MGI:96079] |
| ENSMUSG00000027009 | Itga4 | 2.074185 | 0.0000191 | 0.0028514 | integrin alpha 4 [Source:MGI Symbol;Acc:MGI:96603] |
| ENSMUSG00000062960 | Kdr | 2.045643 | 0.0000277 | 0.0033785 | kinase insert domain protein receptor [Source:MGI Symbol;Acc:MGI:96683] |
| ENSMUSG00000020053 | Igf1 | 2.780445 | 0.0000345 | 0.0036412 | insulin-like growth factor 1 [Source:MGI Symbol;Acc:MGI:96432] |
| ENSMUSG00000031273 | Col4a6 | 3.466810 | 0.0000439 | 0.0041268 | collagen, type IV, alpha 6 [Source:MGI Symbol;Acc:MGI:2152695] |
| ENSMUSG00000028047 | Thbs3 | 1.673809 | 0.0000604 | 0.0048021 | thrombospondin 3 [Source:MGI Symbol;Acc:MGI:98739] |
| ENSMUSG00000026840 | Lamc3 | 3.803842 | 0.0000826 | 0.0053543 | laminin gamma 3 [Source:MGI Symbol;Acc:MGI:1344394] |
| ENSMUSG00000019846 | Lama4 | 1.940280 | 0.0000999 | 0.0059120 | laminin, alpha 4 [Source:MGI Symbol;Acc:MGI:109321] |
| ENSMUSG00000001281 | Itgb7 | 1.806291 | 0.0001350 | 0.0067067 | integrin beta 7 [Source:MGI Symbol;Acc:MGI:96616] |
| ENSMUSG00000000184 | Ccnd2 | 1.705391 | 0.0001366 | 0.0067339 | cyclin D2 [Source:MGI Symbol;Acc:MGI:88314] |
| ENSMUSG00000026193 | Fn1 | 1.969689 | 0.0001369 | 0.0067339 | fibronectin 1 [Source:MGI Symbol;Acc:MGI:95566] |
| ENSMUSG00000021448 | Shc3 | 2.149036 | 0.0001593 | 0.0073164 | src homology 2 domain-containing transforming protein C3 [Source:MGI Symbol;Acc:MGI:106179] |
| ENSMUSG00000024867 | Pip5k1b | 1.500364 | 0.0001979 | 0.0083928 | phosphatidylinositol-4-phosphate 5-kinase, type 1 beta [Source:MGI Symbol;Acc:MGI:107930] |
| ENSMUSG00000042284 | Itga1 | 1.938967 | 0.0003646 | 0.0117800 | integrin alpha 1 [Source:MGI Symbol;Acc:MGI:96599] |
| ENSMUSG00000028626 | Col9a2 | 4.129759 | 0.0003733 | 0.0119508 | collagen, type IX, alpha 2 [Source:MGI Symbol;Acc:MGI:88466] |
| ENSMUSG00000019899 | Lama2 | 1.833935 | 0.0006765 | 0.0165713 | laminin, alpha 2 [Source:MGI Symbol;Acc:MGI:99912] |
| ENSMUSG00000031520 | Vegfc | 2.124547 | 0.0008424 | 0.0189346 | vascular endothelial growth factor C [Source:MGI Symbol;Acc:MGI:109124] |
| ENSMUSG00000022439 | Parvg | 1.770609 | 0.0011712 | 0.0225219 | parvin, gamma [Source:MGI Symbol;Acc:MGI:2158329] |
| ENSMUSG00000025348 | Itga7 | 1.579782 | 0.0011908 | 0.0226598 | integrin alpha 7 [Source:MGI Symbol;Acc:MGI:102700] |
| ENSMUSG00000022438 | Parvb | 1.642556 | 0.0014600 | 0.0259169 | parvin, beta [Source:MGI Symbol;Acc:MGI:2153063] |
| ENSMUSG00000068699 | Flnc | 1.179774 | 0.0018739 | 0.0300212 | filamin C, gamma [Source:MGI Symbol;Acc:MGI:95557] |
| ENSMUSG00000052698 | Tln2 | 1.244836 | 0.0019261 | 0.0305158 | talin 2 [Source:MGI Symbol;Acc:MGI:1917799] |
| ENSMUSG00000019843 | Fyn | 1.178665 | 0.0023041 | 0.0344884 | Fyn proto-oncogene [Source:MGI Symbol;Acc:MGI:95602] |
| ENSMUSG00000019699 | Akt3 | 1.200109 | 0.0027128 | 0.0380460 | thymoma viral proto-oncogene 3 [Source:MGI Symbol;Acc:MGI:1345147] |
