- Data Setup
- Import DGElist Data
- Reactome
- Export Data
Reactome Analysis
Ha M. Tran
22/08/2021
Last updated: 2023-01-23
Checks: 7 0
Knit directory: SRB_2022/1_analysis/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | eb10bef | Ha Manh Tran | 2023-01-22 | workflowr::wflow_publish(here::here("1_analysis/*.Rmd")) |
| html | 8c9178d | tranmanhha135 | 2023-01-21 | added png |
| html | d578f46 | Ha Manh Tran | 2023-01-21 | Build site. |
| html | 159f352 | tranmanhha135 | 2023-01-21 | adding for pathview |
| Rmd | 4d51a4e | tranmanhha135 | 2023-01-20 | test png |
| html | 4d51a4e | tranmanhha135 | 2023-01-20 | test png |
| html | 691cf34 | Ha Manh Tran | 2023-01-20 | Build site. |
| Rmd | 7f6bab2 | Ha Manh Tran | 2023-01-20 | workflowr::wflow_publish(here::here("1_analysis/*.Rmd")) |
| Rmd | b6cf190 | tranmanhha135 | 2023-01-19 | quick commit |
| Rmd | 3119fad | tranmanhha135 | 2022-11-05 | build website |
| html | 3119fad | tranmanhha135 | 2022-11-05 | build website |
Data Setup
# working with data
library(dplyr)
library(magrittr)
library(readr)
library(tibble)
library(reshape2)
library(tidyverse)
# Visualisation:
library(kableExtra)
library(ggplot2)
library(grid)
library(pander)
library(cowplot)
library(pheatmap)
# Custom ggplot
library(ggbiplot)
library(ggrepel)
theme_set(theme_light())
pub <- readRDS(here::here("0_data/RDS_objects/pub.rds"))
# Bioconductor packages:
library(edgeR)
library(limma)
library(Glimma)
library(clusterProfiler)
library(org.Mm.eg.db)
library(enrichplot)
library(ReactomePA)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"))Reactome
p=1reactome=list()
reactome_all=list()
reactome_sig=list()
for (i in 1:length(fc)) {
x <- fc[i] %>% as.character()
reactome[[x]] <- enrichPathway(gene = lmTreat_sig[[x]]$entrezid, organism = "mouse", pvalueCutoff = 0.05, pAdjustMethod = "fdr", readable = T)
reactome_all[[x]] <- reactome[[x]]@result
reactome_sig[[x]] <- reactome_all[[x]] %>% dplyr::filter(p.adjust <= 0.05) %>%
separate(col = BgRatio, sep = "/", into = c("Total", "Universe")) %>%
dplyr::mutate(
logFDR = -log(p.adjust, 10),
GeneRatio = Count / as.numeric(Total))%>%
dplyr::select(c("Description", "GeneRatio", "pvalue", "p.adjust", "logFDR", "qvalue", "geneID", "Count"))
# at the beginnning of a word (after 35 characters), add a newline. shorten the y axis for dot plot
reactome_sig[[x]]$Description <- sub(pattern = "(.{1,55})(?:$| )",
replacement = "\\1\n",
x = reactome_sig[[x]]$Description)
# remove the additional newline at the end of the string
reactome_sig[[x]]$Description <- sub(pattern = "\n$",
replacement = "",
