- Data Setup
- Import DGElist Data
- KEGG Analysis
- Pathway specific heatmaps
- Export Data
KEGG Analysis
Ha M. Tran
22/08/2021
Last updated: 2023-01-22
Checks: 7 0
Knit directory: SRB_2022/1_analysis/
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| Rmd | b6cf190 | tranmanhha135 | 2023-01-19 | quick commit |
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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]]$entrezid,
keyType = "kegg",
organism = "mmu",
pvalueCutoff = 0.05,
pAdjustMethod = "none"
)
enrichKEGG[[x]] <- enrichKEGG[[x]] %>%
clusterProfiler::setReadable(OrgDb = org.Mm.eg.db, keyType = "ENTREZID")
enrichKEGG_all[[x]] <- enrichKEGG[[x]]@result
# filter the significant and print top 30
enrichKEGG_sig[[x]] <- enrichKEGG_all[[x]] %>%
dplyr::filter(pvalue <= 0.05) %>%
separate(col = BgRatio, sep = "/", into = c("Total", "Universe")) %>%
dplyr::mutate(
logPval = -log(pvalue, 10),
GeneRatio = Count / as.numeric(Total)
) %>%
dplyr::select(c("Description", "GeneRatio", "pvalue", "logPval", "p.adjust", "qvalue", "geneID", "Count"))
# # at the beginnning of a word (after 35 characters), add a newline. shorten the y axis for dot plot
# enrichKEGG_sig[[x]]$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]] %>%
dplyr::mutate_if(is.numeric, funs(as.character(signif(.,3)))) %>%
kable(caption = "Significantly enriched KEGG pathways") %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Description | GeneRatio | pvalue | logPval | p.adjust | qvalue | geneID | Count | |
|---|---|---|---|---|---|---|---|---|
| mmu04713 | Circadian entrainment | 0.245 | 1.14e-08 | 7.94 | 1.14e-08 | 2.46e-06 | Kcnj3/Gria4/Cacna1c/Ryr1/Gnai1/Gucy1a2/Grin2b/Adcy3/Gngt2/Plcb1/Gucy1b1/Gucy1a1/Adcy4/Adcy7/Gng11/Gng2/Adcyap1r1/Rps6ka5/Plcb2/Ryr3/Cacna1h/Gnb5/Gng7/Gnb4 | 24 |
| mmu04514 | Cell adhesion molecules | 0.187 | 2.01e-08 | 7.7 | 2.01e-08 | 2.46e-06 | Itga4/Lrrc4c/Ptprd/Nlgn1/Cdh2/Itgb7/Lrrc4b/Icam1/Jam3/Cldn8/Slitrk3/Ptprm/Cdh5/Cd226/Itgal/Esam/H2-Ab1/Nlgn3/Nfasc/H2-Ob/Sele/Pecam1/H2-Eb1/Neo1/Cldn5/H2-Aa/Ntng1/Itga8/Spn/Cldn1/Cd4/Vcan/Nlgn2/Jam2 | 34 |
| mmu04724 | Glutamatergic synapse | 0.212 | 2.13e-07 | 6.67 | 2.13e-07 | 1.74e-05 | Slc1a3/Kcnj3/Gria4/Cacna1c/Grik1/Gnai1/Grin2b/Adcy3/Shank2/Gngt2/Plcb1/Adcy4/Adcy7/Gng11/Grik2/Gng2/Plcb2/Slc38a1/Dlg4/Gnb5/Gng7/Gnb4/Cacna1a/Pld2 | 24 |
| mmu04371 | Apelin signaling pathway | 0.19 | 6.91e-07 | 6.16 | 6.91e-07 | 4.24e-05 | Ryr1/Slc8a1/Nos3/Gnai1/Mef2c/Adcy3/Gngt2/Pik3r6/Plcb1/Slc8a3/Adcy4/Adcy7/Gng11/Aplnr/Agtr1a/Gng2/Myl3/Plcb2/Ryr3/Akt3/Ccn2/Gnb5/Gng7/Apln/Gnb4/Lipe | 26 |
| mmu05414 | Dilated cardiomyopathy | 0.213 | 2.13e-06 | 5.67 | 2.13e-06 | 0.000104 | Cacna1c/Sgcd/Itga4/Igf1/Slc8a1/Itgb7/Cacna2d1/Adcy3/Itga1/Slc8a3/Adcy4/Adcy7/Lama2/Itga7/Myl3/Cacng7/Sgcb/Itga8/Itgb4/Cacnb4 | 20 |
| mmu04340 | Hedgehog signaling pathway | 0.259 | 3.13e-06 | 5.5 | 3.13e-06 | 0.000112 | Gli1/Ihh/Hhip/Evc2/Ptch2/Evc/Kif7/Ccnd2/Gli3/Lrp2/Gpr161/Arrb1/Arrb2/Ptch1/Iqce | 15 |
| mmu04015 | Rap1 signaling pathway | 0.154 | 3.19e-06 | 5.5 | 3.19e-06 | 0.000112 | Hgf/Angpt1/Kdr/Igf1/Evl/Rasgrp3/Gnai1/Pfn2/Lpar4/Grin2b/Prkd1/Adcy3/Tek/Plcb1/Rasgrp2/Kit/Adcy4/Adcy7/Itgal/Vegfc/Magi2/Pard6g/Kitl/Arap3/Tln2/Plcb2/Akt3/Apbb1ip/Lat/Pdgfrb/Lcp2/F2r/Sipa1 | 33 |
| mmu05032 | Morphine addiction | 0.209 | 5.13e-06 | 5.29 | 5.13e-06 | 0.000157 | Kcnj3/Gnai1/Pde1b/Adcy3/Gngt2/Adcy4/Adcy7/Gabra4/Gng11/Pde1a/Gng2/Arrb1/Arrb2/Gnb5/Gng7/Gnb4/Gabbr1/Pde8a/Cacna1a | 19 |
| mmu04022 | cGMP-PKG signaling pathway | 0.162 | 6.96e-06 | 5.16 | 6.96e-06 | 0.000179 | Cacna1c/Adra1a/Slc8a1/Nos3/Gnai1/Ednrb/Mef2c/Gucy1a2/Adcy3/Pik3r6/Plcb1/Slc8a3/Trpc6/Gucy1b1/Gucy1a1/Adcy4/Adcy7/Agtr1a/Kcnma1/Ednra/Bdkrb2/Nfatc4/Plcb2/Pde5a/Akt3/Atp2b4/Atp1a2/Irs1 | 28 |
| mmu05412 | Arrhythmogenic right ventricular cardiomyopathy | 0.221 | 7.29e-06 | 5.14 | 7.29e-06 | 0.000179 | Cacna1c/Lef1/Sgcd/Itga4/Slc8a1/Cdh2/Itgb7/Cacna2d1/Itga1/Slc8a3/Lama2/Itga7/Cacng7/Sgcb/Itga8/Itgb4/Cacnb4 | 17 |
| mmu04512 | ECM-receptor interaction | 0.205 | 1.23e-05 | 4.91 | 1.23e-05 | 0.000273 | Itga4/Col4a6/Thbs3/Npnt/Cd44/Lamc3/Lama4/Itgb7/Fn1/Itga1/Col9a2/Frem1/Lama2/Itga7/Sv2c/Itga8/Itgb4/Col4a5 | 18 |
| mmu04020 | Calcium signaling pathway | 0.142 | 1.5e-05 | 4.82 | 1.5e-05 | 0.000307 | Hgf/Cacna1c/Kdr/Ryr1/Adra1a/Slc8a1/Nos3/P2rx2/Ednrb/Pde1b/Adcy3/Cacna1e/Ptgfr/Plcb1/Slc8a3/Adcy4/Adcy7/Vegfc/Cd38/Agtr1a/Pde1a/Ednra/Bdkrb2/Htr2a/Plcb2/Asph/Ryr3/Cacna1h/Ptger3/Atp2b4/Pdgfrb/Cacna1a/F2r/Camk1 | 34 |
| mmu04924 | Renin secretion | 0.211 | 2.55e-05 | 4.59 | 2.55e-05 | 0.00048 | Cacna1c/Gnai1/Gucy1a2/Pde1b/Edn3/Plcb1/Gucy1b1/Gucy1a1/Agtr1a/Pde1a/Kcnma1/Ednra/Adcyap1r1/Plcb2/Clca2/Ptger2 | 16 |
| mmu04926 | Relaxin signaling pathway | 0.171 | 2.92e-05 | 4.54 | 2.92e-05 | 0.000511 | Col4a6/Nos3/Gnai1/Ednrb/Mmp2/Shc3/Adcy3/Gngt2/Plcb1/Adcy4/Adcy7/Gng11/Vegfc/Gng2/Arrb1/Plcb2/Arrb2/Akt3/Gnb5/Gng7/Gnb4/Col4a5 | 22 |
| mmu04725 | Cholinergic synapse | 0.179 | 3.38e-05 | 4.47 | 3.38e-05 | 0.000552 | Kcnj3/Cacna1c/Gnai1/Kcnq5/Adcy3/Gngt2/Pik3r6/Plcb1/Adcy4/Adcy7/Gng11/Gng2/Plcb2/Fyn/Akt3/Gnb5/Gng7/Gnb4/Kcnq4/Cacna1a | 20 |
| mmu04510 | Focal adhesion | 0.144 | 4.52e-05 | 4.35 | 4.52e-05 | 0.000658 | Hgf/Itga4/Kdr/Igf1/Col4a6/Thbs3/Lamc3/Lama4/Ccnd2/Itgb7/Fn1/Shc3/Pip5k1b/Itga1/Col9a2/Lama2/Vegfc/Itga7/Parvg/Parvb/Flnc/Tln2/Fyn/Akt3/Pdgfrb/Cav1/Itga8/Itgb4/Col4a5 | 29 |
| mmu04360 | Axon guidance | 0.149 | 4.56e-05 | 4.34 | 4.56e-05 | 0.000658 | Epha8/Efnb3/Sema5a/Lrrc4c/Dcc/Plxnb1/Sema5b/Nrp1/Sema7a/Gnai1/Cxcl12/Trpc6/Gdf7/Epha3/Sema3g/Pard6g/Nfatc4/Epha7/Neo1/Ptch1/Fyn/Unc5c/Ngef/Sema6a/Ntng1/Bmp7/Slit3 | 27 |
| mmu04014 | Ras signaling pathway | 0.136 | 5.9e-05 | 4.23 | 5.9e-05 | 0.000772 | Hgf/Angpt1/Pla2g10/Kdr/Igf1/Ets1/Rasgrp3/Shc3/Rasa3/Grin2b/Tek/Gngt2/Rasgrp2/Flt3/Kit/Gng11/Vegfc/Igf2/Gng2/Kitl/Pla1a/Akt3/Gnb5/Gng7/Ets2/Syngap1/Zap70/Gnb4/Lat/Pdgfrb/Pld2/Rasal3 | 32 |
| mmu04728 | Dopaminergic synapse | 0.163 | 5.98e-05 | 4.22 | 5.98e-05 | 0.000772 | Kcnj3/Gria4/Cacna1c/Maob/Drd4/Gnai1/Scn1a/Grin2b/Maoa/Gngt2/Plcb1/Gng11/Gng2/Arrb1/Plcb2/Arrb2/Akt3/Gnb5/Gng7/Gnb4/Cacna1a/Kif5a | 22 |
| mmu04974 | Protein digestion and absorption | 0.176 | 6.53e-05 | 4.19 | 6.53e-05 | 0.000801 | Col11a1/Col26a1/Col14a1/Col4a6/Slc8a1/Pga5/Col16a1/Slc36a4/Slc8a3/Col9a2/Col13a1/Mme/Col5a2/Col15a1/Atp1a2/Slc7a7/Col23a1/Col18a1/Col4a5 | 19 |
| mmu05410 | Hypertrophic cardiomyopathy | 0.187 | 7.22e-05 | 4.14 | 7.22e-05 | 0.000843 | Cacna1c/Sgcd/Itga4/Igf1/Slc8a1/Itgb7/Cacna2d1/Itga1/Slc8a3/Lama2/Itga7/Myl3/Cacng7/Sgcb/Itga8/Itgb4/Cacnb4 | 17 |
| mmu04151 | PI3K-Akt signaling pathway | 0.12 | 7.81e-05 | 4.11 | 7.81e-05 | 0.00087 | Hgf/Angpt1/Itga4/Kdr/Igf1/Col4a6/Thbs3/Nos3/Lamc3/Lama4/Ccnd2/Itgb7/Fn1/Areg/Lpar4/Tek/Gngt2/Pik3r6/Itga1/Col9a2/Flt3/Kit/Gng11/Lama2/Vegfc/Magi2/Igf2/Gng2/Itga7/Kitl/Akt3/Gnb5/Gng7/Gnb4/Pdgfrb/Il2rg/Itga8/Itgb4/F2r/Il7r/Myc/Col4a5/Irs1 | 43 |
| mmu04970 | Salivary secretion | 0.188 | 0.000107 | 3.97 | 0.000107 | 0.00112 | Adra1a/Gucy1a2/Adcy3/Plcb1/Gucy1b1/Gucy1a1/Adcy4/Adcy7/Cd38/Lyz2/Kcnma1/Plcb2/Ryr3/Lyz1/Atp2b4/Atp1a2 | 16 |
| mmu04640 | Hematopoietic cell lineage | 0.181 | 0.00011 | 3.96 | 0.00011 | 0.00112 | Itga4/Cd44/Il11ra1/Cd3g/Itga1/Flt3/Cd1d1/Kit/Mme/H2-Ab1/Cd38/H2-Ob/Kitl/H2-Eb1/H2-Aa/Il7r/Cd4 | 17 |
| mmu04062 | Chemokine signaling pathway | 0.141 | 0.000128 | 3.89 | 0.000128 | 0.00126 | Cxcl15/Gnai1/Shc3/Itk/Adcy3/Cxcr3/Cxcl12/Gngt2/Pik3r6/Plcb1/Dock2/Rasgrp2/Adcy4/Adcy7/Gng11/Gng2/Xcl1/Arrb1/Plcb2/Arrb2/Stat5b/Xcr1/Fgr/Akt3/Gnb5/Gng7/Gnb4 | 27 |
| mmu04727 | GABAergic synapse | 0.18 | 0.000187 | 3.73 | 0.000187 | 0.00177 | Cacna1c/Abat/Gnai1/Adcy3/Gngt2/Adcy4/Adcy7/Gabra4/Gng11/Gng2/Slc38a1/Gnb5/Gng7/Gnb4/Gabbr1/Cacna1a | 16 |
| mmu00514 | Other types of O-glycan biosynthesis | 0.233 | 0.00036 | 3.44 | 0.00036 | 0.00327 | St6gal2/Gxylt2/B4galt2/Galnt16/Lfng/Eogt/Galntl6/Pomt2/Mfng/Galnt18 | 10 |
| mmu04921 | Oxytocin signaling pathway | 0.144 | 0.000386 | 3.41 | 0.000386 | 0.00338 | Kcnj3/Cacna1c/Ryr1/Nos3/Gnai1/Cacna2d1/Mef2c/Gucy1a2/Adcy3/Pik3r6/Plcb1/Gucy1b1/Gucy1a1/Adcy4/Adcy7/Cd38/Nfatc4/Cacng7/Plcb2/Ryr3/Cacnb4/Camk1 | 22 |
| mmu04330 | Notch signaling pathway | 0.2 | 0.000429 | 3.37 | 0.000429 | 0.00362 | Aph1b/Lfng/Jag2/Heyl/Dtx3/Tle1/Mfng/Psen1/Maml3/Tle2/Hey2/Numbl | 12 |
| mmu04670 | Leukocyte transendothelial migration | 0.153 | 0.000629 | 3.2 | 0.000629 | 0.00514 | Itga4/Gnai1/Mmp2/Icam1/Itk/Jam3/Cxcl12/Cldn8/Cdh5/Thy1/Msn/Itgal/Esam/Pecam1/Cldn5/Cldn1/Sipa1/Jam2 | 18 |
| mmu04072 | Phospholipase D signaling pathway | 0.141 | 0.000681 | 3.17 | 0.000681 | 0.00539 | Shc3/Pip5k1b/Lpar4/Adcy3/Ptgfr/Pik3r6/Plcb1/Plpp3/Kit/Adcy4/Adcy7/Dgkb/Agtr1a/Kitl/Plcb2/Fyn/Akt3/Plpp1/Pdgfrb/Pld2/F2r | 21 |
| mmu04310 | Wnt signaling pathway | 0.135 | 0.000752 | 3.12 | 0.000752 | 0.00576 | Sfrp2/Wnt6/Lef1/Apcdd1/Wnt11/Nkd1/Ccnd2/Plcb1/Peg12/Wnt9a/Znrf3/Prickle2/Daam2/Prickle1/Nfatc4/Plcb2/Tle1/Fzd2/Psen1/Nkd2/Tle2/Ror1/Myc | 23 |
| mmu04010 | MAPK signaling pathway | 0.116 | 0.000821 | 3.09 | 0.000821 | 0.0061 | Hgf/Cacna1c/Angpt1/Kdr/Igf1/Rasgrp3/Cacna2d1/Areg/Mef2c/Tek/Mapk8ip1/Cacna1e/Rasgrp2/Rps6ka2/Flt3/Kit/Vegfc/Igf2/Kitl/Rps6ka5/Arrb1/Cacng7/Flnc/Arrb2/Irak4/Cacna1h/Akt3/Pdgfrb/Map4k2/Cacna1a/Mknk2/Cacnb4/Myc/Ptpn7 | 34 |