| ENSMUSG00000007655 | Cav1 | 1.601119 | 0.0036517 | 0.0457046 | caveolin 1, caveolae protein [Source:MGI Symbol;Acc:MGI:102709] |
| ENSMUSG00000026768 | Itga8 | 1.587301 | 0.0038730 | 0.0475073 | integrin alpha 8 [Source:MGI Symbol;Acc:MGI:109442] |
| ENSMUSG00000020758 | Itgb4 | -1.499047 | 0.0041179 | 0.0494897 | integrin beta 4 [Source:MGI Symbol;Acc:MGI:96613] |
q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000029375 | Cxcl15 | 6.916834 | 0.0000000 | 0.0001526 | chemokine (C-X-C motif) ligand 15 [Source:MGI Symbol;Acc:MGI:1339941] |
| ENSMUSG00000034457 | Eda2r | 3.524309 | 0.0000414 | 0.0040532 | ectodysplasin A2 receptor [Source:MGI Symbol;Acc:MGI:2442860] |
| ENSMUSG00000073889 | Il11ra1 | 1.542982 | 0.0001432 | 0.0068940 | interleukin 11 receptor, alpha chain 1 [Source:MGI Symbol;Acc:MGI:107426] |
| ENSMUSG00000050232 | Cxcr3 | 2.280257 | 0.0002218 | 0.0088088 | chemokine (C-X-C motif) receptor 3 [Source:MGI Symbol;Acc:MGI:1277207] |
| ENSMUSG00000061353 | Cxcl12 | 2.574792 | 0.0002222 | 0.0088088 | chemokine (C-X-C motif) ligand 12 [Source:MGI Symbol;Acc:MGI:103556] |
| ENSMUSG00000025352 | Gdf11 | 2.251448 | 0.0002756 | 0.0100961 | growth differentiation factor 11 [Source:MGI Symbol;Acc:MGI:1338027] |
| ENSMUSG00000037660 | Gdf7 | 3.410398 | 0.0004216 | 0.0129205 | growth differentiation factor 7 [Source:MGI Symbol;Acc:MGI:95690] |
| ENSMUSG00000031497 | Tnfsf13b | 2.218370 | 0.0004882 | 0.0139237 | tumor necrosis factor (ligand) superfamily, member 13b [Source:MGI Symbol;Acc:MGI:1344376] |
| ENSMUSG00000021943 | Gdf10 | 2.741543 | 0.0005614 | 0.0148797 | growth differentiation factor 10 [Source:MGI Symbol;Acc:MGI:95684] |
| ENSMUSG00000005465 | Il27ra | 1.937581 | 0.0007697 | 0.0178553 | interleukin 27 receptor, alpha [Source:MGI Symbol;Acc:MGI:1355318] |
| ENSMUSG00000063727 | Tnfrsf11b | 2.131252 | 0.0008294 | 0.0187463 | tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin) [Source:MGI Symbol;Acc:MGI:109587] |
| ENSMUSG00000026573 | Xcl1 | 2.671247 | 0.0011830 | 0.0225865 | chemokine (C motif) ligand 1 [Source:MGI Symbol;Acc:MGI:104593] |
| ENSMUSG00000060509 | Xcr1 | 2.001440 | 0.0019520 | 0.0308129 | chemokine (C motif) receptor 1 [Source:MGI Symbol;Acc:MGI:1346338] |
| ENSMUSG00000071713 | Csf2rb | 2.031328 | 0.0019826 | 0.0310486 | colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage) [Source:MGI Symbol;Acc:MGI:1339759] |
| ENSMUSG00000000791 | Il12rb1 | 2.130604 | 0.0033775 | 0.0436691 | interleukin 12 receptor, beta 1 [Source:MGI Symbol;Acc:MGI:104579] |
| ENSMUSG00000031304 | Il2rg | 1.883060 | 0.0037085 | 0.0462470 | interleukin 2 receptor, gamma chain [Source:MGI Symbol;Acc:MGI:96551] |
| ENSMUSG00000003227 | Edar | 2.573653 | 0.0040571 | 0.0490666 | ectodysplasin-A receptor [Source:MGI Symbol;Acc:MGI:1343498] |