x = reactome_sig[[x]]$Description)
}
reactome_sig[[p]] %>%
dplyr::mutate_if(is.numeric, funs(as.character(signif(., 3)))) %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Description | GeneRatio | pvalue | p.adjust | logFDR | qvalue | geneID | Count | |
|---|---|---|---|---|---|---|---|---|
| R-MMU-112316 | Neuronal System | 0.174 | 3.21e-09 | 2.26e-06 | 5.65 | 1.93e-06 | Kcnk3/Kcnb2/Syn2/Slc1a3/Kcnj3/Gria4/Kcna6/Kcnd2/Ptprd/Kcnd3/Nlgn1/Epb41l3/Abat/Lrrc7/Gnai1/Lrrc4b/Kcnq5/Grin2b/Adcy3/Shank2/Maoa/Gngt2/Plcb1/Ppfia2/Slitrk3/Rps6ka2/Glrb/Ppfia4/Adcy4/Adcy7/Gabra4/Dlg2/Gng11/Lin7a/Nlgn3/Tspan7/Kcnma1/Gjc1/Gng2/Kcnc4/Plcb2/Slc38a1/Lrfn2/Dlg4/Kcng4/Gnb5/Arhgef9/Gnb4/Gabbr1/Kcnq4/Cacna1a/Cacnb4/Prkar1b/Kcnh1/Camk1/Nlgn2 | 56 |
| R-MMU-1474244 | Extracellular matrix organization | 0.19 | 1.13e-08 | 3.98e-06 | 5.4 | 3.4e-06 | Col11a1/Mmp16/Col26a1/Itga4/P3h3/Col14a1/Capn6/Ddr2/Col4a6/Cd44/Lama4/Col16a1/Itgb7/Fn1/Mmp2/Icam1/Nid1/Jam3/Itga1/Col13a1/Loxl3/Itgal/Emilin1/Pecam1/Col5a2/Ltbp3/Mmp19/Bgn/Col15a1/P3h1/Adam19/Efemp2/Crtap/Col23a1/Col18a1/Itga8/Itgb4/Tmprss6/Lum/Nid2/Bmp7/Jam2/Fbln5/Col4a5 | 44 |
| R-MMU-109582 | Hemostasis | 0.145 | 7.52e-08 | 1.76e-05 | 4.75 | 1.5e-05 | Apob/Hgf/Angpt1/Itga4/Cd109/Igf1/Tfpi/Slc8a1/Nos3/Cd44/Pcdh7/P2rx2/Gnai1/Fn1/Pde1b/Serpine2/Jam3/Tek/Gngt2/Pik3r6/Dock2/Rasgrp2/Slc8a3/Trpc6/Sh2b2/Kif26a/Dock10/Maged2/Islr/Procr/Gng11/Itgal/Esam/Dgkb/Tubb4a/Vegfc/Pde1a/Sele/Pecam1/Kif6/Igf2/Gng2/Pros1/Arrb1/Sccpdh/Arrb2/Fyn/Pde5a/Cd84/Tor4a/Fgr/Habp4/Atp2b4/Gnb5/Fam3c/Selenop/Gnb4/Apbb1ip/Sri/Lat/Vps45/Kif16b/Spn/Lcp2/Pafah2/Lhfpl2/F2r/Prkar1b/Kif5a/Plek/Jam2 | 71 |
| R-MMU-418346 | Platelet homeostasis | 0.268 | 9.76e-07 | 0.000172 | 3.77 | 0.000146 | Apob/Slc8a1/Nos3/P2rx2/Pde1b/Gngt2/Slc8a3/Trpc6/Gng11/Pde1a/Pecam1/Gng2/Pde5a/Fgr/Atp2b4/Gnb5/Gnb4/Sri/Pafah2 | 19 |
| R-MMU-216083 | Integrin cell surface interactions | 0.273 | 1.39e-06 | 0.000196 | 3.71 | 0.000167 | Itga4/Col4a6/Cd44/Col16a1/Itgb7/Fn1/Icam1/Jam3/Itga1/Col13a1/Itgal/Pecam1/Col5a2/Col18a1/Itga8/Lum/Jam2/Col4a5 | 18 |
| R-MMU-112315 | Transmission across Chemical Synapses | 0.176 | 2.58e-06 | 0.000299 | 3.52 | 0.000255 | Syn2/Slc1a3/Kcnj3/Gria4/Abat/Lrrc7/Gnai1/Grin2b/Adcy3/Maoa/Gngt2/Plcb1/Ppfia2/Rps6ka2/Glrb/Ppfia4/Adcy4/Adcy7/Gabra4/Dlg2/Gng11/Lin7a/Tspan7/Gng2/Plcb2/Slc38a1/Dlg4/Gnb5/Arhgef9/Gnb4/Gabbr1/Cacna1a/Cacnb4/Prkar1b/Camk1 | 35 |
| R-MMU-5173214 | O-glycosylation of TSR domain-containing proteins | 0.364 | 2.97e-06 | 0.000299 | 3.52 | 0.000255 | Adamts20/Sema5b/Adamts16/Adamts19/Thsd7b/Thsd1/Adamts1/Adamts10/Adamts7/Adamtsl1/Sbspon/Adamts17 | 12 |