| mmu04261 | Adrenergic signaling in cardiomyocytes | 0.135 | 0.00124 | 2.91 | 0.00124 | 0.00878 | Cacna1c/Adra1a/Slc8a1/Scn4b/Gnai1/Cacna2d1/Adcy3/Pik3r6/Plcb1/Slc8a3/Adcy4/Adcy7/Agtr1a/Myl3/Rps6ka5/Cacng7/Plcb2/Akt3/Atp2b4/Atp1a2/Cacnb4 | 21 |
| mmu04611 | Platelet activation | 0.144 | 0.00125 | 2.9 | 0.00125 | 0.00878 | Nos3/Gnai1/Gucy1a2/Adcy3/Pik3r6/Plcb1/Rasgrp2/Gucy1b1/Gucy1a1/Adcy4/Adcy7/Tln2/Plcb2/Fyn/Akt3/Apbb1ip/Lcp2/F2r | 18 |
| mmu04658 | Th1 and Th2 cell differentiation | 0.159 | 0.00163 | 2.79 | 0.00163 | 0.0111 | Cd3g/Jag2/H2-Ab1/H2-Ob/H2-Eb1/Stat5b/Nfkbie/H2-Aa/Zap70/Lat/Il12rb1/Il2rg/Maml3/Cd4 | 14 |
| mmu05205 | Proteoglycans in cancer | 0.122 | 0.00188 | 2.73 | 0.00188 | 0.0125 | Ihh/Hgf/Wnt6/Wnt11/Hoxd10/Kdr/Igf1/Hcls1/Cd44/Gpc3/Fn1/Mmp2/Ank2/Wnt9a/Msn/Igf2/Twist2/Flnc/Ptch1/Fzd2/Akt3/Cav1/Lum/Myc/Twist1 | 25 |
| mmu05217 | Basal cell carcinoma | 0.175 | 0.00236 | 2.63 | 0.00236 | 0.0152 | Gli1/Wnt6/Hhip/Lef1/Wnt11/Ptch2/Kif7/Gli3/Wnt9a/Ptch1/Fzd2 | 11 |
| mmu04024 | cAMP signaling pathway | 0.116 | 0.00309 | 2.51 | 0.00309 | 0.0194 | Gli1/Gria4/Cacna1c/Hhip/Vipr2/Gnai1/Grin2b/Adcy3/Edn3/Gli3/Htr1b/Adcy4/Adcy7/Ednra/Adcyap1r1/Arap3/Ptch1/Akt3/Ptger3/Atp2b4/Atp1a2/Gabbr1/Lipe/Pld2/F2r/Ptger2 | 26 |
| mmu04726 | Serotonergic synapse | 0.13 | 0.00512 | 2.29 | 0.00512 | 0.031 | Kcnj3/Cacna1c/Maob/Kcnd2/Gnai1/Maoa/Gngt2/Plcb1/Htr1b/Gng11/Gng2/Htr2a/Plcb2/Gnb5/Gng7/Gnb4/Cacna1a | 17 |
| mmu04730 | Long-term depression | 0.167 | 0.00519 | 2.28 | 0.00519 | 0.031 | Ryr1/Igf1/Gnai1/Gucy1a2/Plcb1/Gucy1b1/Gucy1a1/Plcb2/Gnaz/Cacna1a | 10 |
| mmu04916 | Melanogenesis | 0.14 | 0.00542 | 2.27 | 0.00542 | 0.0317 | Wnt6/Lef1/Wnt11/Gnai1/Ednrb/Adcy3/Plcb1/Wnt9a/Kit/Adcy4/Adcy7/Kitl/Plcb2/Fzd2 | 14 |
| mmu04933 | AGE-RAGE signaling pathway in diabetic complications | 0.139 | 0.00593 | 2.23 | 0.00593 | 0.0332 | Col4a6/Nos3/Fn1/Mmp2/Icam1/Plcb1/Vegfc/Agtr1a/Nox4/Sele/Plcb2/Stat5b/Akt3/Col4a5 | 14 |
| mmu02010 | ABC transporters | 0.173 | 0.00609 | 2.22 | 0.00609 | 0.0332 | Abcg2/Abca5/Abcg1/Abca8b/Abcd2/Abcb1a/Abcc5/Abcg3/Abcg4 | 9 |
| mmu04672 | Intestinal immune network for IgA production | 0.186 | 0.00609 | 2.22 | 0.00609 | 0.0332 | Itga4/Itgb7/Cxcl12/Tnfsf13b/H2-Ab1/H2-Ob/H2-Eb1/H2-Aa | 8 |
| mmu04925 | Aldosterone synthesis and secretion | 0.137 | 0.00647 | 2.19 | 0.00647 | 0.0345 | Kcnk3/Cacna1c/Prkd1/Adcy3/Plcb1/Adcy4/Adcy7/Agtr1a/Plcb2/Cacna1h/Atp2b4/Atp1a2/Lipe/Camk1 | 14 |
| mmu04742 | Taste transduction | 0.141 | 0.00669 | 2.17 | 0.00669 | 0.0349 | Cacna1c/P2rx2/Pde1b/Plcb1/Htr1b/Scn2a/Adcy4/Gabra4/Pde1a/Plcb2/Scn3a/Gabbr1/Cacna1a | 13 |
| mmu04540 | Gap junction | 0.14 | 0.00992 | 2 | 0.00992 | 0.0507 | Gnai1/Gucy1a2/Adcy3/Plcb1/Gucy1b1/Gucy1a1/Adcy4/Adcy7/Tubb4a/Htr2a/Plcb2/Pdgfrb | 12 |
| mmu00533 | Glycosaminoglycan biosynthesis - keratan sulfate | 0.286 | 0.0108 | 1.97 | 0.0108 | 0.0532 | Chst2/B4galt2/St3gal2/Chst1 | 4 |
| mmu05323 | Rheumatoid arthritis | 0.138 | 0.0108 | 1.96 | 0.0108 | 0.0532 | Angpt1/Icam1/Tek/Cxcl12/Tnfsf13b/Itgal/H2-Ab1/H2-Ob/Atp6v0e2/H2-Eb1/H2-Aa/Atp6v1b2 | 12 |
| mmu04270 | Vascular smooth muscle contraction | 0.118 | 0.0129 | 1.89 | 0.0129 | 0.062 | Cacna1c/Pla2g10/Adra1a/Gucy1a2/Adcy3/Edn3/Plcb1/Calca/Gucy1b1/Gucy1a1/Adcy4/Adcy7/Agtr1a/Kcnma1/Ednra/Plcb2/Calcrl | 17 |
| mmu00260 | Glycine, serine and threonine metabolism | 0.175 | 0.014 | 1.85 | 0.014 | 0.0645 | Maob/Cbs/Maoa/Gamt/Cth/Phgdh/Sardh | 7 |
| mmu00230 | Purine metabolism | 0.119 | 0.0141 | 1.85 | 0.0141 | 0.0645 | Nme4/Gucy1a2/Pde1b/Adcy3/Gucy1b1/Gucy1a1/Adcy4/Adcy7/Enpp1/Pde1a/Hddc3/Lacc1/Pde5a/Impdh1/Pde8a/Papss2 | 16 |
| mmu04390 | Hippo signaling pathway | 0.115 | 0.0142 | 1.85 | 0.0142 | 0.0645 | Wnt6/Lef1/Wnt11/Nkd1/Ccnd2/Areg/Gdf7/Wnt9a/Dlg2/Pard6g/Dlg4/Fzd2/Ccn2/Dlg5/Lats2/Nkd2/Bmp7/Myc | 18 |
| mmu04723 | Retrograde endocannabinoid signaling | 0.115 | 0.0166 | 1.78 | 0.0166 | 0.0739 | Kcnj3/Gria4/Cacna1c/Gnai1/Adcy3/Gngt2/Plcb1/Adcy4/Adcy7/Gabra4/Gng11/Gng2/Plcb2/Gnb5/Gng7/Gnb4/Cacna1a | 17 |
| mmu04927 | Cortisol synthesis and secretion | 0.139 | 0.0183 | 1.74 | 0.0183 | 0.0802 | Kcnk3/Cacna1c/Adcy3/Plcb1/Adcy4/Adcy7/Agtr1a/Plcb2/Cacna1h/Pde8a | 10 |
| mmu04659 | Th17 cell differentiation | 0.124 | 0.0193 | 1.71 | 0.0193 | 0.0831 | Cd3g/H2-Ab1/Il27ra/H2-Ob/H2-Eb1/Stat5b/Nfkbie/H2-Aa/Zap70/Lat/Il12rb1/Il2rg/Cd4 | 13 |
| mmu04929 | GnRH secretion | 0.143 | 0.0207 | 1.68 | 0.0207 | 0.0877 | Kcnj3/Cacna1c/Plcb1/Arrb1/Plcb2/Arrb2/Cacna1h/Akt3/Gabbr1 | 9 |
| mmu00601 | Glycosphingolipid biosynthesis - lacto and neolacto series | 0.192 | 0.0248 | 1.61 | 0.0248 | 0.103 | B4galt2/B3galnt1/Ggta1/B3gnt5/St3gal4 | 5 |
| mmu05100 | Bacterial invasion of epithelial cells | 0.132 | 0.0258 | 1.59 | 0.0258 | 0.105 | Hcls1/Fn1/Shc3/Septin3/Arhgap10/Arhgef26/Elmo2/Cav1/Actr3b/Septin6 | 10 |
| mmu04260 | Cardiac muscle contraction | 0.126 | 0.0261 | 1.58 | 0.0261 | 0.105 | Cacna1c/Slc8a1/Cacna2d1/Slc9a7/Slc8a3/Myl3/Cacng7/Asph/Cox4i2/Atp1a2/Cacnb4 | 11 |
| mmu05416 | Viral myocarditis | 0.125 | 0.0281 | 1.55 | 0.0281 | 0.111 | Sgcd/Icam1/Lama2/Itgal/H2-Ab1/H2-Ob/H2-Eb1/Fyn/H2-Aa/Sgcb/Cav1 | 11 |
| mmu04810 | Regulation of actin cytoskeleton | 0.0996 | 0.029 | 1.54 | 0.029 | 0.113 | Itga4/Itgb7/Fn1/Pip5k1b/Pfn2/Lpar4/Cxcl12/Itga1/Msn/Abi2/Itgal/Itga7/Scin/Nckap1l/Bdkrb2/Fgd1/Akt3/Pdgfrb/Cyfip2/Actr3b/Itga8/Itgb4/F2r | 23 |
| mmu04923 | Regulation of lipolysis in adipocytes | 0.14 | 0.0312 | 1.51 | 0.0312 | 0.12 | Gnai1/Adcy3/Adcy4/Adcy7/Akt3/Ptger3/Lipe/Irs1 | 8 |
| mmu00061 | Fatty acid biosynthesis | 0.211 | 0.0321 | 1.49 | 0.0321 | 0.121 | Acsl6/Acacb/Acsl1/Olah | 4 |
| mmu00565 | Ether lipid metabolism | 0.146 | 0.0354 | 1.45 | 0.0354 | 0.132 | Pla2g10/Plpp3/Lpcat1/Plpp1/Pld2/Enpp2/Pafah2 | 7 |
| mmu00062 | Fatty acid elongation | 0.172 | 0.0381 | 1.42 | 0.0381 | 0.139 | Elovl4/Them5/Echs1/Acot7/Hacd1 | 5 |
| mmu04961 | Endocrine and other factor-regulated calcium reabsorption | 0.131 | 0.0444 | 1.35 | 0.0444 | 0.16 | Slc8a1/Plcb1/Slc8a3/Pth1r/Bdkrb2/Plcb2/Atp2b4/Atp1a2 | 8 |
| mmu01212 | Fatty acid metabolism | 0.129 | 0.0482 | 1.32 | 0.0482 | 0.171 | Acsl6/Fads2/Fads1/Elovl4/Echs1/Cpt1c/Acsl1/Hacd1 | 8 |
| mmu04350 | TGF-beta signaling pathway | 0.115 | 0.0487 | 1.31 | 0.0487 | 0.171 | Nog/Fst/Id3/Id4/Gdf7/Tgif2/Smad9/Neo1/Zfyve9/Bmp7/Myc | 11 |
| mmu04928 | Parathyroid hormone synthesis, secretion and action | 0.111 | 0.0496 | 1.3 | 0.0496 | 0.171 | Mmp16/Gnai1/Mef2c/Adcy3/Plcb1/Pth1r/Adcy4/Adcy7/Arrb1/Plcb2/Arrb2/Pld2 | 12 |
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(1.5,5)) +
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]] + pub, path = here::here("2_plots/kegg/"),
width = 250, height = 130, 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/"),
width = 170, height = 130, units = "mm")
}
kegg_dot[[p]]
upset[[p]]
p=p+1enrichKEGG_sig[[p]] %>%
dplyr::mutate_if(is.numeric, funs(as.character(signif(.,3)))) %>%
kable(caption = "Significantly enriched KEGG pathways") %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Description | GeneRatio | pvalue | logPval | p.adjust | qvalue | geneID | Count | |
|---|---|---|---|---|---|---|---|---|
| mmu04713 | Circadian entrainment | 0.245 | 8.02e-10 | 9.1 | 8.02e-10 | 1.95e-07 | Kcnj3/Gria4/Cacna1c/Ryr1/Gnai1/Gucy1a2/Grin2b/Adcy3/Gngt2/Plcb1/Gucy1b1/Gucy1a1/Adcy4/Gng11/Adcy7/Adcyap1r1/Gng2/Rps6ka5/Plcb2/Ryr3/Cacna1h/Gng7/Gnb5/Gnb4 | 24 |
| mmu04371 | Apelin signaling pathway | 0.19 | 4.99e-08 | 7.3 | 4.99e-08 | 6.07e-06 | Ryr1/Nos3/Slc8a1/Gnai1/Mef2c/Adcy3/Gngt2/Pik3r6/Slc8a3/Plcb1/Adcy4/Gng11/Aplnr/Adcy7/Agtr1a/Myl3/Gng2/Plcb2/Ryr3/Ccn2/Apln/Gng7/Akt3/Gnb5/Gnb4/Lipe | 26 |
| mmu04724 | Glutamatergic synapse | 0.204 | 7.78e-08 | 7.11 | 7.78e-08 | 6.31e-06 | Kcnj3/Slc1a3/Gria4/Grik1/Cacna1c/Gnai1/Grin2b/Adcy3/Shank2/Gngt2/Plcb1/Adcy4/Gng11/Adcy7/Grik2/Gng2/Plcb2/Slc38a1/Dlg4/Gng7/Gnb5/Gnb4/Cacna1a | 23 |
| mmu05414 | Dilated cardiomyopathy | 0.213 | 2.58e-07 | 6.59 | 2.58e-07 | 1.57e-05 | Sgcd/Cacna1c/Itga4/Igf1/Slc8a1/Itgb7/Cacna2d1/Adcy3/Slc8a3/Itga1/Adcy4/Lama2/Adcy7/Itga7/Myl3/Cacng7/Sgcb/Itga8/Itgb4/Cacnb4 | 20 |
| mmu04514 | Cell adhesion molecules | 0.159 | 4.43e-07 | 6.35 | 4.43e-07 | 2.16e-05 | Itga4/Lrrc4c/Ptprd/Nlgn1/Cdh2/Lrrc4b/Itgb7/Icam1/Jam3/Cldn8/Slitrk3/Cdh5/Ptprm/Cd226/Nlgn3/Esam/Itgal/H2-Ab1/Nfasc/Sele/H2-Ob/Pecam1/H2-Eb1/Cldn5/Neo1/H2-Aa/Ntng1/Itga8/Cldn1 | 29 |
| mmu05412 | Arrhythmogenic right ventricular cardiomyopathy | 0.221 | 1.19e-06 | 5.93 | 1.19e-06 | 4.81e-05 | Lef1/Sgcd/Cacna1c/Itga4/Slc8a1/Cdh2/Itgb7/Cacna2d1/Slc8a3/Itga1/Lama2/Itga7/Cacng7/Sgcb/Itga8/Itgb4/Cacnb4 | 17 |
| mmu04022 | cGMP-PKG signaling pathway | 0.156 | 1.68e-06 | 5.77 | 1.68e-06 | 5.85e-05 | Cacna1c/Adra1a/Nos3/Slc8a1/Gnai1/Ednrb/Mef2c/Gucy1a2/Adcy3/Pik3r6/Slc8a3/Plcb1/Gucy1b1/Trpc6/Gucy1a1/Adcy4/Adcy7/Agtr1a/Kcnma1/Ednra/Bdkrb2/Plcb2/Pde5a/Nfatc4/Atp2b4/Akt3/Atp1a2 | 27 |
| mmu05032 | Morphine addiction | 0.198 | 3.14e-06 | 5.5 | 3.14e-06 | 9.19e-05 | Kcnj3/Gnai1/Pde1b/Adcy3/Gngt2/Gabra4/Adcy4/Gng11/Adcy7/Pde1a/Gng2/Arrb1/Arrb2/Gng7/Gnb5/Gnb4/Gabbr1/Cacna1a | 18 |
| mmu04340 | Hedgehog signaling pathway | 0.241 | 3.4e-06 | 5.47 | 3.4e-06 | 9.19e-05 | Gli1/Ihh/Hhip/Evc2/Ptch2/Evc/Kif7/Ccnd2/Gli3/Lrp2/Gpr161/Arrb1/Ptch1/Arrb2 | 14 |