p=p+1enrichKEGG_sig[[p]][1:20, ] %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Count | GeneRatio | pvalue | logPval | p.adjust | qvalue | Description | geneID | |
|---|---|---|---|---|---|---|---|---|
| mmu04340 | 8 | 0.1379310 | 0.0000028 | 5.557687 | 0.0000028 | 0.0006063 | Hedgehog signaling pathway | 14632/16147/15245/19207/68525/59056/14725/16576 |
| mmu05217 | 7 | 0.1111111 | 0.0000504 | 4.297777 | 0.0000504 | 0.0045810 | Basal cell carcinoma | 14632/22420/15245/22411/16842/19207/16576 |
| mmu04512 | 8 | 0.0909091 | 0.0000628 | 4.202261 | 0.0000628 | 0.0045810 | ECM-receptor interaction | 94216/23928/16401/114249/12505/12840/329872/16775 |
| mmu04360 | 11 | 0.0607735 | 0.0001136 | 3.944594 | 0.0001136 | 0.0062185 | Axon guidance | 13842/13643/20356/13176/241568/20357/235611/14677/20361/20315/238057 |
| mmu05205 | 10 | 0.0487805 | 0.0013117 | 2.882157 | 0.0013117 | 0.0519047 | Proteoglycans in cancer | 16147/15234/22420/22411/15430/16000/16542/14734/12505/17390 |
| mmu04974 | 7 | 0.0648148 | 0.0014224 | 2.846982 | 0.0014224 | 0.0519047 | Protein digestion and absorption | 12814/140709/12818/94216/58803/12840/110893 |
| mmu04020 | 10 | 0.0416667 | 0.0041455 | 2.382427 | 0.0041455 | 0.1296624 | Calcium signaling pathway | 15234/20190/11549/16542/13618/18127/231602/19220/12290/110893 |
| mmu04728 | 7 | 0.0518519 | 0.0049990 | 2.301116 | 0.0049990 | 0.1368149 | Dopaminergic synapse | 16519/109731/14802/13491/20265/14677/14812 |
| mmu05412 | 5 | 0.0649351 | 0.0068058 | 2.167120 | 0.0068058 | 0.1520052 | Arrhythmogenic right ventricular cardiomyopathy | 16842/24052/16401/12558/110893 |
| mmu04080 | 13 | 0.0336788 | 0.0069425 | 2.158481 | 0.0069425 | 0.1520052 | Neuroactive ligand-receptor interaction | 14803/14805/22355/14802/11549/13491/13618/12310/13616/231602/19220/14812/14397 |
| mmu04724 | 6 | 0.0530973 | 0.0082096 | 2.085675 | 0.0082096 | 0.1634073 | Glutamatergic synapse | 16519/20512/14805/14802/14677/14812 |
| mmu04510 | 8 | 0.0398010 | 0.0129835 | 1.886608 | 0.0129835 | 0.2368921 | Focal adhesion | 15234/94216/16000/23928/16401/16542/12840/16775 |
| mmu04713 | 5 | 0.0510204 | 0.0180879 | 1.742612 | 0.0180879 | 0.2856467 | Circadian entrainment | 16519/14802/20190/14677/14812 |
| mmu04015 | 8 | 0.0373832 | 0.0183037 | 1.737462 | 0.0183037 | 0.2856467 | Rap1 signaling pathway | 15234/11600/16000/16542/14677/14026/14812/240168 |
| mmu04916 | 5 | 0.0500000 | 0.0195695 | 1.708419 | 0.0195695 | 0.2856467 | Melanogenesis | 22420/22411/16842/13618/14677 |
| mmu05033 | 3 | 0.0750000 | 0.0238642 | 1.622254 | 0.0238642 | 0.3078051 | Nicotine addiction | 14802/14812/14397 |
| mmu04151 | 11 | 0.0306407 | 0.0238993 | 1.621615 | 0.0238993 | 0.3078051 | PI3K-Akt signaling pathway | 15234/11600/94216/16000/23928/11839/16401/16542/18127/12840/16775 |
| mmu00910 | 2 | 0.1176471 | 0.0279885 | 1.553020 | 0.0279885 | 0.3404451 | Nitrogen metabolism | 12351/12319 |