| R-MMU-5173105 | O-linked glycosylation | 0.219 | 8.98e-06 | 0.000789 | 3.1 | 0.000674 | Adamts20/Sema5b/Adamts16/Adamts19/Thsd7b/Thsd1/Adamts1/Galnt16/St3gal2/St6galnac4/Adamts10/Adamts7/Galntl6/Adamtsl1/Pomt2/Large1/B3gnt5/St3gal4/Sbspon/Adamts17/Galnt18 | 21 |
| R-MMU-112314 | Neurotransmitter receptors and postsynaptic signal transmission | 0.184 | 3.25e-05 | 0.00254 | 2.6 | 0.00216 | Kcnj3/Gria4/Lrrc7/Gnai1/Grin2b/Adcy3/Gngt2/Plcb1/Rps6ka2/Glrb/Adcy4/Adcy7/Gabra4/Dlg2/Gng11/Tspan7/Gng2/Plcb2/Dlg4/Gnb5/Arhgef9/Gnb4/Gabbr1/Prkar1b/Camk1 | 25 |
| R-MMU-416482 | G alpha (12/13) signalling events | 0.229 | 5.92e-05 | 0.00416 | 2.38 | 0.00355 | Plxnb1/Adra1a/Arhgef25/Gngt2/Gng11/Arhgef15/Gng2/Arhgef26/Net1/Fgd1/Gnb5/Ngef/Arhgef9/Gnb4/Fgd2/Plekhg5 | 16 |
| R-MMU-418597 | G alpha (z) signalling events | 0.323 | 6.65e-05 | 0.00425 | 2.37 | 0.00363 | Rgs16/Adcy3/Gngt2/Adcy4/Adcy7/Gng11/Gng2/Gnaz/Gnb5/Gnb4 | 10 |
| R-MMU-6794362 | Protein-protein interactions at synapses | 0.227 | 0.000107 | 0.00629 | 2.2 | 0.00537 | Gria4/Ptprd/Nlgn1/Epb41l3/Lrrc4b/Grin2b/Shank2/Ppfia2/Slitrk3/Ppfia4/Dlg2/Nlgn3/Lrfn2/Dlg4/Nlgn2 | 15 |
| R-MMU-1650814 | Collagen biosynthesis and modifying enzymes | 0.233 | 0.000134 | 0.00689 | 2.16 | 0.00588 | Col11a1/Col26a1/P3h3/Col14a1/Col4a6/Col16a1/Col13a1/Col5a2/Col15a1/P3h1/Crtap/Col23a1/Col18a1/Col4a5 | 14 |
| R-MMU-977444 | GABA B receptor activation | 0.275 | 0.000147 | 0.00689 | 2.16 | 0.00588 | Kcnj3/Gnai1/Adcy3/Gngt2/Adcy4/Adcy7/Gng11/Gng2/Gnb5/Gnb4/Gabbr1 | 11 |
| R-MMU-991365 | Activation of GABAB receptors | 0.275 | 0.000147 | 0.00689 | 2.16 | 0.00588 | Kcnj3/Gnai1/Adcy3/Gngt2/Adcy4/Adcy7/Gng11/Gng2/Gnb5/Gnb4/Gabbr1 | 11 |
| R-MMU-76002 | Platelet activation, signaling and aggregation | 0.144 | 2e-04 | 0.0088 | 2.06 | 0.00751 | Hgf/Cd109/Igf1/Pcdh7/Gnai1/Fn1/Gngt2/Pik3r6/Rasgrp2/Trpc6/Maged2/Islr/Gng11/Dgkb/Vegfc/Pecam1/Igf2/Gng2/Pros1/Arrb1/Sccpdh/Arrb2/Fyn/Tor4a/Habp4/Gnb5/Fam3c/Selenop/Gnb4/Apbb1ip/Lat/Lcp2/Lhfpl2/F2r/Plek | 35 |
| R-MMU-977443 | GABA receptor activation | 0.232 | 0.000245 | 0.0101 | 1.99 | 0.00864 | Kcnj3/Gnai1/Adcy3/Gngt2/Adcy4/Adcy7/Gabra4/Gng11/Gng2/Gnb5/Arhgef9/Gnb4/Gabbr1 | 13 |
| R-MMU-397795 | G-protein beta:gamma signalling | 0.3 | 0.000288 | 0.0111 | 1.95 | 0.0095 | Gngt2/Pik3r6/Plcb1/Gng11/Gng2/Plcb2/Akt3/Gnb5/Gnb4 | 9 |
| R-MMU-1296071 | Potassium Channels | 0.188 | 0.000314 | 0.0111 | 1.95 | 0.0095 | Kcnk3/Kcnb2/Kcnj3/Kcna6/Kcnd2/Kcnd3/Kcnq5/Gngt2/Gng11/Kcnma1/Gng2/Kcnc4/Kcng4/Gnb5/Gnb4/Gabbr1/Kcnq4/Kcnh1 | 18 |