| mmu04725 | Cholinergic synapse | 0.179 | 4.74e-06 | 5.32 | 4.74e-06 | 0.000115 | Kcnj3/Cacna1c/Gnai1/Kcnq5/Adcy3/Gngt2/Pik3r6/Plcb1/Adcy4/Gng11/Adcy7/Gng2/Plcb2/Fyn/Gng7/Akt3/Gnb5/Gnb4/Kcnq4/Cacna1a | 20 |
| mmu04512 | ECM-receptor interaction | 0.193 | 8.23e-06 | 5.08 | 8.23e-06 | 0.000182 | Itga4/Col4a6/Npnt/Thbs3/Lamc3/Cd44/Lama4/Itgb7/Fn1/Itga1/Col9a2/Frem1/Lama2/Itga7/Sv2c/Itga8/Itgb4 | 17 |
| mmu04926 | Relaxin signaling pathway | 0.163 | 1.24e-05 | 4.91 | 1.24e-05 | 0.000213 | Col4a6/Nos3/Gnai1/Ednrb/Mmp2/Shc3/Adcy3/Gngt2/Plcb1/Adcy4/Gng11/Adcy7/Vegfc/Gng2/Arrb1/Plcb2/Arrb2/Gng7/Akt3/Gnb5/Gnb4 | 21 |
| mmu04015 | Rap1 signaling pathway | 0.136 | 1.25e-05 | 4.9 | 1.25e-05 | 0.000213 | Hgf/Angpt1/Kdr/Igf1/Evl/Rasgrp3/Gnai1/Pfn2/Grin2b/Lpar4/Prkd1/Tek/Adcy3/Plcb1/Rasgrp2/Adcy4/Kit/Adcy7/Itgal/Vegfc/Magi2/Arap3/Pard6g/Kitl/Plcb2/Tln2/Akt3/Lat/Apbb1ip | 29 |
| mmu04062 | Chemokine signaling pathway | 0.141 | 1.26e-05 | 4.9 | 1.26e-05 | 0.000213 | Cxcl15/Gnai1/Shc3/Itk/Cxcr3/Cxcl12/Adcy3/Gngt2/Pik3r6/Plcb1/Rasgrp2/Dock2/Adcy4/Gng11/Adcy7/Xcl1/Gng2/Arrb1/Plcb2/Xcr1/Arrb2/Gng7/Fgr/Stat5b/Akt3/Gnb5/Gnb4 | 27 |
| mmu05410 | Hypertrophic cardiomyopathy | 0.187 | 1.31e-05 | 4.88 | 1.31e-05 | 0.000213 | Sgcd/Cacna1c/Itga4/Igf1/Slc8a1/Itgb7/Cacna2d1/Slc8a3/Itga1/Lama2/Itga7/Myl3/Cacng7/Sgcb/Itga8/Itgb4/Cacnb4 | 17 |
| mmu04020 | Calcium signaling pathway | 0.129 | 1.67e-05 | 4.78 | 1.67e-05 | 0.000254 | Hgf/Cacna1c/Ryr1/Kdr/Adra1a/Nos3/Slc8a1/P2rx2/Ednrb/Pde1b/Adcy3/Cacna1e/Ptgfr/Slc8a3/Plcb1/Adcy4/Adcy7/Vegfc/Pde1a/Cd38/Agtr1a/Ednra/Bdkrb2/Htr2a/Plcb2/Asph/Ryr3/Cacna1h/Ptger3/Atp2b4/Cacna1a | 31 |
| mmu04970 | Salivary secretion | 0.188 | 2.13e-05 | 4.67 | 2.13e-05 | 0.000288 | Adra1a/Gucy1a2/Adcy3/Plcb1/Gucy1b1/Gucy1a1/Adcy4/Adcy7/Cd38/Lyz2/Kcnma1/Plcb2/Ryr3/Lyz1/Atp2b4/Atp1a2 | 16 |
| mmu04924 | Renin secretion | 0.197 | 2.13e-05 | 4.67 | 2.13e-05 | 0.000288 | Cacna1c/Gnai1/Gucy1a2/Pde1b/Edn3/Plcb1/Gucy1b1/Gucy1a1/Pde1a/Agtr1a/Kcnma1/Ednra/Adcyap1r1/Plcb2/Clca2 | 15 |
| mmu04728 | Dopaminergic synapse | 0.156 | 2.53e-05 | 4.6 | 2.53e-05 | 0.000323 | Kcnj3/Gria4/Maob/Cacna1c/Drd4/Gnai1/Scn1a/Grin2b/Maoa/Gngt2/Plcb1/Gng11/Gng2/Arrb1/Plcb2/Arrb2/Gng7/Akt3/Gnb5/Gnb4/Cacna1a | 21 |
| mmu04510 | Focal adhesion | 0.134 | 2.91e-05 | 4.54 | 2.91e-05 | 0.000354 | Hgf/Itga4/Kdr/Igf1/Col4a6/Thbs3/Lamc3/Lama4/Itgb7/Ccnd2/Fn1/Shc3/Pip5k1b/Itga1/Col9a2/Lama2/Vegfc/Parvg/Itga7/Parvb/Flnc/Tln2/Fyn/Akt3/Cav1/Itga8/Itgb4 | 27 |
| mmu04360 | Axon guidance | 0.138 | 3.58e-05 | 4.45 | 3.58e-05 | 0.000408 | Epha8/Efnb3/Sema5a/Lrrc4c/Dcc/Plxnb1/Sema5b/Sema7a/Nrp1/Gnai1/Cxcl12/Gdf7/Trpc6/Epha3/Sema3g/Pard6g/Epha7/Ptch1/Nfatc4/Neo1/Fyn/Unc5c/Sema6a/Ngef/Ntng1 | 25 |
| mmu04974 | Protein digestion and absorption | 0.167 | 3.72e-05 | 4.43 | 3.72e-05 | 0.000408 | Col11a1/Col26a1/Col14a1/Col4a6/Slc8a1/Pga5/Col16a1/Slc36a4/Slc8a3/Col9a2/Col13a1/Mme/Col5a2/Col15a1/Atp1a2/Col23a1/Slc7a7/Col18a1 | 18 |
| mmu04727 | GABAergic synapse | 0.18 | 3.86e-05 | 4.41 | 3.86e-05 | 0.000408 | Cacna1c/Abat/Gnai1/Adcy3/Gngt2/Gabra4/Adcy4/Gng11/Adcy7/Gng2/Slc38a1/Gng7/Gnb5/Gnb4/Gabbr1/Cacna1a | 16 |
| mmu04014 | Ras signaling pathway | 0.123 | 7.28e-05 | 4.14 | 7.28e-05 | 0.000737 | Hgf/Angpt1/Pla2g10/Kdr/Igf1/Rasgrp3/Ets1/Shc3/Rasa3/Grin2b/Tek/Gngt2/Rasgrp2/Flt3/Gng11/Kit/Vegfc/Igf2/Gng2/Pla1a/Kitl/Gng7/Ets2/Akt3/Zap70/Gnb5/Lat/Syngap1/Gnb4 | 29 |
| mmu04921 | Oxytocin signaling pathway | 0.137 | 0.000163 | 3.79 | 0.000163 | 0.00159 | Kcnj3/Cacna1c/Ryr1/Nos3/Gnai1/Cacna2d1/Mef2c/Gucy1a2/Adcy3/Pik3r6/Plcb1/Gucy1b1/Gucy1a1/Adcy4/Adcy7/Cd38/Cacng7/Plcb2/Ryr3/Nfatc4/Cacnb4 | 21 |
| mmu04261 | Adrenergic signaling in cardiomyocytes | 0.135 | 0.000215 | 3.67 | 0.000215 | 0.00201 | Cacna1c/Adra1a/Slc8a1/Scn4b/Gnai1/Cacna2d1/Adcy3/Pik3r6/Slc8a3/Plcb1/Adcy4/Adcy7/Agtr1a/Myl3/Rps6ka5/Cacng7/Plcb2/Atp2b4/Akt3/Atp1a2/Cacnb4 | 21 |
| mmu04640 | Hematopoietic cell lineage | 0.16 | 0.000269 | 3.57 | 0.000269 | 0.00242 | Itga4/Cd44/Il11ra1/Cd3g/Itga1/Flt3/Mme/Cd1d1/Kit/H2-Ab1/Cd38/H2-Ob/Kitl/H2-Eb1/H2-Aa | 15 |
| mmu04151 | PI3K-Akt signaling pathway | 0.103 | 0.000352 | 3.45 | 0.000352 | 0.00306 | Hgf/Angpt1/Itga4/Kdr/Igf1/Col4a6/Thbs3/Nos3/Lamc3/Lama4/Areg/Itgb7/Ccnd2/Fn1/Lpar4/Tek/Gngt2/Pik3r6/Itga1/Col9a2/Flt3/Gng11/Kit/Lama2/Vegfc/Magi2/Igf2/Itga7/Gng2/Kitl/Gng7/Akt3/Gnb5/Gnb4/Il2rg/Itga8/Itgb4 | 37 |
| mmu05217 | Basal cell carcinoma | 0.175 | 0.000802 | 3.1 | 0.000802 | 0.00673 | Gli1/Wnt6/Hhip/Lef1/Wnt11/Ptch2/Kif7/Gli3/Wnt9a/Ptch1/Fzd2 | 11 |
| mmu04670 | Leukocyte transendothelial migration | 0.136 | 0.00109 | 2.96 | 0.00109 | 0.00886 | Itga4/Gnai1/Mmp2/Icam1/Itk/Cxcl12/Jam3/Cldn8/Cdh5/Thy1/Msn/Esam/Itgal/Pecam1/Cldn5/Cldn1 | 16 |
| mmu04726 | Serotonergic synapse | 0.13 | 0.00127 | 2.9 | 0.00127 | 0.00998 | Kcnj3/Maob/Cacna1c/Kcnd2/Gnai1/Maoa/Gngt2/Plcb1/Htr1b/Gng11/Htr2a/Gng2/Plcb2/Gng7/Gnb5/Gnb4/Cacna1a | 17 |
| mmu04916 | Melanogenesis | 0.14 | 0.00161 | 2.79 | 0.00161 | 0.0122 | Wnt6/Lef1/Wnt11/Gnai1/Ednrb/Adcy3/Plcb1/Wnt9a/Adcy4/Kit/Adcy7/Kitl/Plcb2/Fzd2 | 14 |
| mmu04730 | Long-term depression | 0.167 | 0.00198 | 2.7 | 0.00198 | 0.0145 | Ryr1/Igf1/Gnai1/Gucy1a2/Plcb1/Gucy1b1/Gucy1a1/Plcb2/Gnaz/Cacna1a | 10 |
| mmu04611 | Platelet activation | 0.128 | 0.00202 | 2.69 | 0.00202 | 0.0145 | Nos3/Gnai1/Gucy1a2/Adcy3/Pik3r6/Plcb1/Rasgrp2/Gucy1b1/Gucy1a1/Adcy4/Adcy7/Plcb2/Tln2/Fyn/Akt3/Apbb1ip | 16 |
| mmu04072 | Phospholipase D signaling pathway | 0.121 | 0.00211 | 2.68 | 0.00211 | 0.0145 | Shc3/Lpar4/Pip5k1b/Adcy3/Ptgfr/Pik3r6/Plcb1/Plpp3/Adcy4/Kit/Adcy7/Dgkb/Agtr1a/Kitl/Plcb2/Fyn/Akt3/Plpp1 | 18 |
| mmu04742 | Taste transduction | 0.141 | 0.00215 | 2.67 | 0.00215 | 0.0145 | Cacna1c/P2rx2/Pde1b/Plcb1/Htr1b/Gabra4/Scn2a/Adcy4/Pde1a/Plcb2/Scn3a/Gabbr1/Cacna1a | 13 |
| mmu00514 | Other types of O-glycan biosynthesis | 0.186 | 0.0027 | 2.57 | 0.0027 | 0.0173 | St6gal2/Gxylt2/B4galt2/Galnt16/Lfng/Eogt/Galntl6/Mfng | 8 |
| mmu04672 | Intestinal immune network for IgA production | 0.186 | 0.0027 | 2.57 | 0.0027 | 0.0173 | Itga4/Itgb7/Cxcl12/Tnfsf13b/H2-Ab1/H2-Ob/H2-Eb1/H2-Aa | 8 |
| mmu04010 | MAPK signaling pathway | 0.0986 | 0.00291 | 2.54 | 0.00291 | 0.0181 | Hgf/Angpt1/Cacna1c/Kdr/Igf1/Rasgrp3/Areg/Cacna2d1/Mef2c/Tek/Mapk8ip1/Cacna1e/Rasgrp2/Rps6ka2/Flt3/Kit/Vegfc/Igf2/Rps6ka5/Kitl/Arrb1/Cacng7/Flnc/Irak4/Cacna1h/Arrb2/Akt3/Cacna1a/Cacnb4 | 29 |
| mmu05205 | Proteoglycans in cancer | 0.107 | 0.0033 | 2.48 | 0.0033 | 0.0201 | Ihh/Hgf/Wnt6/Wnt11/Hoxd10/Kdr/Igf1/Cd44/Hcls1/Gpc3/Fn1/Mmp2/Ank2/Wnt9a/Msn/Igf2/Twist2/Ptch1/Flnc/Fzd2/Akt3/Cav1 | 22 |
| mmu04270 | Vascular smooth muscle contraction | 0.118 | 0.00354 | 2.45 | 0.00354 | 0.021 | Cacna1c/Pla2g10/Adra1a/Gucy1a2/Adcy3/Edn3/Calca/Plcb1/Gucy1b1/Gucy1a1/Adcy4/Adcy7/Agtr1a/Kcnma1/Ednra/Plcb2/Calcrl | 17 |
| mmu04310 | Wnt signaling pathway | 0.111 | 0.00418 | 2.38 | 0.00418 | 0.0239 | Sfrp2/Wnt6/Lef1/Apcdd1/Wnt11/Nkd1/Ccnd2/Plcb1/Peg12/Wnt9a/Prickle2/Znrf3/Daam2/Prickle1/Tle1/Plcb2/Nfatc4/Fzd2/Nkd2 | 19 |
| mmu04658 | Th1 and Th2 cell differentiation | 0.136 | 0.00423 | 2.37 | 0.00423 | 0.0239 | Cd3g/Jag2/H2-Ab1/H2-Ob/H2-Eb1/Nfkbie/H2-Aa/Stat5b/Zap70/Lat/Il12rb1/Il2rg | 12 |
| mmu04024 | cAMP signaling pathway | 0.103 | 0.00468 | 2.33 | 0.00468 | 0.0253 | Gli1/Gria4/Hhip/Cacna1c/Vipr2/Gnai1/Grin2b/Adcy3/Edn3/Gli3/Htr1b/Adcy4/Adcy7/Ednra/Adcyap1r1/Arap3/Ptch1/Ptger3/Atp2b4/Akt3/Atp1a2/Gabbr1/Lipe | 23 |
| mmu04723 | Retrograde endocannabinoid signaling | 0.115 | 0.00469 | 2.33 | 0.00469 | 0.0253 | Kcnj3/Gria4/Cacna1c/Gnai1/Adcy3/Gngt2/Plcb1/Gabra4/Adcy4/Gng11/Adcy7/Gng2/Plcb2/Gng7/Gnb5/Gnb4/Cacna1a | 17 |
| mmu04933 | AGE-RAGE signaling pathway in diabetic complications | 0.129 | 0.00491 | 2.31 | 0.00491 | 0.026 | Col4a6/Nos3/Fn1/Mmp2/Icam1/Plcb1/Vegfc/Nox4/Sele/Agtr1a/Plcb2/Stat5b/Akt3 | 13 |
| mmu04925 | Aldosterone synthesis and secretion | 0.127 | 0.00534 | 2.27 | 0.00534 | 0.0276 | Kcnk3/Cacna1c/Prkd1/Adcy3/Plcb1/Adcy4/Adcy7/Agtr1a/Plcb2/Cacna1h/Atp2b4/Atp1a2/Lipe | 13 |
| mmu00533 | Glycosaminoglycan biosynthesis - keratan sulfate | 0.286 | 0.00674 | 2.17 | 0.00674 | 0.0341 | Chst2/B4galt2/St3gal2/Chst1 | 4 |
| mmu02010 | ABC transporters | 0.154 | 0.00893 | 2.05 | 0.00893 | 0.0443 | Abcg2/Abca5/Abcg1/Abca8b/Abcd2/Abcb1a/Abcc5/Abcg3 | 8 |
| mmu04929 | GnRH secretion | 0.143 | 0.00927 | 2.03 | 0.00927 | 0.0451 | Kcnj3/Cacna1c/Plcb1/Arrb1/Plcb2/Cacna1h/Arrb2/Akt3/Gabbr1 | 9 |
| mmu04540 | Gap junction | 0.128 | 0.00974 | 2.01 | 0.00974 | 0.0464 | Gnai1/Gucy1a2/Adcy3/Plcb1/Gucy1b1/Gucy1a1/Adcy4/Adcy7/Tubb4a/Htr2a/Plcb2 | 11 |
| mmu04260 | Cardiac muscle contraction | 0.126 | 0.0106 | 1.98 | 0.0106 | 0.0486 | Cacna1c/Slc8a1/Cacna2d1/Slc9a7/Slc8a3/Myl3/Cacng7/Asph/Cox4i2/Atp1a2/Cacnb4 | 11 |
| mmu05323 | Rheumatoid arthritis | 0.126 | 0.0106 | 1.98 | 0.0106 | 0.0486 | Angpt1/Icam1/Tek/Cxcl12/Tnfsf13b/Itgal/H2-Ab1/H2-Ob/Atp6v0e2/H2-Eb1/H2-Aa | 11 |
| mmu05416 | Viral myocarditis | 0.125 | 0.0115 | 1.94 | 0.0115 | 0.0518 | Sgcd/Icam1/Lama2/Itgal/H2-Ab1/H2-Ob/H2-Eb1/Fyn/H2-Aa/Sgcb/Cav1 | 11 |
| mmu00601 | Glycosphingolipid biosynthesis - lacto and neolacto series | 0.192 | 0.0147 | 1.83 | 0.0147 | 0.0648 | B3galnt1/B4galt2/Ggta1/B3gnt5/St3gal4 | 5 |