| mmu04390 | 6 | 0.0382166 | 0.0354622 | 1.450235 | 0.0354622 | 0.4086500 | Hippo signaling pathway | 22420/22411/16842/11839/93960/238057 |
| mmu05030 | 3 | 0.0625000 | 0.0382166 | 1.417748 | 0.0382166 | 0.4183712 | Cocaine addiction | 109731/14677/14812 |
kegg_dot[[p]]
upset[[p]]
q=1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000027009 | Itga4 | 2.074185 | 0.0002323 | 0.0204195 | integrin alpha 4 [Source:MGI Symbol;Acc:MGI:96603] |
| ENSMUSG00000057614 | Gnai1 | 2.405667 | 0.0006615 | 0.0368704 | guanine nucleotide binding protein (G protein), alpha inhibiting 1 [Source:MGI Symbol;Acc:MGI:95771] |
| ENSMUSG00000031740 | Mmp2 | 2.270956 | 0.0009560 | 0.0456079 | matrix metallopeptidase 2 [Source:MGI Symbol;Acc:MGI:97009] |
| ENSMUSG00000061353 | Cxcl12 | 2.574792 | 0.0009762 | 0.0460594 | chemokine (C-X-C motif) ligand 12 [Source:MGI Symbol;Acc:MGI:103556] |
q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000027009 | Itga4 | 2.074185 | 0.0002323 | 0.0204195 | integrin alpha 4 [Source:MGI Symbol;Acc:MGI:96603] |
| ENSMUSG00000002033 | Cd3g | 3.645674 | 0.0005422 | 0.0332987 | CD3 antigen, gamma polypeptide [Source:MGI Symbol;Acc:MGI:88333] |
| ENSMUSG00000005087 | Cd44 | 2.271713 | 0.0005912 | 0.0346913 | CD44 antigen [Source:MGI Symbol;Acc:MGI:88338] |
q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000022683 | Pla2g10 | 5.773220 | 0.0000322 | 0.0076044 | phospholipase A2, group X [Source:MGI Symbol;Acc:MGI:1347522] |
| ENSMUSG00000045875 | Adra1a | 4.131590 | 0.0001383 | 0.0158943 | adrenergic receptor, alpha 1a [Source:MGI Symbol;Acc:MGI:104773] |
| ENSMUSG00000030669 | Calca | 5.762174 | 0.0005474 | 0.0333098 | calcitonin/calcitonin-related polypeptide, alpha [Source:MGI Symbol;Acc:MGI:2151253] |
| ENSMUSG00000027524 | Edn3 | 3.849271 | 0.0006811 | 0.0374735 | endothelin 3 [Source:MGI Symbol;Acc:MGI:95285] |
q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000028864 | Hgf | 4.125312 | 0.0000135 | 0.0045661 | hepatocyte growth factor [Source:MGI Symbol;Acc:MGI:96079] |
| ENSMUSG00000022309 | Angpt1 | 3.388586 | 0.0000423 | 0.0085432 | angiopoietin 1 [Source:MGI Symbol;Acc:MGI:108448] |
| ENSMUSG00000031273 | Col4a6 | 3.466810 | 0.0001389 | 0.0158943 | collagen, type IV, alpha 6 [Source:MGI Symbol;Acc:MGI:2152695] |
| ENSMUSG00000020053 | Igf1 | 2.780445 | 0.0001735 | 0.0173062 | insulin-like growth factor 1 [Source:MGI Symbol;Acc:MGI:96432] |
| ENSMUSG00000026840 | Lamc3 | 3.803842 | 0.0002111 | 0.0190302 | laminin gamma 3 [Source:MGI Symbol;Acc:MGI:1344394] |
| ENSMUSG00000029378 | Areg | 5.246523 | 0.0002264 | 0.0200946 | amphiregulin [Source:MGI Symbol;Acc:MGI:88068] |
| ENSMUSG00000027009 | Itga4 | 2.074185 | 0.0002323 | 0.0204195 | integrin alpha 4 [Source:MGI Symbol;Acc:MGI:96603] |
| ENSMUSG00000062960 | Kdr | 2.045643 | 0.0003273 | 0.0254005 | kinase insert domain protein receptor [Source:MGI Symbol;Acc:MGI:96683] |