| R-MMU-202433 | Generation of second messenger molecules | 0.368 | 0.000337 | 0.0111 | 1.95 | 0.0095 | Itk/Cd3g/Zap70/Lat/Lcp2/Grap2/Cd4 | 7 |
| R-MMU-418217 | G beta:gamma signalling through PLC beta | 0.368 | 0.000337 | 0.0111 | 1.95 | 0.0095 | Gngt2/Plcb1/Gng11/Gng2/Plcb2/Gnb5/Gnb4 | 7 |
| R-MMU-1474290 | Collagen formation | 0.205 | 0.000352 | 0.0111 | 1.95 | 0.0095 | Col11a1/Col26a1/P3h3/Col14a1/Col4a6/Col16a1/Col13a1/Loxl3/Col5a2/Col15a1/P3h1/Crtap/Col23a1/Col18a1/Col4a5 | 15 |
| R-MMU-202733 | Cell surface interactions at the vascular wall | 0.191 | 0.000364 | 0.0111 | 1.95 | 0.0095 | Apob/Angpt1/Itga4/Cd44/Fn1/Jam3/Tek/Procr/Itgal/Esam/Sele/Pecam1/Pros1/Fyn/Cd84/Spn/Jam2 | 17 |
| R-MMU-3000157 | Laminin interactions | 0.5 | 0.000477 | 0.0136 | 1.87 | 0.0116 | Col4a6/Lama4/Nid1/Nid2/Col4a5 | 5 |
| R-MMU-500657 | Presynaptic function of Kainate receptors | 0.35 | 0.000485 | 0.0136 | 1.87 | 0.0116 | Gngt2/Plcb1/Gng11/Gng2/Plcb2/Gnb5/Gnb4 | 7 |
| R-MMU-111885 | Opioid Signalling | 0.203 | 0.000628 | 0.0164 | 1.79 | 0.014 | Gnai1/Pde1b/Adcy3/Gngt2/Plcb1/Adcy4/Adcy7/Gng11/Pde1a/Gng2/Plcb2/Gnb5/Gnb4/Prkar1b | 14 |
| R-MMU-4085001 | Sialic acid metabolism | 0.273 | 0.000629 | 0.0164 | 1.79 | 0.014 | St6gal2/St8sia2/St8sia4/Npl/St3gal2/St6galnac4/St8sia6/St6galnac6/St3gal4 | 9 |
| R-MMU-8948216 | Collagen chain trimerization | 0.257 | 0.001 | 0.0252 | 1.6 | 0.0215 | Col11a1/Col26a1/Col14a1/Col16a1/Col13a1/Col5a2/Col15a1/Col23a1/Col18a1 | 9 |
| R-MMU-451326 | Activation of kainate receptors upon glutamate binding | 0.276 | 0.00116 | 0.0281 | 1.55 | 0.024 | Gngt2/Plcb1/Gng11/Gng2/Plcb2/Dlg4/Gnb5/Gnb4 | 8 |
| R-MMU-4086398 | Ca2+ pathway | 0.233 | 0.00124 | 0.0291 | 1.54 | 0.0248 | Lef1/Wnt11/Gngt2/Plcb1/Gng11/Gng2/Plcb2/Fzd2/Gnb5/Gnb4 | 10 |
| R-MMU-9013149 | RAC1 GTPase cycle | 0.148 | 0.00131 | 0.0291 | 1.54 | 0.0248 | Nhs/Mcam/Fermt2/Wasf3/Arhgap45/Arhgef25/Arhgap25/Dock2/Dock10/Abi2/Sh3bp1/Arhgef15/Nckap1l/Arap3/Prex2/Arhgap10/Dlc1/Arhgap31/Ngef/Fgd5/Arhgap15/Cav1/Cyfip2/Pld2 | 24 |
| R-MMU-9012999 | RHO GTPase cycle | 0.12 | 0.00132 | 0.0291 | 1.54 | 0.0248 | Nhs/Mcam/Plxnb1/Ccdc88a/Pcdh7/Fermt2/Wasf3/Arhgap45/Arhgef25/Akap12/Arhgap25/Dock2/Slitrk3/Myo9a/Plxnd1/Dock10/Abi2/Sh3bp1/Arhgap6/Arhgef15/Nckap1l/Arap3/Prex2/Arhgap10/Dlc1/Arhgef26/Arhgap28/Net1/Pde5a/Fgd1/Dlg5/Arhgap31/Arfgap3/Zap70/Cep97/Ngef/Arhgef9/Fgd5/Arhgap15/Elmo2/Cav1/Cyfip2/Pld2/Wdr6/Fmnl3/Fgd2/Plekhg5 | 47 |
| R-MMU-1630316 | Glycosaminoglycan metabolism | 0.162 | 0.00137 | 0.0293 | 1.53 | 0.025 | Gpc6/Chst2/Cd44/Cspg4/Gpc3/B4galt2/Has2/St3gal2/Chst1/Glb1l/Bgn/Dse/Xylt1/St3gal4/Arsb/Abcc5/Gpc2/Lum/Papss2 | 19 |