| mmu04659 | Th17 cell differentiation | 0.114 | 0.0167 | 1.78 | 0.0167 | 0.0726 | Cd3g/Il27ra/H2-Ab1/H2-Ob/H2-Eb1/Nfkbie/H2-Aa/Stat5b/Zap70/Lat/Il12rb1/Il2rg | 12 |
| mmu04390 | Hippo signaling pathway | 0.102 | 0.0178 | 1.75 | 0.0178 | 0.0761 | Wnt6/Lef1/Wnt11/Nkd1/Areg/Ccnd2/Gdf7/Wnt9a/Dlg2/Pard6g/Ccn2/Fzd2/Dlg4/Dlg5/Lats2/Nkd2 | 16 |
| mmu00230 | Purine metabolism | 0.104 | 0.0212 | 1.67 | 0.0212 | 0.0874 | Nme4/Gucy1a2/Pde1b/Adcy3/Gucy1b1/Gucy1a1/Adcy4/Adcy7/Pde1a/Enpp1/Hddc3/Lacc1/Pde5a/Impdh1 | 14 |
| mmu04927 | Cortisol synthesis and secretion | 0.125 | 0.0212 | 1.67 | 0.0212 | 0.0874 | Kcnk3/Cacna1c/Adcy3/Plcb1/Adcy4/Adcy7/Agtr1a/Plcb2/Cacna1h | 9 |
| mmu04961 | Endocrine and other factor-regulated calcium reabsorption | 0.131 | 0.0224 | 1.65 | 0.0224 | 0.0906 | Slc8a1/Slc8a3/Plcb1/Pth1r/Bdkrb2/Plcb2/Atp2b4/Atp1a2 | 8 |
| mmu04810 | Regulation of actin cytoskeleton | 0.0909 | 0.0241 | 1.62 | 0.0241 | 0.0962 | Itga4/Itgb7/Fn1/Pfn2/Lpar4/Pip5k1b/Cxcl12/Itga1/Msn/Abi2/Itgal/Scin/Bdkrb2/Itga7/Nckap1l/Fgd1/Akt3/Actr3b/Cyfip2/Itga8/Itgb4 | 21 |
| mmu04918 | Thyroid hormone synthesis | 0.122 | 0.0249 | 1.6 | 0.0249 | 0.0971 | Ttr/Adcy3/Plcb1/Lrp2/Adcy4/Adcy7/Plcb2/Gpx7/Atp1a2 | 9 |
| mmu00260 | Glycine, serine and threonine metabolism | 0.15 | 0.0251 | 1.6 | 0.0251 | 0.0971 | Maob/Cbs/Maoa/Gamt/Cth/Phgdh | 6 |
| mmu00380 | Tryptophan metabolism | 0.135 | 0.0279 | 1.56 | 0.0279 | 0.106 | Cyp1b1/Maob/Maoa/Kyat1/Dhtkd1/Echs1/Aox4 | 7 |
| mmu04923 | Regulation of lipolysis in adipocytes | 0.123 | 0.0432 | 1.36 | 0.0432 | 0.157 | Gnai1/Adcy3/Adcy4/Adcy7/Ptger3/Akt3/Lipe | 7 |
| mmu05144 | Malaria | 0.123 | 0.0432 | 1.36 | 0.0432 | 0.157 | Hgf/Thbs3/Icam1/Gypc/Itgal/Sele/Pecam1 | 7 |
| mmu04915 | Estrogen signaling pathway | 0.097 | 0.0434 | 1.36 | 0.0434 | 0.157 | Krt23/Kcnj3/Nos3/Gnai1/Mmp2/Shc3/Adcy3/Plcb1/Adcy4/Adcy7/Plcb2/Akt3/Gabbr1 | 13 |
| mmu04934 | Cushing syndrome | 0.0926 | 0.0449 | 1.35 | 0.0449 | 0.158 | Kcnk3/Wnt6/Lef1/Wnt11/Cacna1c/Gnai1/Adcy3/Plcb1/Wnt9a/Adcy4/Adcy7/Agtr1a/Plcb2/Cacna1h/Fzd2 | 15 |
| mmu04928 | Parathyroid hormone synthesis, secretion and action | 0.102 | 0.0449 | 1.35 | 0.0449 | 0.158 | Mmp16/Gnai1/Mef2c/Adcy3/Plcb1/Pth1r/Adcy4/Adcy7/Arrb1/Plcb2/Arrb2 | 11 |
kegg_dot[[p]]
upset[[p]]
p=p+1enrichKEGG_sig[[p]] %>%
dplyr::mutate_if(is.numeric, funs(as.character(signif(.,3)))) %>%
kable(caption = "Significantly enriched KEGG pathways") %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Description | GeneRatio | pvalue | logPval | p.adjust | qvalue | geneID | Count | |
|---|---|---|---|---|---|---|---|---|
| mmu04340 | Hedgehog signaling pathway | 0.138 | 2.71e-06 | 5.57 | 2.71e-06 | 0.000588 | Gli1/Ihh/Hhip/Ptch2/Evc2/Evc/Lrp2/Kif7 | 8 |
| mmu05217 | Basal cell carcinoma | 0.111 | 4.95e-05 | 4.31 | 4.95e-05 | 0.00445 | Gli1/Wnt6/Hhip/Wnt11/Lef1/Ptch2/Kif7 | 7 |
| mmu04512 | ECM-receptor interaction | 0.0909 | 6.16e-05 | 4.21 | 6.16e-05 | 0.00445 | Col4a6/Lamc3/Itga4/Npnt/Cd44/Col9a2/Frem1/Lama4 | 8 |
| mmu04360 | Axon guidance | 0.0608 | 0.000111 | 3.96 | 0.000111 | 0.00601 | Epha8/Efnb3/Sema5a/Dcc/Lrrc4c/Sema5b/Plxnb1/Gnai1/Sema7a/Cxcl12/Gdf7 | 11 |
| mmu05205 | Proteoglycans in cancer | 0.0488 | 0.00128 | 2.89 | 0.00128 | 0.0506 | Ihh/Hgf/Wnt6/Wnt11/Hoxd10/Igf1/Kdr/Gpc3/Cd44/Mmp2 | 10 |
| mmu04974 | Protein digestion and absorption | 0.0648 | 0.0014 | 2.85 | 0.0014 | 0.0506 | Col11a1/Col26a1/Col14a1/Col4a6/Pga5/Col9a2/Slc8a3 | 7 |
| mmu04020 | Calcium signaling pathway | 0.0417 | 0.00407 | 2.39 | 0.00407 | 0.126 | Hgf/Ryr1/Adra1a/Kdr/Ednrb/Nos3/P2rx2/Ptgfr/Cacna1e/Slc8a3 | 10 |
| mmu04728 | Dopaminergic synapse | 0.0519 | 0.00493 | 2.31 | 0.00493 | 0.134 | Kcnj3/Maob/Gria4/Drd4/Scn1a/Gnai1/Grin2b | 7 |
| mmu05412 | Arrhythmogenic right ventricular cardiomyopathy | 0.0649 | 0.00673 | 2.17 | 0.00673 | 0.16 | Lef1/Sgcd/Itga4/Cdh2/Slc8a3 | 5 |
| mmu04080 | Neuroactive ligand-receptor interaction | 0.0332 | 0.00753 | 2.12 | 0.00753 | 0.16 | Grid1/Grik1/Vipr2/Gria4/Adra1a/Drd4/Ednrb/Calca/Edn3/P2rx2/Ptgfr/Grin2b/Gabra4 | 13 |
| mmu04724 | Glutamatergic synapse | 0.0531 | 0.0081 | 2.09 | 0.0081 | 0.16 | Kcnj3/Slc1a3/Grik1/Gria4/Gnai1/Grin2b | 6 |
| mmu04510 | Focal adhesion | 0.0398 | 0.0128 | 1.89 | 0.0128 | 0.231 | Hgf/Col4a6/Igf1/Lamc3/Itga4/Kdr/Col9a2/Lama4 | 8 |
| mmu04713 | Circadian entrainment | 0.051 | 0.0179 | 1.75 | 0.0179 | 0.279 | Kcnj3/Gria4/Ryr1/Gnai1/Grin2b | 5 |
| mmu04015 | Rap1 signaling pathway | 0.0374 | 0.018 | 1.74 | 0.018 | 0.279 | Hgf/Angpt1/Igf1/Kdr/Gnai1/Evl/Grin2b/Rasgrp3 | 8 |
| mmu04916 | Melanogenesis | 0.05 | 0.0194 | 1.71 | 0.0194 | 0.28 | Wnt6/Wnt11/Lef1/Ednrb/Gnai1 | 5 |
| mmu04151 | PI3K-Akt signaling pathway | 0.0306 | 0.0235 | 1.63 | 0.0235 | 0.302 | Hgf/Angpt1/Col4a6/Igf1/Lamc3/Areg/Itga4/Kdr/Nos3/Col9a2/Lama4 | 11 |
| mmu05033 | Nicotine addiction | 0.075 | 0.0237 | 1.63 | 0.0237 | 0.302 | Gria4/Grin2b/Gabra4 | 3 |
| mmu00910 | Nitrogen metabolism | 0.118 | 0.0278 | 1.56 | 0.0278 | 0.335 | Car4/Car8 | 2 |
| mmu04390 | Hippo signaling pathway | 0.0382 | 0.0351 | 1.46 | 0.0351 | 0.4 | Wnt6/Wnt11/Lef1/Areg/Nkd1/Gdf7 | 6 |
| mmu05030 | Cocaine addiction | 0.0625 | 0.038 | 1.42 | 0.038 | 0.411 | Maob/Gnai1/Grin2b | 3 |
| mmu04979 | Cholesterol metabolism | 0.06 | 0.0421 | 1.38 | 0.0421 | 0.434 | Apob/Lrp2/Soat1 | 3 |
| mmu04310 | Wnt signaling pathway | 0.0351 | 0.0497 | 1.3 | 0.0497 | 0.458 | Wnt6/Sfrp2/Wnt11/Lef1/Apcdd1/Nkd1 | 6 |
| mmu04926 | Relaxin signaling pathway | 0.0388 | 0.0499 | 1.3 | 0.0499 | 0.458 | Col4a6/Ednrb/Nos3/Gnai1/Mmp2 | 5 |
kegg_dot[[p]]
upset[[p]]
Pathway specific heatmaps
p=1q=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
# 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", "#a3a500")
names(anno_colours) <- c("Control", "Intact")matrix <- list()
display_matrix <- list()
kegg_heat=list()
my_palette <- colorRampPalette(c(
rgb(32,121,226, maxColorValue = 255),
# rgb(144,203,180, maxColorValue = 255),
rgb(254,248,239, maxColorValue = 255),
# rgb(251,192,52, maxColorValue = 255),
rgb(226,46,45, maxColorValue = 255)))(n = 201)
for (i in 1:length(fc)) {
x <- fc[i] %>% as.character()
for (j in 1:length(kegg_id)) {
y <- kegg_pathway[[j]]$PATHWAY_MAP
partial <- enrichKEGG_all[[x]][, c("ID", "geneID")]
partial <- partial[kegg_id[j], "geneID"] %>% as.data.frame()
partial <- separate_rows(partial, ., sep = "/")
colnames(partial) <- "entrezid"
# heatmap matrix
match <- rownames(logCPM) %in% partial$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]][, "gene_name"] %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 = 10,
fontsize_col = 11,
fontsize_number = 7,
fontsize_row = 10,
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 = 166,
height = 250,
units = "mm")}
}kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
dplyr::mutate_if(is.numeric, funs(as.character(signif(.,3)))) %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000027009 | Itga4 | 2.07 | 1.55e-05 | 0.00251 | integrin alpha 4 [Source:MGI Symbol;Acc:MGI:96603] |
| ENSMUSG00000057614 | Gnai1 | 2.41 | 0.000101 | 0.0055 | guanine nucleotide binding protein (G protein), alpha inhibiting 1 [Source:MGI Symbol;Acc:MGI:95771] |
| ENSMUSG00000031740 | Mmp2 | 2.27 | 0.000133 | 0.00629 | matrix metallopeptidase 2 [Source:MGI Symbol;Acc:MGI:97009] |
| ENSMUSG00000037405 | Icam1 | 1.99 | 0.000159 | 0.00687 | intercellular adhesion molecule 1 [Source:MGI Symbol;Acc:MGI:96392] |
| ENSMUSG00000020395 | Itk | 2.08 | 0.00019 | 0.00747 | IL2 inducible T cell kinase [Source:MGI Symbol;Acc:MGI:96621] |
| ENSMUSG00000031990 | Jam3 | 1.93 | 0.000193 | 0.00752 | junction adhesion molecule 3 [Source:MGI Symbol;Acc:MGI:1933825] |
| ENSMUSG00000061353 | Cxcl12 | 2.57 | 0.000201 | 0.00769 | chemokine (C-X-C motif) ligand 12 [Source:MGI Symbol;Acc:MGI:103556] |
| ENSMUSG00000050520 | Cldn8 | 1.95 | 0.00027 | 0.00934 | claudin 8 [Source:MGI Symbol;Acc:MGI:1859286] |
| ENSMUSG00000031871 | Cdh5 | 2.5 | 4e-04 | 0.0117 | cadherin 5 [Source:MGI Symbol;Acc:MGI:105057] |
| ENSMUSG00000032011 | Thy1 | 1.78 | 0.000413 | 0.0118 | thymus cell antigen 1, theta [Source:MGI Symbol;Acc:MGI:98747] |
| ENSMUSG00000031207 | Msn | 1.38 | 0.000449 | 0.0122 | moesin [Source:MGI Symbol;Acc:MGI:97167] |
| ENSMUSG00000030830 | Itgal | 1.82 | 0.000648 | 0.015 | integrin alpha L [Source:MGI Symbol;Acc:MGI:96606] |
| ENSMUSG00000001946 | Esam | 1.94 | 0.000649 | 0.015 | endothelial cell-specific adhesion molecule [Source:MGI Symbol;Acc:MGI:1916774] |
| ENSMUSG00000020717 | Pecam1 | 1.73 | 9e-04 | 0.0179 | platelet/endothelial cell adhesion molecule 1 [Source:MGI Symbol;Acc:MGI:97537] |
| ENSMUSG00000041378 | Cldn5 | 1.92 | 0.00188 | 0.0281 | claudin 5 [Source:MGI Symbol;Acc:MGI:1276112] |
| ENSMUSG00000022512 | Cldn1 | 1.84 | 0.00378 | 0.0436 | claudin 1 [Source:MGI Symbol;Acc:MGI:1276109] |
| ENSMUSG00000056917 | Sipa1 | 1.25 | 0.00423 | 0.0466 | signal-induced proliferation associated gene 1 [Source:MGI Symbol;Acc:MGI:107576] |
| ENSMUSG00000053062 | Jam2 | 3.16 | 0.00463 | 0.0493 | 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("docs/figure/kegg.Rmd/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."