| ENSMUSG00000028978 | Nos3 | 2.148682 | 0.0005850 | 0.0346913 | nitric oxide synthase 3, endothelial cell [Source:MGI Symbol;Acc:MGI:97362] |
| ENSMUSG00000028626 | Col9a2 | 4.129759 | 0.0007333 | 0.0389401 | collagen, type IX, alpha 2 [Source:MGI Symbol;Acc:MGI:88466] |
| ENSMUSG00000019846 | Lama4 | 1.940280 | 0.0010516 | 0.0475346 | laminin, alpha 4 [Source:MGI Symbol;Acc:MGI:109321] |
q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000028864 | Hgf | 4.125312 | 0.0000135 | 0.0045661 | hepatocyte growth factor [Source:MGI Symbol;Acc:MGI:96079] |
| ENSMUSG00000031273 | Col4a6 | 3.466810 | 0.0001389 | 0.0158943 | collagen, type IV, alpha 6 [Source:MGI Symbol;Acc:MGI:2152695] |
| ENSMUSG00000020053 | Igf1 | 2.780445 | 0.0001735 | 0.0173062 | insulin-like growth factor 1 [Source:MGI Symbol;Acc:MGI:96432] |
| ENSMUSG00000026840 | Lamc3 | 3.803842 | 0.0002111 | 0.0190302 | laminin gamma 3 [Source:MGI Symbol;Acc:MGI:1344394] |
| ENSMUSG00000027009 | Itga4 | 2.074185 | 0.0002323 | 0.0204195 | integrin alpha 4 [Source:MGI Symbol;Acc:MGI:96603] |
| ENSMUSG00000062960 | Kdr | 2.045643 | 0.0003273 | 0.0254005 | kinase insert domain protein receptor [Source:MGI Symbol;Acc:MGI:96683] |
| ENSMUSG00000028626 | Col9a2 | 4.129759 | 0.0007333 | 0.0389401 | collagen, type IX, alpha 2 [Source:MGI Symbol;Acc:MGI:88466] |
| ENSMUSG00000019846 | Lama4 | 1.940280 | 0.0010516 | 0.0475346 | laminin, alpha 4 [Source:MGI Symbol;Acc:MGI:109321] |
q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000029375 | Cxcl15 | 6.916834 | 0.0000000 | 0.0002795 | chemokine (C-X-C motif) ligand 15 [Source:MGI Symbol;Acc:MGI:1339941] |
| ENSMUSG00000034457 | Eda2r | 3.524309 | 0.0001283 | 0.0153427 | ectodysplasin A2 receptor [Source:MGI Symbol;Acc:MGI:2442860] |
| ENSMUSG00000061353 | Cxcl12 | 2.574792 | 0.0009762 | 0.0460594 | chemokine (C-X-C motif) ligand 12 [Source:MGI Symbol;Acc:MGI:103556] |
| ENSMUSG00000037660 | Gdf7 | 3.410398 | 0.0010346 | 0.0472634 | growth differentiation factor 7 [Source:MGI Symbol;Acc:MGI:95690] |
Export Data
# save to csv
writexl::write_xlsx(x = enrichKEGG_all, here::here("3_output/enrichKEGG_all.xlsx"))
writexl::write_xlsx(x = enrichKEGG_sig, here::here("3_output/enrichKEGG_sig.xlsx"))
sessionInfo()R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=English_Australia.utf8 LC_CTYPE=English_Australia.utf8
[3] LC_MONETARY=English_Australia.utf8 LC_NUMERIC=C
[5] LC_TIME=English_Australia.utf8
attached base packages:
[1] stats4 grid stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] pathview_1.36.1 enrichplot_1.16.2 org.Mm.eg.db_3.15.0
[4] AnnotationDbi_1.58.0 IRanges_2.30.1 S4Vectors_0.34.0
[7] Biobase_2.56.0 BiocGenerics_0.42.0 clusterProfiler_4.4.4
[10] Glimma_2.6.0 edgeR_3.38.4 limma_3.52.4
[13] ggrepel_0.9.1 ggbiplot_0.55 scales_1.2.1
[16] plyr_1.8.7 ggpubr_0.4.0 ggplotify_0.1.0