| R-MMU-9013148 | CDC42 GTPase cycle | 0.181 | 0.00144 | 0.0297 | 1.53 | 0.0254 | Arhgap45/Arhgef25/Dock10/Arhgef15/Arap3/Prex2/Arhgap10/Dlc1/Arhgef26/Fgd1/Arhgap31/Ngef/Arhgef9/Cav1/Fgd2 | 15 |
| R-MMU-392451 | G beta:gamma signalling through PI3Kgamma | 0.292 | 0.00165 | 0.0332 | 1.48 | 0.0283 | Gngt2/Pik3r6/Gng11/Gng2/Akt3/Gnb5/Gnb4 | 7 |
| R-MMU-456926 | Thrombin signalling through proteinase activated receptors (PARs) | 0.258 | 0.00186 | 0.0363 | 1.44 | 0.031 | Gngt2/Gng11/Gng2/Arrb1/Arrb2/Gnb5/Gnb4/F2r | 8 |
react_dot=list()
upset=list()
for (i in 1:length(fc)) {
x <- fc[i] %>% as.character()
react_dot[[x]] <- ggplot(reactome_sig[[x]][1:12, ]) +
geom_point(aes(x = GeneRatio, y = reorder(Description, GeneRatio), colour = logFDR, size = Count)) +
scale_color_gradient(low = "dodgerblue3", high = "firebrick3", limits = c(0, NA)) +
scale_size(range = c(1.5,5)) +
ggtitle("Reactome Pathways") +
ylab(label = "") +
xlab(label = "Gene Ratio") +
labs(color = expression("-log"[10] * "FDR"), size = "Gene Counts")
ggsave(filename = paste0("react_dot_", x, ".svg"), plot = react_dot[[x]] + pub, path = here::here("2_plots/reactome/"),
width = 250, height = 130, units = "mm")
upset[[x]] <- upsetplot(x = reactome[[x]], 9)
ggsave(filename = paste0("upset_react_", fc[i], ".svg"), plot = upset[[x]], path = here::here("2_plots/reactome/"))
}
react_dot[[p]]
upset[[p]]
p=p+1reactome_sig[[p]] %>%
dplyr::mutate_if(is.numeric, funs(as.character(signif(., 3)))) %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Description | GeneRatio | pvalue | p.adjust | logFDR | qvalue | geneID | Count | |
|---|---|---|---|---|---|---|---|---|
| R-MMU-112316 | Neuronal System | 0.162 | 1.41e-09 | 9.38e-07 | 6.03 | 7.93e-07 | Kcnk3/Kcnb2/Syn2/Kcnj3/Slc1a3/Gria4/Kcna6/Kcnd2/Ptprd/Kcnd3/Nlgn1/Epb41l3/Lrrc7/Abat/Gnai1/Lrrc4b/Kcnq5/Grin2b/Adcy3/Maoa/Shank2/Gngt2/Ppfia2/Plcb1/Slitrk3/Rps6ka2/Glrb/Gabra4/Dlg2/Adcy4/Ppfia4/Gng11/Nlgn3/Lin7a/Adcy7/Tspan7/Kcnma1/Kcnc4/Gjc1/Gng2/Plcb2/Lrfn2/Kcng4/Slc38a1/Dlg4/Gnb5/Arhgef9/Gnb4/Kcnq4/Gabbr1/Cacna1a/Cacnb4 | 52 |
| R-MMU-1474244 | Extracellular matrix organization | 0.165 | 1.69e-07 | 5.61e-05 | 4.25 | 4.74e-05 | Col11a1/Mmp16/Col26a1/Itga4/P3h3/Col14a1/Capn6/Col4a6/Ddr2/Cd44/Lama4/Itgb7/Fn1/Mmp2/Col16a1/Icam1/Nid1/Jam3/Itga1/Col13a1/Loxl3/Itgal/Emilin1/Pecam1/Col5a2/Col15a1/Ltbp3/Mmp19/Bgn/P3h1/Adam19/Crtap/Efemp2/Col23a1/Col18a1/Itga8/Tmprss6/Itgb4 | 38 |
| R-MMU-5173214 | O-glycosylation of TSR domain-containing proteins | 0.364 | 6.86e-07 | 0.000152 | 3.82 | 0.000129 | Adamts20/Sema5b/Adamts16/Adamts19/Thsd7b/Thsd1/Adamts1/Adamts10/Adamts7/Adamtsl1/Sbspon/Adamts17 | 12 |