Pathview
q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
dplyr::mutate_if(is.numeric, funs(as.character(signif(.,3)))) %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000027009 | Itga4 | 2.07 | 1.55e-05 | 0.00251 | integrin alpha 4 [Source:MGI Symbol;Acc:MGI:96603] |
| ENSMUSG00000005087 | Cd44 | 2.27 | 7.24e-05 | 0.00467 | CD44 antigen [Source:MGI Symbol;Acc:MGI:88338] |
| ENSMUSG00000073889 | Il11ra1 | 1.54 | 0.000108 | 0.00566 | interleukin 11 receptor, alpha chain 1 [Source:MGI Symbol;Acc:MGI:107426] |
| ENSMUSG00000002033 | Cd3g | 3.65 | 0.000212 | 0.00797 | CD3 antigen, gamma polypeptide [Source:MGI Symbol;Acc:MGI:88333] |
| ENSMUSG00000042284 | Itga1 | 1.94 | 0.000311 | 0.0102 | integrin alpha 1 [Source:MGI Symbol;Acc:MGI:96599] |
| ENSMUSG00000042817 | Flt3 | 2.08 | 0.00041 | 0.0118 | FMS-like tyrosine kinase 3 [Source:MGI Symbol;Acc:MGI:95559] |
| ENSMUSG00000028076 | Cd1d1 | 2.34 | 0.000506 | 0.0131 | CD1d1 antigen [Source:MGI Symbol;Acc:MGI:107674] |
| ENSMUSG00000005672 | Kit | 1.52 | 0.000531 | 0.0134 | KIT proto-oncogene receptor tyrosine kinase [Source:MGI Symbol;Acc:MGI:96677] |
| ENSMUSG00000027820 | Mme | 3.74 | 0.000535 | 0.0135 | membrane metallo endopeptidase [Source:MGI Symbol;Acc:MGI:97004] |
| ENSMUSG00000073421 | H2-Ab1 | 1.74 | 0.00065 | 0.015 | histocompatibility 2, class II antigen A, beta 1 [Source:MGI Symbol;Acc:MGI:103070] |
| ENSMUSG00000029084 | Cd38 | 1.71 | 0.000756 | 0.0163 | CD38 antigen [Source:MGI Symbol;Acc:MGI:107474] |
| ENSMUSG00000041538 | H2-Ob | 1.72 | 0.000831 | 0.0171 | histocompatibility 2, O region beta locus [Source:MGI Symbol;Acc:MGI:95925] |
| ENSMUSG00000019966 | Kitl | 1.31 | 0.00107 | 0.0201 | kit ligand [Source:MGI Symbol;Acc:MGI:96974] |
| ENSMUSG00000060586 | H2-Eb1 | 1.69 | 0.00138 | 0.0232 | histocompatibility 2, class II antigen E beta [Source:MGI Symbol;Acc:MGI:95901] |
| ENSMUSG00000036594 | H2-Aa | 1.67 | 0.00216 | 0.0309 | histocompatibility 2, class II antigen A, alpha [Source:MGI Symbol;Acc:MGI:95895] |
| ENSMUSG00000003882 | Il7r | 2.26 | 0.00405 | 0.0455 | interleukin 7 receptor [Source:MGI Symbol;Acc:MGI:96562] |
| ENSMUSG00000023274 | Cd4 | 2.41 | 0.00408 | 0.0457 | CD4 antigen [Source:MGI Symbol;Acc:MGI:88335] |
Pathview
q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
dplyr::mutate_if(is.numeric, funs(as.character(signif(.,3)))) %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000051331 | Cacna1c | 1.12 | 9.35e-06 | 0.00199 | calcium channel, voltage-dependent, L type, alpha 1C subunit [Source:MGI Symbol;Acc:MGI:103013] |
| ENSMUSG00000022683 | Pla2g10 | 5.77 | 1.8e-05 | 0.00256 | phospholipase A2, group X [Source:MGI Symbol;Acc:MGI:1347522] |
| ENSMUSG00000045875 | Adra1a | 4.13 | 5.6e-05 | 0.00427 | adrenergic receptor, alpha 1a [Source:MGI Symbol;Acc:MGI:104773] |
| ENSMUSG00000041624 | Gucy1a2 | 2.2 | 0.000165 | 0.00701 | guanylate cyclase 1, soluble, alpha 2 [Source:MGI Symbol;Acc:MGI:2660877] |
| ENSMUSG00000020654 | Adcy3 | 1.65 | 0.00019 | 0.00747 | adenylate cyclase 3 [Source:MGI Symbol;Acc:MGI:99675] |
| ENSMUSG00000027524 | Edn3 | 3.85 | 3e-04 | 0.01 | endothelin 3 [Source:MGI Symbol;Acc:MGI:95285] |
| ENSMUSG00000051177 | Plcb1 | 1.96 | 0.00032 | 0.0104 | phospholipase C, beta 1 [Source:MGI Symbol;Acc:MGI:97613] |
| ENSMUSG00000030669 | Calca | 5.76 | 0.000366 | 0.0111 | calcitonin/calcitonin-related polypeptide, alpha [Source:MGI Symbol;Acc:MGI:2151253] |
| ENSMUSG00000028005 | Gucy1b1 | 1.86 | 0.000413 | 0.0118 | guanylate cyclase 1, soluble, beta 1 [Source:MGI Symbol;Acc:MGI:1860604] |
| ENSMUSG00000033910 | Gucy1a1 | 1.99 | 0.000517 | 0.0132 | guanylate cyclase 1, soluble, alpha 1 [Source:MGI Symbol;Acc:MGI:1926562] |
| ENSMUSG00000022220 | Adcy4 | 1.87 | 0.000549 | 0.0136 | adenylate cyclase 4 [Source:MGI Symbol;Acc:MGI:99674] |
| ENSMUSG00000031659 | Adcy7 | 1.31 | 0.000557 | 0.0137 | adenylate cyclase 7 [Source:MGI Symbol;Acc:MGI:102891] |
| ENSMUSG00000049115 | Agtr1a | 1.76 | 0.000765 | 0.0165 | angiotensin II receptor, type 1a [Source:MGI Symbol;Acc:MGI:87964] |
| ENSMUSG00000063142 | Kcnma1 | 2.43 | 0.000843 | 0.0172 | potassium large conductance calcium-activated channel, subfamily M, alpha member 1 [Source:MGI Symbol;Acc:MGI:99923] |
| ENSMUSG00000031616 | Ednra | 1.78 | 0.00087 | 0.0175 | endothelin receptor type A [Source:MGI Symbol;Acc:MGI:105923] |
| ENSMUSG00000040061 | Plcb2 | 1.5 | 0.00154 | 0.0249 | phospholipase C, beta 2 [Source:MGI Symbol;Acc:MGI:107465] |
| ENSMUSG00000059588 | Calcrl | 1.49 | 0.00189 | 0.0281 | calcitonin receptor-like [Source:MGI Symbol;Acc:MGI:1926944] |
Pathview
q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
dplyr::mutate_if(is.numeric, funs(as.character(signif(.,3)))) %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000028864 | Hgf | 4.13 | 4.39e-06 | 0.0015 | hepatocyte growth factor [Source:MGI Symbol;Acc:MGI:96079] |
| ENSMUSG00000022309 | Angpt1 | 3.39 | 1.02e-05 | 0.00211 | angiopoietin 1 [Source:MGI Symbol;Acc:MGI:108448] |
| ENSMUSG00000027009 | Itga4 | 2.07 | 1.55e-05 | 0.00251 | integrin alpha 4 [Source:MGI Symbol;Acc:MGI:96603] |
| ENSMUSG00000062960 | Kdr | 2.05 | 2.26e-05 | 0.0028 | kinase insert domain protein receptor [Source:MGI Symbol;Acc:MGI:96683] |
| ENSMUSG00000020053 | Igf1 | 2.78 | 3.09e-05 | 0.00326 | insulin-like growth factor 1 [Source:MGI Symbol;Acc:MGI:96432] |
| ENSMUSG00000031273 | Col4a6 | 3.47 | 4.09e-05 | 0.00373 | collagen, type IV, alpha 6 [Source:MGI Symbol;Acc:MGI:2152695] |
| ENSMUSG00000028047 | Thbs3 | 1.67 | 4.61e-05 | 0.00399 | thrombospondin 3 [Source:MGI Symbol;Acc:MGI:98739] |
| ENSMUSG00000028978 | Nos3 | 2.15 | 5.81e-05 | 0.00435 | nitric oxide synthase 3, endothelial cell [Source:MGI Symbol;Acc:MGI:97362] |
| ENSMUSG00000026840 | Lamc3 | 3.8 | 7.83e-05 | 0.00483 | laminin gamma 3 [Source:MGI Symbol;Acc:MGI:1344394] |
| ENSMUSG00000019846 | Lama4 | 1.94 | 8.23e-05 | 0.00498 | laminin, alpha 4 [Source:MGI Symbol;Acc:MGI:109321] |
| ENSMUSG00000000184 | Ccnd2 | 1.71 | 0.000108 | 0.00566 | cyclin D2 [Source:MGI Symbol;Acc:MGI:88314] |
| ENSMUSG00000001281 | Itgb7 | 1.81 | 0.000109 | 0.00566 | integrin beta 7 [Source:MGI Symbol;Acc:MGI:96616] |
| ENSMUSG00000026193 | Fn1 | 1.97 | 0.000114 | 0.00576 | fibronectin 1 [Source:MGI Symbol;Acc:MGI:95566] |
| ENSMUSG00000029378 | Areg | 5.25 | 0.00013 | 0.00622 | amphiregulin [Source:MGI Symbol;Acc:MGI:88068] |
| ENSMUSG00000049929 | Lpar4 | 2.15 | 0.000166 | 0.00701 | lysophosphatidic acid receptor 4 [Source:MGI Symbol;Acc:MGI:1925384] |
| ENSMUSG00000006386 | Tek | 2.34 | 0.000195 | 0.00753 | TEK receptor tyrosine kinase [Source:MGI Symbol;Acc:MGI:98664] |
| ENSMUSG00000038811 | Gngt2 | 1.82 | 0.000221 | 0.00818 | guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2 [Source:MGI Symbol;Acc:MGI:893584] |
| ENSMUSG00000046207 | Pik3r6 | 1.69 | 0.00027 | 0.00934 | phosphoinositide-3-kinase regulatory subunit 5 [Source:MGI Symbol;Acc:MGI:2144613] |
| ENSMUSG00000042284 | Itga1 | 1.94 | 0.000311 | 0.0102 | integrin alpha 1 [Source:MGI Symbol;Acc:MGI:96599] |
| ENSMUSG00000028626 | Col9a2 | 4.13 | 0.00036 | 0.0111 | collagen, type IX, alpha 2 [Source:MGI Symbol;Acc:MGI:88466] |
| ENSMUSG00000042817 | Flt3 | 2.08 | 0.00041 | 0.0118 | FMS-like tyrosine kinase 3 [Source:MGI Symbol;Acc:MGI:95559] |
| ENSMUSG00000005672 | Kit | 1.52 | 0.000531 | 0.0134 | KIT proto-oncogene receptor tyrosine kinase [Source:MGI Symbol;Acc:MGI:96677] |
| ENSMUSG00000032766 | Gng11 | 2.02 | 0.000574 | 0.0139 | guanine nucleotide binding protein (G protein), gamma 11 [Source:MGI Symbol;Acc:MGI:1913316] |
| ENSMUSG00000019899 | Lama2 | 1.83 | 0.000577 | 0.014 | laminin, alpha 2 [Source:MGI Symbol;Acc:MGI:99912] |
| ENSMUSG00000031520 | Vegfc | 2.12 | 0.000751 | 0.0163 | vascular endothelial growth factor C [Source:MGI Symbol;Acc:MGI:109124] |
| ENSMUSG00000040003 | Magi2 | 1.52 | 0.000798 | 0.0167 | membrane associated guanylate kinase, WW and PDZ domain containing 2 [Source:MGI Symbol;Acc:MGI:1354953] |
| ENSMUSG00000048583 | Igf2 | 2.43 | 0.000933 | 0.0183 | insulin-like growth factor 2 [Source:MGI Symbol;Acc:MGI:96434] |
| ENSMUSG00000043004 | Gng2 | 1.24 | 0.00094 | 0.0184 | guanine nucleotide binding protein (G protein), gamma 2 [Source:MGI Symbol;Acc:MGI:102705] |
| ENSMUSG00000025348 | Itga7 | 1.58 | 0.000987 | 0.0189 | integrin alpha 7 [Source:MGI Symbol;Acc:MGI:102700] |
| ENSMUSG00000019966 | Kitl | 1.31 | 0.00107 | 0.0201 | kit ligand [Source:MGI Symbol;Acc:MGI:96974] |
| ENSMUSG00000019699 | Akt3 | 1.2 | 0.00209 | 0.0302 | thymoma viral proto-oncogene 3 [Source:MGI Symbol;Acc:MGI:1345147] |
| ENSMUSG00000032192 | Gnb5 | 1.03 | 0.00219 | 0.0311 | guanine nucleotide binding protein (G protein), beta 5 [Source:MGI Symbol;Acc:MGI:101848] |
| ENSMUSG00000048240 | Gng7 | 2.31 | 0.00227 | 0.0316 | guanine nucleotide binding protein (G protein), gamma 7 [Source:MGI Symbol;Acc:MGI:95787] |
| ENSMUSG00000027669 | Gnb4 | 1.16 | 0.00273 | 0.0356 | guanine nucleotide binding protein (G protein), beta 4 [Source:MGI Symbol;Acc:MGI:104581] |
| ENSMUSG00000024620 | Pdgfrb | 0.957 | 0.00298 | 0.0376 | platelet derived growth factor receptor, beta polypeptide [Source:MGI Symbol;Acc:MGI:97531] |
| ENSMUSG00000031304 | Il2rg | 1.88 | 0.00336 | 0.0405 | interleukin 2 receptor, gamma chain [Source:MGI Symbol;Acc:MGI:96551] |
| ENSMUSG00000026768 | Itga8 | 1.59 | 0.00337 | 0.0407 | integrin alpha 8 [Source:MGI Symbol;Acc:MGI:109442] |
| ENSMUSG00000020758 | Itgb4 | -1.5 | 0.00354 | 0.042 | integrin beta 4 [Source:MGI Symbol;Acc:MGI:96613] |
| ENSMUSG00000048376 | F2r | 2.19 | 0.00405 | 0.0455 | coagulation factor II (thrombin) receptor [Source:MGI Symbol;Acc:MGI:101802] |
| ENSMUSG00000003882 | Il7r | 2.26 | 0.00405 | 0.0455 | interleukin 7 receptor [Source:MGI Symbol;Acc:MGI:96562] |
| ENSMUSG00000022346 | Myc | 1.81 | 0.00431 | 0.0471 | myelocytomatosis oncogene [Source:MGI Symbol;Acc:MGI:97250] |
| ENSMUSG00000031274 | Col4a5 | 1.7 | 0.00471 | 0.0498 | collagen, type IV, alpha 5 [Source:MGI Symbol;Acc:MGI:88456] |