[19] pheatmap_1.0.12 cowplot_1.1.1 viridis_0.6.2
[22] viridisLite_0.4.1 pander_0.6.5 kableExtra_1.3.4
[25] KEGGREST_1.36.3 forcats_0.5.2 stringr_1.4.1
[28] purrr_0.3.5 tidyr_1.2.1 ggplot2_3.3.6
[31] tidyverse_1.3.2 reshape2_1.4.4 tibble_3.1.8
[34] readr_2.1.3 magrittr_2.0.3 dplyr_1.0.10
loaded via a namespace (and not attached):
[1] utf8_1.2.2 tidyselect_1.2.0
[3] RSQLite_2.2.18 htmlwidgets_1.5.4
[5] BiocParallel_1.30.3 scatterpie_0.1.8
[7] munsell_0.5.0 ragg_1.2.3
[9] codetools_0.2-18 withr_2.5.0
[11] colorspace_2.0-3 GOSemSim_2.22.0
[13] highr_0.9 knitr_1.40
[15] rstudioapi_0.14 ggsignif_0.6.3
[17] DOSE_3.22.1 labeling_0.4.2
[19] MatrixGenerics_1.8.1 KEGGgraph_1.56.0
[21] git2r_0.30.1 GenomeInfoDbData_1.2.8
[23] polyclip_1.10-0 bit64_4.0.5
[25] farver_2.1.1 rprojroot_2.0.3
[27] downloader_0.4 treeio_1.20.2
[29] vctrs_0.4.2 generics_0.1.3
[31] xfun_0.33 R6_2.5.1
[33] GenomeInfoDb_1.32.4 graphlayouts_0.8.2
[35] locfit_1.5-9.6 bitops_1.0-7
[37] cachem_1.0.6 fgsea_1.22.0
[39] gridGraphics_0.5-1 DelayedArray_0.22.0
[41] assertthat_0.2.1 promises_1.2.0.1
[43] ggraph_2.1.0 googlesheets4_1.0.1
[45] gtable_0.3.1 tidygraph_1.2.2
[47] workflowr_1.7.0 rlang_1.0.6
[49] genefilter_1.78.0 systemfonts_1.0.4
[51] splines_4.2.1 lazyeval_0.2.2
[53] rstatix_0.7.0 gargle_1.2.1
[55] broom_1.0.1 yaml_2.3.5
[57] abind_1.4-5 modelr_0.1.9
[59] backports_1.4.1 httpuv_1.6.6
[61] qvalue_2.28.0 tools_4.2.1
[63] ellipsis_0.3.2 jquerylib_0.1.4
[65] RColorBrewer_1.1-3 Rcpp_1.0.9
[67] zlibbioc_1.42.0 RCurl_1.98-1.9
[69] SummarizedExperiment_1.26.1 haven_2.5.1
[71] here_1.0.1 fs_1.5.2
[73] data.table_1.14.2 DO.db_2.9
[75] reprex_2.0.2 googledrive_2.0.0
[77] matrixStats_0.62.0 hms_1.1.2
[79] patchwork_1.1.2 evaluate_0.17
[81] xtable_1.8-4 XML_3.99-0.11
[83] readxl_1.4.1 gridExtra_2.3
[85] ggupset_0.3.0 compiler_4.2.1
[87] writexl_1.4.0 shadowtext_0.1.2
[89] crayon_1.5.2 htmltools_0.5.3
[91] ggfun_0.0.7 later_1.3.0
[93] tzdb_0.3.0 geneplotter_1.74.0
[95] aplot_0.1.8 lubridate_1.8.0
[97] DBI_1.1.3 tweenr_2.0.2
[99] dbplyr_2.2.1 MASS_7.3-57
[101] Matrix_1.5-1 car_3.1-0
[103] cli_3.4.1 parallel_4.2.1
[105] igraph_1.3.5 GenomicRanges_1.48.0
[107] pkgconfig_2.0.3 xml2_1.3.3
[109] ggtree_3.4.4 svglite_2.1.0
[111] annotate_1.74.0 bslib_0.4.0
[113] webshot_0.5.4 XVector_0.36.0
[115] rvest_1.0.3 yulab.utils_0.0.5
[117] digest_0.6.29 graph_1.74.0
[119] Biostrings_2.64.1 rmarkdown_2.17
[121] cellranger_1.1.0 fastmatch_1.1-3
[123] tidytree_0.4.1 curl_4.3.3
[125] nlme_3.1-157 lifecycle_1.0.3
[127] jsonlite_1.8.2 carData_3.0-5
[129] fansi_1.0.3 pillar_1.8.1
[131] lattice_0.20-45 fastmap_1.1.0
[133] httr_1.4.4 survival_3.3-1
[135] GO.db_3.15.0 glue_1.6.2
[137] png_0.1-7 Rgraphviz_2.40.0
[139] bit_4.0.4 ggforce_0.4.1
[141] stringi_1.7.8 sass_0.4.2
[143] blob_1.2.3 textshaping_0.3.6
[145] org.Hs.eg.db_3.15.0 DESeq2_1.36.0
[147] memoise_2.0.1 ape_5.6-2