| R-MMU-112315 | Transmission across Chemical Synapses | 0.166 | 9.22e-07 | 0.000153 | 3.81 | 0.00013 | Syn2/Kcnj3/Slc1a3/Gria4/Lrrc7/Abat/Gnai1/Grin2b/Adcy3/Maoa/Gngt2/Ppfia2/Plcb1/Rps6ka2/Glrb/Gabra4/Dlg2/Adcy4/Ppfia4/Gng11/Lin7a/Adcy7/Tspan7/Gng2/Plcb2/Slc38a1/Dlg4/Gnb5/Arhgef9/Gnb4/Gabbr1/Cacna1a/Cacnb4 | 33 |
| R-MMU-109582 | Hemostasis | 0.123 | 2.41e-06 | 0.00032 | 3.49 | 0.00027 | Apob/Hgf/Angpt1/Itga4/Cd109/Igf1/Tfpi/Nos3/Slc8a1/Cd44/Pcdh7/P2rx2/Gnai1/Fn1/Serpine2/Tek/Pde1b/Jam3/Gngt2/Pik3r6/Slc8a3/Rasgrp2/Dock2/Sh2b2/Kif26a/Dock10/Trpc6/Procr/Gng11/Islr/Esam/Itgal/Dgkb/Vegfc/Tubb4a/Pde1a/Maged2/Sele/Kif6/Igf2/Pecam1/Pros1/Gng2/Arrb1/Sccpdh/Pde5a/Cd84/Arrb2/Fyn/Fgr/Atp2b4/Tor4a/Selenop/Gnb5/Lat/Fam3c/Habp4/Apbb1ip/Gnb4/Kif16b | 60 |
| R-MMU-418346 | Platelet homeostasis | 0.239 | 2.91e-06 | 0.000322 | 3.49 | 0.000272 | Apob/Nos3/Slc8a1/P2rx2/Pde1b/Gngt2/Slc8a3/Trpc6/Gng11/Pde1a/Pecam1/Gng2/Pde5a/Fgr/Atp2b4/Gnb5/Gnb4 | 17 |
| R-MMU-5173105 | O-linked glycosylation | 0.198 | 1.53e-05 | 0.00146 | 2.84 | 0.00123 | Adamts20/Sema5b/Adamts16/Adamts19/Thsd7b/Thsd1/Adamts1/Galnt16/St6galnac4/St3gal2/Adamts10/Adamts7/Galntl6/Adamtsl1/B3gnt5/Sbspon/St3gal4/Large1/Adamts17 | 19 |
| R-MMU-418597 | G alpha (z) signalling events | 0.323 | 2.02e-05 | 0.00161 | 2.79 | 0.00136 | Rgs16/Adcy3/Gngt2/Adcy4/Gng11/Adcy7/Gng2/Gnaz/Gnb5/Gnb4 | 10 |
| R-MMU-216083 | Integrin cell surface interactions | 0.227 | 2.18e-05 | 0.00161 | 2.79 | 0.00136 | Itga4/Col4a6/Cd44/Itgb7/Fn1/Col16a1/Icam1/Jam3/Itga1/Col13a1/Itgal/Pecam1/Col5a2/Col18a1/Itga8 | 15 |
| R-MMU-112314 | Neurotransmitter receptors and postsynaptic signal transmission | 0.169 | 3.02e-05 | 0.00201 | 2.7 | 0.0017 | Kcnj3/Gria4/Lrrc7/Gnai1/Grin2b/Adcy3/Gngt2/Plcb1/Rps6ka2/Glrb/Gabra4/Dlg2/Adcy4/Gng11/Adcy7/Tspan7/Gng2/Plcb2/Dlg4/Gnb5/Arhgef9/Gnb4/Gabbr1 | 23 |
| R-MMU-977444 | GABA B receptor activation | 0.275 | 4.2e-05 | 0.00233 | 2.63 | 0.00197 | Kcnj3/Gnai1/Adcy3/Gngt2/Adcy4/Gng11/Adcy7/Gng2/Gnb5/Gnb4/Gabbr1 | 11 |
| R-MMU-991365 | Activation of GABAB receptors | 0.275 | 4.2e-05 | 0.00233 | 2.63 | 0.00197 | Kcnj3/Gnai1/Adcy3/Gngt2/Adcy4/Gng11/Adcy7/Gng2/Gnb5/Gnb4/Gabbr1 | 11 |
| R-MMU-977443 | GABA receptor activation | 0.232 | 6.06e-05 | 0.0031 | 2.51 | 0.00262 | Kcnj3/Gnai1/Adcy3/Gngt2/Gabra4/Adcy4/Gng11/Adcy7/Gng2/Gnb5/Arhgef9/Gnb4/Gabbr1 | 13 |
| R-MMU-6794362 | Protein-protein interactions at synapses | 0.212 | 9.17e-05 | 0.00436 | 2.36 | 0.00368 | Gria4/Ptprd/Nlgn1/Epb41l3/Lrrc4b/Grin2b/Shank2/Ppfia2/Slitrk3/Dlg2/Ppfia4/Nlgn3/Lrfn2/Dlg4 | 14 |