| ENSMUSG00000055980 | Irs1 | 0.95 | 0.00472 | 0.0499 | insulin receptor substrate 1 [Source:MGI Symbol;Acc:MGI:99454] |
Pathview
q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
dplyr::mutate_if(is.numeric, funs(as.character(signif(.,3)))) %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000028864 | Hgf | 4.13 | 4.39e-06 | 0.0015 | hepatocyte growth factor [Source:MGI Symbol;Acc:MGI:96079] |
| ENSMUSG00000027009 | Itga4 | 2.07 | 1.55e-05 | 0.00251 | integrin alpha 4 [Source:MGI Symbol;Acc:MGI:96603] |
| ENSMUSG00000062960 | Kdr | 2.05 | 2.26e-05 | 0.0028 | kinase insert domain protein receptor [Source:MGI Symbol;Acc:MGI:96683] |
| ENSMUSG00000020053 | Igf1 | 2.78 | 3.09e-05 | 0.00326 | insulin-like growth factor 1 [Source:MGI Symbol;Acc:MGI:96432] |
| ENSMUSG00000031273 | Col4a6 | 3.47 | 4.09e-05 | 0.00373 | collagen, type IV, alpha 6 [Source:MGI Symbol;Acc:MGI:2152695] |
| ENSMUSG00000028047 | Thbs3 | 1.67 | 4.61e-05 | 0.00399 | thrombospondin 3 [Source:MGI Symbol;Acc:MGI:98739] |
| ENSMUSG00000026840 | Lamc3 | 3.8 | 7.83e-05 | 0.00483 | laminin gamma 3 [Source:MGI Symbol;Acc:MGI:1344394] |
| ENSMUSG00000019846 | Lama4 | 1.94 | 8.23e-05 | 0.00498 | laminin, alpha 4 [Source:MGI Symbol;Acc:MGI:109321] |
| ENSMUSG00000000184 | Ccnd2 | 1.71 | 0.000108 | 0.00566 | cyclin D2 [Source:MGI Symbol;Acc:MGI:88314] |
| ENSMUSG00000001281 | Itgb7 | 1.81 | 0.000109 | 0.00566 | integrin beta 7 [Source:MGI Symbol;Acc:MGI:96616] |
| ENSMUSG00000026193 | Fn1 | 1.97 | 0.000114 | 0.00576 | fibronectin 1 [Source:MGI Symbol;Acc:MGI:95566] |
| ENSMUSG00000021448 | Shc3 | 2.15 | 0.000137 | 0.00632 | src homology 2 domain-containing transforming protein C3 [Source:MGI Symbol;Acc:MGI:106179] |
| ENSMUSG00000024867 | Pip5k1b | 1.5 | 0.000149 | 0.00668 | phosphatidylinositol-4-phosphate 5-kinase, type 1 beta [Source:MGI Symbol;Acc:MGI:107930] |
| ENSMUSG00000042284 | Itga1 | 1.94 | 0.000311 | 0.0102 | integrin alpha 1 [Source:MGI Symbol;Acc:MGI:96599] |
| ENSMUSG00000028626 | Col9a2 | 4.13 | 0.00036 | 0.0111 | collagen, type IX, alpha 2 [Source:MGI Symbol;Acc:MGI:88466] |
| ENSMUSG00000019899 | Lama2 | 1.83 | 0.000577 | 0.014 | laminin, alpha 2 [Source:MGI Symbol;Acc:MGI:99912] |
| ENSMUSG00000031520 | Vegfc | 2.12 | 0.000751 | 0.0163 | vascular endothelial growth factor C [Source:MGI Symbol;Acc:MGI:109124] |
| ENSMUSG00000025348 | Itga7 | 1.58 | 0.000987 | 0.0189 | integrin alpha 7 [Source:MGI Symbol;Acc:MGI:102700] |
| ENSMUSG00000022439 | Parvg | 1.77 | 0.00101 | 0.0192 | parvin, gamma [Source:MGI Symbol;Acc:MGI:2158329] |
| ENSMUSG00000022438 | Parvb | 1.64 | 0.00124 | 0.0215 | parvin, beta [Source:MGI Symbol;Acc:MGI:2153063] |
| ENSMUSG00000068699 | Flnc | 1.18 | 0.0014 | 0.0234 | filamin C, gamma [Source:MGI Symbol;Acc:MGI:95557] |
| ENSMUSG00000052698 | Tln2 | 1.24 | 0.00148 | 0.0244 | talin 2 [Source:MGI Symbol;Acc:MGI:1917799] |
| ENSMUSG00000019843 | Fyn | 1.18 | 0.00174 | 0.0267 | Fyn proto-oncogene [Source:MGI Symbol;Acc:MGI:95602] |
| ENSMUSG00000019699 | Akt3 | 1.2 | 0.00209 | 0.0302 | thymoma viral proto-oncogene 3 [Source:MGI Symbol;Acc:MGI:1345147] |
| ENSMUSG00000024620 | Pdgfrb | 0.957 | 0.00298 | 0.0376 | platelet derived growth factor receptor, beta polypeptide [Source:MGI Symbol;Acc:MGI:97531] |
| ENSMUSG00000007655 | Cav1 | 1.6 | 0.00318 | 0.0393 | caveolin 1, caveolae protein [Source:MGI Symbol;Acc:MGI:102709] |
| ENSMUSG00000026768 | Itga8 | 1.59 | 0.00337 | 0.0407 | integrin alpha 8 [Source:MGI Symbol;Acc:MGI:109442] |
| ENSMUSG00000020758 | Itgb4 | -1.5 | 0.00354 | 0.042 | integrin beta 4 [Source:MGI Symbol;Acc:MGI:96613] |
| ENSMUSG00000031274 | Col4a5 | 1.7 | 0.00471 | 0.0498 | collagen, type IV, alpha 5 [Source:MGI Symbol;Acc:MGI:88456] |
Pathview
q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
dplyr::mutate_if(is.numeric, funs(as.character(signif(.,3)))) %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000029375 | Cxcl15 | 6.92 | 1.72e-08 | 0.000148 | chemokine (C-X-C motif) ligand 15 [Source:MGI Symbol;Acc:MGI:1339941] |
| ENSMUSG00000034457 | Eda2r | 3.52 | 3.87e-05 | 0.00366 | ectodysplasin A2 receptor [Source:MGI Symbol;Acc:MGI:2442860] |
| ENSMUSG00000073889 | Il11ra1 | 1.54 | 0.000108 | 0.00566 | interleukin 11 receptor, alpha chain 1 [Source:MGI Symbol;Acc:MGI:107426] |
| ENSMUSG00000050232 | Cxcr3 | 2.28 | 0.000195 | 0.00753 | chemokine (C-X-C motif) receptor 3 [Source:MGI Symbol;Acc:MGI:1277207] |
| ENSMUSG00000061353 | Cxcl12 | 2.57 | 0.000201 | 0.00769 | chemokine (C-X-C motif) ligand 12 [Source:MGI Symbol;Acc:MGI:103556] |
| ENSMUSG00000025352 | Gdf11 | 2.25 | 0.000243 | 0.00876 | growth differentiation factor 11 [Source:MGI Symbol;Acc:MGI:1338027] |
| ENSMUSG00000037660 | Gdf7 | 3.41 | 4e-04 | 0.0117 | growth differentiation factor 7 [Source:MGI Symbol;Acc:MGI:95690] |
| ENSMUSG00000031497 | Tnfsf13b | 2.22 | 0.000434 | 0.012 | tumor necrosis factor (ligand) superfamily, member 13b [Source:MGI Symbol;Acc:MGI:1344376] |
| ENSMUSG00000021943 | Gdf10 | 2.74 | 0.000521 | 0.0133 | growth differentiation factor 10 [Source:MGI Symbol;Acc:MGI:95684] |
| ENSMUSG00000005465 | Il27ra | 1.94 | 0.00067 | 0.0153 | interleukin 27 receptor, alpha [Source:MGI Symbol;Acc:MGI:1355318] |
| ENSMUSG00000063727 | Tnfrsf11b | 2.13 | 0.00074 | 0.0162 | tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin) [Source:MGI Symbol;Acc:MGI:109587] |
| ENSMUSG00000026573 | Xcl1 | 2.67 | 0.00111 | 0.0204 | chemokine (C motif) ligand 1 [Source:MGI Symbol;Acc:MGI:104593] |
| ENSMUSG00000060509 | Xcr1 | 2 | 0.00176 | 0.0269 | chemokine (C motif) receptor 1 [Source:MGI Symbol;Acc:MGI:1346338] |
| ENSMUSG00000071713 | Csf2rb | 2.03 | 0.00179 | 0.0271 | colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage) [Source:MGI Symbol;Acc:MGI:1339759] |
| ENSMUSG00000000791 | Il12rb1 | 2.13 | 0.00312 | 0.0387 | interleukin 12 receptor, beta 1 [Source:MGI Symbol;Acc:MGI:104579] |
| ENSMUSG00000031304 | Il2rg | 1.88 | 0.00336 | 0.0405 | interleukin 2 receptor, gamma chain [Source:MGI Symbol;Acc:MGI:96551] |
| ENSMUSG00000003227 | Edar | 2.57 | 0.00385 | 0.044 | ectodysplasin-A receptor [Source:MGI Symbol;Acc:MGI:1343498] |
| ENSMUSG00000008999 | Bmp7 | 1.59 | 0.00405 | 0.0455 | bone morphogenetic protein 7 [Source:MGI Symbol;Acc:MGI:103302] |
| ENSMUSG00000003882 | Il7r | 2.26 | 0.00405 | 0.0455 | interleukin 7 receptor [Source:MGI Symbol;Acc:MGI:96562] |
| ENSMUSG00000023274 | Cd4 | 2.41 | 0.00408 | 0.0457 | CD4 antigen [Source:MGI Symbol;Acc:MGI:88335] |
Pathview
p=p+1q=1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
dplyr::mutate_if(is.numeric, funs(as.character(signif(.,3)))) %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000027009 | Itga4 | 2.07 | 1.91e-05 | 0.00285 | integrin alpha 4 [Source:MGI Symbol;Acc:MGI:96603] |
| ENSMUSG00000057614 | Gnai1 | 2.41 | 0.000115 | 0.0064 | guanine nucleotide binding protein (G protein), alpha inhibiting 1 [Source:MGI Symbol;Acc:MGI:95771] |
| ENSMUSG00000031740 | Mmp2 | 2.27 | 0.000153 | 0.00716 | matrix metallopeptidase 2 [Source:MGI Symbol;Acc:MGI:97009] |
| ENSMUSG00000037405 | Icam1 | 1.99 | 0.000189 | 0.00826 | intercellular adhesion molecule 1 [Source:MGI Symbol;Acc:MGI:96392] |
| ENSMUSG00000020395 | Itk | 2.08 | 0.000221 | 0.0088 | IL2 inducible T cell kinase [Source:MGI Symbol;Acc:MGI:96621] |
| ENSMUSG00000061353 | Cxcl12 | 2.57 | 0.000222 | 0.00881 | chemokine (C-X-C motif) ligand 12 [Source:MGI Symbol;Acc:MGI:103556] |
| ENSMUSG00000031990 | Jam3 | 1.93 | 0.00023 | 0.00892 | junction adhesion molecule 3 [Source:MGI Symbol;Acc:MGI:1933825] |
| ENSMUSG00000050520 | Cldn8 | 1.95 | 0.000318 | 0.0111 | claudin 8 [Source:MGI Symbol;Acc:MGI:1859286] |
| ENSMUSG00000031871 | Cdh5 | 2.5 | 0.00044 | 0.0132 | cadherin 5 [Source:MGI Symbol;Acc:MGI:105057] |
| ENSMUSG00000032011 | Thy1 | 1.78 | 0.000493 | 0.014 | thymus cell antigen 1, theta [Source:MGI Symbol;Acc:MGI:98747] |
| ENSMUSG00000031207 | Msn | 1.38 | 0.000594 | 0.0154 | moesin [Source:MGI Symbol;Acc:MGI:97167] |
| ENSMUSG00000001946 | Esam | 1.94 | 0.000747 | 0.0177 | endothelial cell-specific adhesion molecule [Source:MGI Symbol;Acc:MGI:1916774] |
| ENSMUSG00000030830 | Itgal | 1.82 | 0.000759 | 0.0179 | integrin alpha L [Source:MGI Symbol;Acc:MGI:96606] |
| ENSMUSG00000020717 | Pecam1 | 1.73 | 0.00106 | 0.0212 | platelet/endothelial cell adhesion molecule 1 [Source:MGI Symbol;Acc:MGI:97537] |
| ENSMUSG00000041378 | Cldn5 | 1.92 | 0.0021 | 0.0325 | claudin 5 [Source:MGI Symbol;Acc:MGI:1276112] |
| ENSMUSG00000022512 | Cldn1 | 1.84 | 0.00418 | 0.0498 | claudin 1 [Source:MGI Symbol;Acc:MGI:1276109] |
Pathview
q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
dplyr::mutate_if(is.numeric, funs(as.character(signif(.,3)))) %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000027009 | Itga4 | 2.07 | 1.91e-05 | 0.00285 | integrin alpha 4 [Source:MGI Symbol;Acc:MGI:96603] |
| ENSMUSG00000005087 | Cd44 | 2.27 | 8.38e-05 | 0.00539 | CD44 antigen [Source:MGI Symbol;Acc:MGI:88338] |
| ENSMUSG00000073889 | Il11ra1 | 1.54 | 0.000143 | 0.00689 | interleukin 11 receptor, alpha chain 1 [Source:MGI Symbol;Acc:MGI:107426] |
| ENSMUSG00000002033 | Cd3g | 3.65 | 0.000223 | 0.00881 | CD3 antigen, gamma polypeptide [Source:MGI Symbol;Acc:MGI:88333] |
| ENSMUSG00000042284 | Itga1 | 1.94 | 0.000365 | 0.0118 | integrin alpha 1 [Source:MGI Symbol;Acc:MGI:96599] |
| ENSMUSG00000042817 | Flt3 | 2.08 | 0.000469 | 0.0137 | FMS-like tyrosine kinase 3 [Source:MGI Symbol;Acc:MGI:95559] |
| ENSMUSG00000027820 | Mme | 3.74 | 0.000558 | 0.0149 | membrane metallo endopeptidase [Source:MGI Symbol;Acc:MGI:97004] |
| ENSMUSG00000028076 | Cd1d1 | 2.34 | 0.000561 | 0.0149 | CD1d1 antigen [Source:MGI Symbol;Acc:MGI:107674] |
| ENSMUSG00000005672 | Kit | 1.52 | 0.000667 | 0.0164 | KIT proto-oncogene receptor tyrosine kinase [Source:MGI Symbol;Acc:MGI:96677] |
| ENSMUSG00000073421 | H2-Ab1 | 1.74 | 0.000771 | 0.0179 | histocompatibility 2, class II antigen A, beta 1 [Source:MGI Symbol;Acc:MGI:103070] |
| ENSMUSG00000029084 | Cd38 | 1.71 | 0.000897 | 0.0194 | CD38 antigen [Source:MGI Symbol;Acc:MGI:107474] |
| ENSMUSG00000041538 | H2-Ob | 1.72 | 0.000982 | 0.0204 | histocompatibility 2, O region beta locus [Source:MGI Symbol;Acc:MGI:95925] |
| ENSMUSG00000019966 | Kitl | 1.31 | 0.00138 | 0.0249 | kit ligand [Source:MGI Symbol;Acc:MGI:96974] |
| ENSMUSG00000060586 | H2-Eb1 | 1.69 | 0.00161 | 0.0274 | histocompatibility 2, class II antigen E beta [Source:MGI Symbol;Acc:MGI:95901] |
| ENSMUSG00000036594 | H2-Aa | 1.67 | 0.00249 | 0.036 | histocompatibility 2, class II antigen A, alpha [Source:MGI Symbol;Acc:MGI:95895] |
Pathview
q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
dplyr::mutate_if(is.numeric, funs(as.character(signif(.,3)))) %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000051331 | Cacna1c | 1.12 | 1.72e-05 | 0.00285 | calcium channel, voltage-dependent, L type, alpha 1C subunit [Source:MGI Symbol;Acc:MGI:103013] |
| ENSMUSG00000022683 | Pla2g10 | 5.77 | 1.85e-05 | 0.00285 | phospholipase A2, group X [Source:MGI Symbol;Acc:MGI:1347522] |
| ENSMUSG00000045875 | Adra1a | 4.13 | 5.88e-05 | 0.0048 | adrenergic receptor, alpha 1a [Source:MGI Symbol;Acc:MGI:104773] |
| ENSMUSG00000041624 | Gucy1a2 | 2.2 | 0.00019 | 0.00828 | guanylate cyclase 1, soluble, alpha 2 [Source:MGI Symbol;Acc:MGI:2660877] |
| ENSMUSG00000020654 | Adcy3 | 1.65 | 0.00024 | 0.0092 | adenylate cyclase 3 [Source:MGI Symbol;Acc:MGI:99675] |
| ENSMUSG00000027524 | Edn3 | 3.85 | 0.000313 | 0.011 | endothelin 3 [Source:MGI Symbol;Acc:MGI:95285] |
| ENSMUSG00000030669 | Calca | 5.76 | 0.000373 | 0.012 | calcitonin/calcitonin-related polypeptide, alpha [Source:MGI Symbol;Acc:MGI:2151253] |
| ENSMUSG00000051177 | Plcb1 | 1.96 | 0.000374 | 0.012 | phospholipase C, beta 1 [Source:MGI Symbol;Acc:MGI:97613] |
| ENSMUSG00000028005 | Gucy1b1 | 1.86 | 0.000486 | 0.0139 | guanylate cyclase 1, soluble, beta 1 [Source:MGI Symbol;Acc:MGI:1860604] |
| ENSMUSG00000033910 | Gucy1a1 | 1.99 | 0.000594 | 0.0154 | guanylate cyclase 1, soluble, alpha 1 [Source:MGI Symbol;Acc:MGI:1926562] |
| ENSMUSG00000022220 | Adcy4 | 1.87 | 0.000641 | 0.0161 | adenylate cyclase 4 [Source:MGI Symbol;Acc:MGI:99674] |
| ENSMUSG00000031659 | Adcy7 | 1.31 | 0.000747 | 0.0177 | adenylate cyclase 7 [Source:MGI Symbol;Acc:MGI:102891] |
| ENSMUSG00000049115 | Agtr1a | 1.76 | 0.000899 | 0.0194 | angiotensin II receptor, type 1a [Source:MGI Symbol;Acc:MGI:87964] |
| ENSMUSG00000063142 | Kcnma1 | 2.43 | 0.000919 | 0.0196 | potassium large conductance calcium-activated channel, subfamily M, alpha member 1 [Source:MGI Symbol;Acc:MGI:99923] |
| ENSMUSG00000031616 | Ednra | 1.78 | 0.00102 | 0.0206 | endothelin receptor type A [Source:MGI Symbol;Acc:MGI:105923] |
| ENSMUSG00000040061 | Plcb2 | 1.5 | 0.00185 | 0.03 | phospholipase C, beta 2 [Source:MGI Symbol;Acc:MGI:107465] |
| ENSMUSG00000059588 | Calcrl | 1.49 | 0.00226 | 0.0341 | calcitonin receptor-like [Source:MGI Symbol;Acc:MGI:1926944] |
Pathview
q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
dplyr::mutate_if(is.numeric, funs(as.character(signif(.,3)))) %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000028864 | Hgf | 4.13 | 4.67e-06 | 0.00158 | hepatocyte growth factor [Source:MGI Symbol;Acc:MGI:96079] |
| ENSMUSG00000022309 | Angpt1 | 3.39 | 1.11e-05 | 0.00231 | angiopoietin 1 [Source:MGI Symbol;Acc:MGI:108448] |
| ENSMUSG00000027009 | Itga4 | 2.07 | 1.91e-05 | 0.00285 | integrin alpha 4 [Source:MGI Symbol;Acc:MGI:96603] |
| ENSMUSG00000062960 | Kdr | 2.05 | 2.77e-05 | 0.00338 | kinase insert domain protein receptor [Source:MGI Symbol;Acc:MGI:96683] |
| ENSMUSG00000020053 | Igf1 | 2.78 | 3.45e-05 | 0.00364 | insulin-like growth factor 1 [Source:MGI Symbol;Acc:MGI:96432] |
| ENSMUSG00000031273 | Col4a6 | 3.47 | 4.39e-05 | 0.00413 | collagen, type IV, alpha 6 [Source:MGI Symbol;Acc:MGI:2152695] |
| ENSMUSG00000028047 | Thbs3 | 1.67 | 6.04e-05 | 0.0048 | thrombospondin 3 [Source:MGI Symbol;Acc:MGI:98739] |
| ENSMUSG00000028978 | Nos3 | 2.15 | 6.87e-05 | 0.00515 | nitric oxide synthase 3, endothelial cell [Source:MGI Symbol;Acc:MGI:97362] |
| ENSMUSG00000026840 | Lamc3 | 3.8 | 8.26e-05 | 0.00535 | laminin gamma 3 [Source:MGI Symbol;Acc:MGI:1344394] |
| ENSMUSG00000019846 | Lama4 | 1.94 | 9.99e-05 | 0.00591 | laminin, alpha 4 [Source:MGI Symbol;Acc:MGI:109321] |
| ENSMUSG00000029378 | Areg | 5.25 | 0.000134 | 0.00671 | amphiregulin [Source:MGI Symbol;Acc:MGI:88068] |
| ENSMUSG00000001281 | Itgb7 | 1.81 | 0.000135 | 0.00671 | integrin beta 7 [Source:MGI Symbol;Acc:MGI:96616] |
| ENSMUSG00000000184 | Ccnd2 | 1.71 | 0.000137 | 0.00673 | cyclin D2 [Source:MGI Symbol;Acc:MGI:88314] |
| ENSMUSG00000026193 | Fn1 | 1.97 | 0.000137 | 0.00673 | fibronectin 1 [Source:MGI Symbol;Acc:MGI:95566] |
| ENSMUSG00000049929 | Lpar4 | 2.15 | 0.000192 | 0.0083 | lysophosphatidic acid receptor 4 [Source:MGI Symbol;Acc:MGI:1925384] |
| ENSMUSG00000006386 | Tek | 2.34 | 0.000221 | 0.0088 | TEK receptor tyrosine kinase [Source:MGI Symbol;Acc:MGI:98664] |
| ENSMUSG00000038811 | Gngt2 | 1.82 | 0.000267 | 0.00986 | guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2 [Source:MGI Symbol;Acc:MGI:893584] |
| ENSMUSG00000046207 | Pik3r6 | 1.69 | 0.000332 | 0.0114 | phosphoinositide-3-kinase regulatory subunit 5 [Source:MGI Symbol;Acc:MGI:2144613] |
| ENSMUSG00000042284 | Itga1 | 1.94 | 0.000365 | 0.0118 | integrin alpha 1 [Source:MGI Symbol;Acc:MGI:96599] |
| ENSMUSG00000028626 | Col9a2 | 4.13 | 0.000373 | 0.012 | collagen, type IX, alpha 2 [Source:MGI Symbol;Acc:MGI:88466] |
| ENSMUSG00000042817 | Flt3 | 2.08 | 0.000469 | 0.0137 | FMS-like tyrosine kinase 3 [Source:MGI Symbol;Acc:MGI:95559] |
| ENSMUSG00000032766 | Gng11 | 2.02 | 0.000655 | 0.0163 | guanine nucleotide binding protein (G protein), gamma 11 [Source:MGI Symbol;Acc:MGI:1913316] |
| ENSMUSG00000005672 | Kit | 1.52 | 0.000667 | 0.0164 | KIT proto-oncogene receptor tyrosine kinase [Source:MGI Symbol;Acc:MGI:96677] |
| ENSMUSG00000019899 | Lama2 | 1.83 | 0.000677 | 0.0166 | laminin, alpha 2 [Source:MGI Symbol;Acc:MGI:99912] |
| ENSMUSG00000031520 | Vegfc | 2.12 | 0.000842 | 0.0189 | vascular endothelial growth factor C [Source:MGI Symbol;Acc:MGI:109124] |
| ENSMUSG00000040003 | Magi2 | 1.52 | 0.000983 | 0.0204 | membrane associated guanylate kinase, WW and PDZ domain containing 2 [Source:MGI Symbol;Acc:MGI:1354953] |
| ENSMUSG00000048583 | Igf2 | 2.43 | 0.00102 | 0.0206 | insulin-like growth factor 2 [Source:MGI Symbol;Acc:MGI:96434] |
| ENSMUSG00000025348 | Itga7 | 1.58 | 0.00119 | 0.0227 | integrin alpha 7 [Source:MGI Symbol;Acc:MGI:102700] |
| ENSMUSG00000043004 | Gng2 | 1.24 | 0.00126 | 0.0235 | guanine nucleotide binding protein (G protein), gamma 2 [Source:MGI Symbol;Acc:MGI:102705] |
| ENSMUSG00000019966 | Kitl | 1.31 | 0.00138 | 0.0249 | kit ligand [Source:MGI Symbol;Acc:MGI:96974] |
| ENSMUSG00000048240 | Gng7 | 2.31 | 0.00245 | 0.0356 | guanine nucleotide binding protein (G protein), gamma 7 [Source:MGI Symbol;Acc:MGI:95787] |
| ENSMUSG00000019699 | Akt3 | 1.2 | 0.00271 | 0.038 | thymoma viral proto-oncogene 3 [Source:MGI Symbol;Acc:MGI:1345147] |
| ENSMUSG00000032192 | Gnb5 | 1.03 | 0.00306 | 0.0413 | guanine nucleotide binding protein (G protein), beta 5 [Source:MGI Symbol;Acc:MGI:101848] |
| ENSMUSG00000027669 | Gnb4 | 1.16 | 0.00354 | 0.0449 | guanine nucleotide binding protein (G protein), beta 4 [Source:MGI Symbol;Acc:MGI:104581] |
| ENSMUSG00000031304 | Il2rg | 1.88 | 0.00371 | 0.0462 | interleukin 2 receptor, gamma chain [Source:MGI Symbol;Acc:MGI:96551] |
| ENSMUSG00000026768 | Itga8 | 1.59 | 0.00387 | 0.0475 | integrin alpha 8 [Source:MGI Symbol;Acc:MGI:109442] |
| ENSMUSG00000020758 | Itgb4 | -1.5 | 0.00412 | 0.0495 | integrin beta 4 [Source:MGI Symbol;Acc:MGI:96613] |
Pathview
q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
dplyr::mutate_if(is.numeric, funs(as.character(signif(.,3)))) %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000028864 | Hgf | 4.13 | 4.67e-06 | 0.00158 | hepatocyte growth factor [Source:MGI Symbol;Acc:MGI:96079] |
| ENSMUSG00000027009 | Itga4 | 2.07 | 1.91e-05 | 0.00285 | integrin alpha 4 [Source:MGI Symbol;Acc:MGI:96603] |
| ENSMUSG00000062960 | Kdr | 2.05 | 2.77e-05 | 0.00338 | kinase insert domain protein receptor [Source:MGI Symbol;Acc:MGI:96683] |
| ENSMUSG00000020053 | Igf1 | 2.78 | 3.45e-05 | 0.00364 | insulin-like growth factor 1 [Source:MGI Symbol;Acc:MGI:96432] |
| ENSMUSG00000031273 | Col4a6 | 3.47 | 4.39e-05 | 0.00413 | collagen, type IV, alpha 6 [Source:MGI Symbol;Acc:MGI:2152695] |
| ENSMUSG00000028047 | Thbs3 | 1.67 | 6.04e-05 | 0.0048 | thrombospondin 3 [Source:MGI Symbol;Acc:MGI:98739] |
| ENSMUSG00000026840 | Lamc3 | 3.8 | 8.26e-05 | 0.00535 | laminin gamma 3 [Source:MGI Symbol;Acc:MGI:1344394] |
| ENSMUSG00000019846 | Lama4 | 1.94 | 9.99e-05 | 0.00591 | laminin, alpha 4 [Source:MGI Symbol;Acc:MGI:109321] |
| ENSMUSG00000001281 | Itgb7 | 1.81 | 0.000135 | 0.00671 | integrin beta 7 [Source:MGI Symbol;Acc:MGI:96616] |
| ENSMUSG00000000184 | Ccnd2 | 1.71 | 0.000137 | 0.00673 | cyclin D2 [Source:MGI Symbol;Acc:MGI:88314] |
| ENSMUSG00000026193 | Fn1 | 1.97 | 0.000137 | 0.00673 | fibronectin 1 [Source:MGI Symbol;Acc:MGI:95566] |
| ENSMUSG00000021448 | Shc3 | 2.15 | 0.000159 | 0.00732 | src homology 2 domain-containing transforming protein C3 [Source:MGI Symbol;Acc:MGI:106179] |
| ENSMUSG00000024867 | Pip5k1b | 1.5 | 0.000198 | 0.00839 | phosphatidylinositol-4-phosphate 5-kinase, type 1 beta [Source:MGI Symbol;Acc:MGI:107930] |
| ENSMUSG00000042284 | Itga1 | 1.94 | 0.000365 | 0.0118 | integrin alpha 1 [Source:MGI Symbol;Acc:MGI:96599] |
| ENSMUSG00000028626 | Col9a2 | 4.13 | 0.000373 | 0.012 | collagen, type IX, alpha 2 [Source:MGI Symbol;Acc:MGI:88466] |
| ENSMUSG00000019899 | Lama2 | 1.83 | 0.000677 | 0.0166 | laminin, alpha 2 [Source:MGI Symbol;Acc:MGI:99912] |
| ENSMUSG00000031520 | Vegfc | 2.12 | 0.000842 | 0.0189 | vascular endothelial growth factor C [Source:MGI Symbol;Acc:MGI:109124] |