| R-MMU-397795 | G-protein beta:gamma signalling | 0.3 | 1e-04 | 0.00445 | 2.35 | 0.00376 | Gngt2/Pik3r6/Plcb1/Gng11/Gng2/Plcb2/Akt3/Gnb5/Gnb4 | 9 |
| R-MMU-1650814 | Collagen biosynthesis and modifying enzymes | 0.217 | 0.000129 | 0.00538 | 2.27 | 0.00455 | Col11a1/Col26a1/P3h3/Col14a1/Col4a6/Col16a1/Col13a1/Col5a2/Col15a1/P3h1/Crtap/Col23a1/Col18a1 | 13 |
| R-MMU-418217 | G beta:gamma signalling through PLC beta | 0.368 | 0.000143 | 0.00558 | 2.25 | 0.00471 | Gngt2/Plcb1/Gng11/Gng2/Plcb2/Gnb5/Gnb4 | 7 |
| R-MMU-416482 | G alpha (12/13) signalling events | 0.2 | 0.000179 | 0.00638 | 2.2 | 0.00539 | Plxnb1/Adra1a/Arhgef25/Gngt2/Gng11/Arhgef15/Gng2/Arhgef26/Net1/Fgd1/Gnb5/Ngef/Arhgef9/Gnb4 | 14 |
| R-MMU-1296071 | Potassium Channels | 0.177 | 0.000182 | 0.00638 | 2.2 | 0.00539 | Kcnk3/Kcnb2/Kcnj3/Kcna6/Kcnd2/Kcnd3/Kcnq5/Gngt2/Gng11/Kcnma1/Kcnc4/Gng2/Kcng4/Gnb5/Gnb4/Kcnq4/Gabbr1 | 17 |
| R-MMU-500657 | Presynaptic function of Kainate receptors | 0.35 | 0.000207 | 0.00688 | 2.16 | 0.00581 | Gngt2/Plcb1/Gng11/Gng2/Plcb2/Gnb5/Gnb4 | 7 |
| R-MMU-4085001 | Sialic acid metabolism | 0.273 | 0.000226 | 0.00715 | 2.15 | 0.00604 | St6gal2/St8sia2/St8sia4/Npl/St6galnac4/St3gal2/St8sia6/St6galnac6/St3gal4 | 9 |
| R-MMU-1474290 | Collagen formation | 0.192 | 0.000284 | 0.00858 | 2.07 | 0.00725 | Col11a1/Col26a1/P3h3/Col14a1/Col4a6/Col16a1/Col13a1/Loxl3/Col5a2/Col15a1/P3h1/Crtap/Col23a1/Col18a1 | 14 |
| R-MMU-76002 | Platelet activation, signaling and aggregation | 0.128 | 0.000359 | 0.0102 | 1.99 | 0.00858 | Hgf/Cd109/Igf1/Pcdh7/Gnai1/Fn1/Gngt2/Pik3r6/Rasgrp2/Trpc6/Gng11/Islr/Dgkb/Vegfc/Maged2/Igf2/Pecam1/Pros1/Gng2/Arrb1/Sccpdh/Arrb2/Fyn/Tor4a/Selenop/Gnb5/Lat/Fam3c/Habp4/Apbb1ip/Gnb4 | 31 |
| R-MMU-8948216 | Collagen chain trimerization | 0.257 | 0.000366 | 0.0102 | 1.99 | 0.00858 | Col11a1/Col26a1/Col14a1/Col16a1/Col13a1/Col5a2/Col15a1/Col23a1/Col18a1 | 9 |
| R-MMU-4086398 | Ca2+ pathway | 0.233 | 0.000422 | 0.0112 | 1.95 | 0.00948 | Lef1/Wnt11/Gngt2/Plcb1/Gng11/Gng2/Plcb2/Fzd2/Gnb5/Gnb4 | 10 |
| R-MMU-9013149 | RAC1 GTPase cycle | 0.142 | 0.000455 | 0.0114 | 1.94 | 0.00965 | Nhs/Mcam/Fermt2/Wasf3/Arhgap45/Arhgef25/Arhgap25/Dock2/Dock10/Abi2/Sh3bp1/Arhgef15/Nckap1l/Arap3/Prex2/Arhgap10/Dlc1/Arhgap31/Ngef/Fgd5/Arhgap15/Cav1/Cyfip2 | 23 |
| R-MMU-451326 | Activation of kainate receptors upon glutamate binding | 0.276 | 0.000464 | 0.0114 | 1.94 | 0.00965 | Gngt2/Plcb1/Gng11/Gng2/Plcb2/Dlg4/Gnb5/Gnb4 | 8 |
| R-MMU-111885 | Opioid Signalling | 0.188 | 0.000556 | 0.0132 | 1.88 | 0.0112 | Gnai1/Pde1b/Adcy3/Gngt2/Plcb1/Adcy4/Gng11/Adcy7/Pde1a/Gng2/Plcb2/Gnb5/Gnb4 | 13 |