| ENSMUSG00000022439 | Parvg | 1.77 | 0.00117 | 0.0225 | parvin, gamma [Source:MGI Symbol;Acc:MGI:2158329] |
| ENSMUSG00000025348 | Itga7 | 1.58 | 0.00119 | 0.0227 | integrin alpha 7 [Source:MGI Symbol;Acc:MGI:102700] |
| ENSMUSG00000022438 | Parvb | 1.64 | 0.00146 | 0.0259 | parvin, beta [Source:MGI Symbol;Acc:MGI:2153063] |
| ENSMUSG00000068699 | Flnc | 1.18 | 0.00187 | 0.03 | filamin C, gamma [Source:MGI Symbol;Acc:MGI:95557] |
| ENSMUSG00000052698 | Tln2 | 1.24 | 0.00193 | 0.0305 | talin 2 [Source:MGI Symbol;Acc:MGI:1917799] |
| ENSMUSG00000019843 | Fyn | 1.18 | 0.0023 | 0.0345 | Fyn proto-oncogene [Source:MGI Symbol;Acc:MGI:95602] |
| ENSMUSG00000019699 | Akt3 | 1.2 | 0.00271 | 0.038 | thymoma viral proto-oncogene 3 [Source:MGI Symbol;Acc:MGI:1345147] |
| ENSMUSG00000007655 | Cav1 | 1.6 | 0.00365 | 0.0457 | caveolin 1, caveolae protein [Source:MGI Symbol;Acc:MGI:102709] |
| ENSMUSG00000026768 | Itga8 | 1.59 | 0.00387 | 0.0475 | integrin alpha 8 [Source:MGI Symbol;Acc:MGI:109442] |
| ENSMUSG00000020758 | Itgb4 | -1.5 | 0.00412 | 0.0495 | integrin beta 4 [Source:MGI Symbol;Acc:MGI:96613] |
Pathview
q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
dplyr::mutate_if(is.numeric, funs(as.character(signif(.,3)))) %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000029375 | Cxcl15 | 6.92 | 1.77e-08 | 0.000153 | chemokine (C-X-C motif) ligand 15 [Source:MGI Symbol;Acc:MGI:1339941] |
| ENSMUSG00000034457 | Eda2r | 3.52 | 4.14e-05 | 0.00405 | ectodysplasin A2 receptor [Source:MGI Symbol;Acc:MGI:2442860] |
| ENSMUSG00000073889 | Il11ra1 | 1.54 | 0.000143 | 0.00689 | interleukin 11 receptor, alpha chain 1 [Source:MGI Symbol;Acc:MGI:107426] |
| ENSMUSG00000050232 | Cxcr3 | 2.28 | 0.000222 | 0.00881 | chemokine (C-X-C motif) receptor 3 [Source:MGI Symbol;Acc:MGI:1277207] |
| ENSMUSG00000061353 | Cxcl12 | 2.57 | 0.000222 | 0.00881 | chemokine (C-X-C motif) ligand 12 [Source:MGI Symbol;Acc:MGI:103556] |
| ENSMUSG00000025352 | Gdf11 | 2.25 | 0.000276 | 0.0101 | growth differentiation factor 11 [Source:MGI Symbol;Acc:MGI:1338027] |
| ENSMUSG00000037660 | Gdf7 | 3.41 | 0.000422 | 0.0129 | growth differentiation factor 7 [Source:MGI Symbol;Acc:MGI:95690] |
| ENSMUSG00000031497 | Tnfsf13b | 2.22 | 0.000488 | 0.0139 | tumor necrosis factor (ligand) superfamily, member 13b [Source:MGI Symbol;Acc:MGI:1344376] |
| ENSMUSG00000021943 | Gdf10 | 2.74 | 0.000561 | 0.0149 | growth differentiation factor 10 [Source:MGI Symbol;Acc:MGI:95684] |
| ENSMUSG00000005465 | Il27ra | 1.94 | 0.00077 | 0.0179 | interleukin 27 receptor, alpha [Source:MGI Symbol;Acc:MGI:1355318] |
| ENSMUSG00000063727 | Tnfrsf11b | 2.13 | 0.000829 | 0.0187 | tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin) [Source:MGI Symbol;Acc:MGI:109587] |
| ENSMUSG00000026573 | Xcl1 | 2.67 | 0.00118 | 0.0226 | chemokine (C motif) ligand 1 [Source:MGI Symbol;Acc:MGI:104593] |
| ENSMUSG00000060509 | Xcr1 | 2 | 0.00195 | 0.0308 | chemokine (C motif) receptor 1 [Source:MGI Symbol;Acc:MGI:1346338] |
| ENSMUSG00000071713 | Csf2rb | 2.03 | 0.00198 | 0.031 | colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage) [Source:MGI Symbol;Acc:MGI:1339759] |
| ENSMUSG00000000791 | Il12rb1 | 2.13 | 0.00338 | 0.0437 | interleukin 12 receptor, beta 1 [Source:MGI Symbol;Acc:MGI:104579] |
| ENSMUSG00000031304 | Il2rg | 1.88 | 0.00371 | 0.0462 | interleukin 2 receptor, gamma chain [Source:MGI Symbol;Acc:MGI:96551] |
| ENSMUSG00000003227 | Edar | 2.57 | 0.00406 | 0.0491 | ectodysplasin-A receptor [Source:MGI Symbol;Acc:MGI:1343498] |
Pathview
p=p+1q=1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
dplyr::mutate_if(is.numeric, funs(as.character(signif(.,3)))) %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000027009 | Itga4 | 2.07 | 0.000232 | 0.0204 | integrin alpha 4 [Source:MGI Symbol;Acc:MGI:96603] |
| ENSMUSG00000057614 | Gnai1 | 2.41 | 0.000662 | 0.0369 | guanine nucleotide binding protein (G protein), alpha inhibiting 1 [Source:MGI Symbol;Acc:MGI:95771] |
| ENSMUSG00000031740 | Mmp2 | 2.27 | 0.000956 | 0.0456 | matrix metallopeptidase 2 [Source:MGI Symbol;Acc:MGI:97009] |
| ENSMUSG00000061353 | Cxcl12 | 2.57 | 0.000976 | 0.0461 | chemokine (C-X-C motif) ligand 12 [Source:MGI Symbol;Acc:MGI:103556] |
Pathview
q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
dplyr::mutate_if(is.numeric, funs(as.character(signif(.,3)))) %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000027009 | Itga4 | 2.07 | 0.000232 | 0.0204 | integrin alpha 4 [Source:MGI Symbol;Acc:MGI:96603] |
| ENSMUSG00000002033 | Cd3g | 3.65 | 0.000542 | 0.0333 | CD3 antigen, gamma polypeptide [Source:MGI Symbol;Acc:MGI:88333] |
| ENSMUSG00000005087 | Cd44 | 2.27 | 0.000591 | 0.0347 | CD44 antigen [Source:MGI Symbol;Acc:MGI:88338] |
Pathview
q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
dplyr::mutate_if(is.numeric, funs(as.character(signif(.,3)))) %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000022683 | Pla2g10 | 5.77 | 3.22e-05 | 0.0076 | phospholipase A2, group X [Source:MGI Symbol;Acc:MGI:1347522] |
| ENSMUSG00000045875 | Adra1a | 4.13 | 0.000138 | 0.0159 | adrenergic receptor, alpha 1a [Source:MGI Symbol;Acc:MGI:104773] |
| ENSMUSG00000030669 | Calca | 5.76 | 0.000547 | 0.0333 | calcitonin/calcitonin-related polypeptide, alpha [Source:MGI Symbol;Acc:MGI:2151253] |
| ENSMUSG00000027524 | Edn3 | 3.85 | 0.000681 | 0.0375 | endothelin 3 [Source:MGI Symbol;Acc:MGI:95285] |
Pathview
q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
dplyr::mutate_if(is.numeric, funs(as.character(signif(.,3)))) %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000028864 | Hgf | 4.13 | 1.35e-05 | 0.00457 | hepatocyte growth factor [Source:MGI Symbol;Acc:MGI:96079] |
| ENSMUSG00000022309 | Angpt1 | 3.39 | 4.23e-05 | 0.00854 | angiopoietin 1 [Source:MGI Symbol;Acc:MGI:108448] |
| ENSMUSG00000031273 | Col4a6 | 3.47 | 0.000139 | 0.0159 | collagen, type IV, alpha 6 [Source:MGI Symbol;Acc:MGI:2152695] |
| ENSMUSG00000020053 | Igf1 | 2.78 | 0.000173 | 0.0173 | insulin-like growth factor 1 [Source:MGI Symbol;Acc:MGI:96432] |
| ENSMUSG00000026840 | Lamc3 | 3.8 | 0.000211 | 0.019 | laminin gamma 3 [Source:MGI Symbol;Acc:MGI:1344394] |
| ENSMUSG00000029378 | Areg | 5.25 | 0.000226 | 0.0201 | amphiregulin [Source:MGI Symbol;Acc:MGI:88068] |
| ENSMUSG00000027009 | Itga4 | 2.07 | 0.000232 | 0.0204 | integrin alpha 4 [Source:MGI Symbol;Acc:MGI:96603] |
| ENSMUSG00000062960 | Kdr | 2.05 | 0.000327 | 0.0254 | kinase insert domain protein receptor [Source:MGI Symbol;Acc:MGI:96683] |
| ENSMUSG00000028978 | Nos3 | 2.15 | 0.000585 | 0.0347 | nitric oxide synthase 3, endothelial cell [Source:MGI Symbol;Acc:MGI:97362] |
| ENSMUSG00000028626 | Col9a2 | 4.13 | 0.000733 | 0.0389 | collagen, type IX, alpha 2 [Source:MGI Symbol;Acc:MGI:88466] |
| ENSMUSG00000019846 | Lama4 | 1.94 | 0.00105 | 0.0475 | laminin, alpha 4 [Source:MGI Symbol;Acc:MGI:109321] |
Pathview
q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
dplyr::mutate_if(is.numeric, funs(as.character(signif(.,3)))) %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000028864 | Hgf | 4.13 | 1.35e-05 | 0.00457 | hepatocyte growth factor [Source:MGI Symbol;Acc:MGI:96079] |
| ENSMUSG00000031273 | Col4a6 | 3.47 | 0.000139 | 0.0159 | collagen, type IV, alpha 6 [Source:MGI Symbol;Acc:MGI:2152695] |
| ENSMUSG00000020053 | Igf1 | 2.78 | 0.000173 | 0.0173 | insulin-like growth factor 1 [Source:MGI Symbol;Acc:MGI:96432] |
| ENSMUSG00000026840 | Lamc3 | 3.8 | 0.000211 | 0.019 | laminin gamma 3 [Source:MGI Symbol;Acc:MGI:1344394] |
| ENSMUSG00000027009 | Itga4 | 2.07 | 0.000232 | 0.0204 | integrin alpha 4 [Source:MGI Symbol;Acc:MGI:96603] |
| ENSMUSG00000062960 | Kdr | 2.05 | 0.000327 | 0.0254 | kinase insert domain protein receptor [Source:MGI Symbol;Acc:MGI:96683] |
| ENSMUSG00000028626 | Col9a2 | 4.13 | 0.000733 | 0.0389 | collagen, type IX, alpha 2 [Source:MGI Symbol;Acc:MGI:88466] |
| ENSMUSG00000019846 | Lama4 | 1.94 | 0.00105 | 0.0475 | laminin, alpha 4 [Source:MGI Symbol;Acc:MGI:109321] |
Pathview
q=q+1kegg_heat[[p]][[q]]
display_matrix[[p]][[q]] %>%
dplyr::mutate_if(is.numeric, funs(as.character(signif(.,3)))) %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Gene Name | logFC | P Value | Adjusted P Value | Description | |
|---|---|---|---|---|---|
| ENSMUSG00000029375 | Cxcl15 | 6.92 | 3.25e-08 | 0.00028 | chemokine (C-X-C motif) ligand 15 [Source:MGI Symbol;Acc:MGI:1339941] |
| ENSMUSG00000034457 | Eda2r | 3.52 | 0.000128 | 0.0153 | ectodysplasin A2 receptor [Source:MGI Symbol;Acc:MGI:2442860] |
| ENSMUSG00000061353 | Cxcl12 | 2.57 | 0.000976 | 0.0461 | chemokine (C-X-C motif) ligand 12 [Source:MGI Symbol;Acc:MGI:103556] |
| ENSMUSG00000037660 | Gdf7 | 3.41 | 0.00103 | 0.0473 | growth differentiation factor 7 [Source:MGI Symbol;Acc:MGI:95690] |
Pathview
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] whisker_0.4 matrixStats_0.62.0
[79] patchwork_1.1.2 hms_1.1.2
[81] evaluate_0.17 xtable_1.8-4
[83] XML_3.99-0.11 readxl_1.4.1
[85] gridExtra_2.3 ggupset_0.3.0
[87] compiler_4.2.1 writexl_1.4.0
[89] shadowtext_0.1.2 crayon_1.5.2
[91] htmltools_0.5.3 ggfun_0.0.7
[93] later_1.3.0 tzdb_0.3.0
[95] geneplotter_1.74.0 aplot_0.1.8
[97] lubridate_1.8.0 DBI_1.1.3
[99] tweenr_2.0.2 dbplyr_2.2.1
[101] MASS_7.3-57 Matrix_1.5-1
[103] car_3.1-0 cli_3.4.1
[105] parallel_4.2.1 igraph_1.3.5
[107] GenomicRanges_1.48.0 pkgconfig_2.0.3
[109] xml2_1.3.3 ggtree_3.4.4
[111] svglite_2.1.0 annotate_1.74.0
[113] bslib_0.4.0 webshot_0.5.4
[115] XVector_0.36.0 rvest_1.0.3
[117] yulab.utils_0.0.5 digest_0.6.29
[119] graph_1.74.0 Biostrings_2.64.1
[121] rmarkdown_2.17 cellranger_1.1.0
[123] fastmatch_1.1-3 tidytree_0.4.1
[125] curl_4.3.3 nlme_3.1-157
[127] lifecycle_1.0.3 jsonlite_1.8.2
[129] carData_3.0-5 fansi_1.0.3
[131] pillar_1.8.1 lattice_0.20-45
[133] fastmap_1.1.0 httr_1.4.4
[135] survival_3.3-1 GO.db_3.15.0
[137] glue_1.6.2 png_0.1-7
[139] Rgraphviz_2.40.0 bit_4.0.4
[141] ggforce_0.4.1 stringi_1.7.8
[143] sass_0.4.2 blob_1.2.3
[145] textshaping_0.3.6 org.Hs.eg.db_3.15.0
[147] DESeq2_1.36.0 memoise_2.0.1
[149] ape_5.6-2