| R-MMU-392451 | G beta:gamma signalling through PI3Kgamma | 0.292 | 0.00073 | 0.0164 | 1.78 | 0.0139 | Gngt2/Pik3r6/Gng11/Gng2/Akt3/Gnb5/Gnb4 | 7 |
| R-MMU-202733 | Cell surface interactions at the vascular wall | 0.169 | 0.000742 | 0.0164 | 1.78 | 0.0139 | Apob/Angpt1/Itga4/Cd44/Fn1/Tek/Jam3/Procr/Esam/Itgal/Sele/Pecam1/Pros1/Cd84/Fyn | 15 |
| R-MMU-446728 | Cell junction organization | 0.188 | 0.000941 | 0.0202 | 1.7 | 0.0171 | Sdk2/Fermt2/Cdh2/Cdh6/Cdh13/Cdh10/Cdh5/Cdh11/Pard6g/Parvb/Flnc/Itgb4 | 12 |
| R-MMU-9013148 | CDC42 GTPase cycle | 0.169 | 0.00109 | 0.0227 | 1.64 | 0.0192 | Arhgap45/Arhgef25/Dock10/Arhgef15/Arap3/Prex2/Arhgef26/Arhgap10/Dlc1/Fgd1/Arhgap31/Ngef/Arhgef9/Cav1 | 14 |
| R-MMU-397014 | Muscle contraction | 0.137 | 0.00124 | 0.0249 | 1.6 | 0.0211 | Kcnk3/Cacna1c/Kcnd2/Ryr1/Kcnd3/Slc8a1/Tmod2/Gucy1a2/Slc8a3/Itga1/Gucy1b1/Mme/Gucy1a1/Myl3/Cacng7/Kcnip3/Asph/Ryr3/Pde5a/Atp2b4/Atp1a2 | 21 |
| R-MMU-1296041 | Activation of G protein gated Potassium channels | 0.259 | 0.00157 | 0.029 | 1.54 | 0.0245 | Kcnj3/Gngt2/Gng11/Gng2/Gnb5/Gnb4/Gabbr1 | 7 |
| R-MMU-1296059 | G protein gated Potassium channels | 0.259 | 0.00157 | 0.029 | 1.54 | 0.0245 | Kcnj3/Gngt2/Gng11/Gng2/Gnb5/Gnb4/Gabbr1 | 7 |
| R-MMU-997272 | Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits | 0.259 | 0.00157 | 0.029 | 1.54 | 0.0245 | Kcnj3/Gngt2/Gng11/Gng2/Gnb5/Gnb4/Gabbr1 | 7 |
| R-MMU-1630316 | Glycosaminoglycan metabolism | 0.145 | 0.00189 | 0.034 | 1.47 | 0.0287 | Gpc6/Chst2/Cd44/Cspg4/Gpc3/B4galt2/Has2/St3gal2/Chst1/Glb1l/Bgn/Xylt1/Dse/St3gal4/Arsb/Gpc2/Abcc5 | 17 |
| R-MMU-392170 | ADP signalling through P2Y purinoceptor 12 | 0.286 | 0.00198 | 0.0347 | 1.46 | 0.0293 | Gnai1/Gngt2/Gng11/Gng2/Gnb5/Gnb4 | 6 |
| R-MMU-400042 | Adrenaline,noradrenaline inhibits insulin secretion | 0.273 | 0.00257 | 0.0438 | 1.36 | 0.037 | Gnai1/Gngt2/Gng11/Gng2/Gnb5/Gnb4 | 6 |
| R-MMU-9012999 | RHO GTPase cycle | 0.105 | 0.00263 | 0.0438 | 1.36 | 0.037 | Nhs/Mcam/Plxnb1/Ccdc88a/Pcdh7/Fermt2/Wasf3/Arhgap45/Arhgef25/Akap12/Arhgap25/Dock2/Slitrk3/Plxnd1/Dock10/Abi2/Myo9a/Sh3bp1/Arhgef15/Arhgap6/Nckap1l/Arap3/Prex2/Arhgef26/Arhgap10/Arhgap28/Pde5a/Dlc1/Net1/Fgd1/Zap70/Dlg5/Arhgap31/Ngef/Fgd5/Arhgef9/Cep97/Arhgap15/Arfgap3/Cav1/Cyfip2 | 41 |
| R-MMU-416476 | G alpha (q) signalling events | 0.122 | 0.003 | 0.0486 | 1.31 | 0.0411 | Adra1a/Rgs16/Ednrb/Lpar4/Arhgef25/Gngt2/Ptgfr/Edn3/Plcb1/Rps6ka2/Trpc6/Gng11/Dgkb/Rgs5/Agtr1a/Ednra/Bdkrb2/Xcl1/Htr2a/Gng2/Plcb2/Gnb5/Prokr1/Gnb4 | 24 |
| R-MMU-373080 | Class B/2 (Secretin family receptors) | 0.182 | 0.00312 | 0.0486 | 1.31 | 0.0411 | Vipr2/Gngt2/Calca/Pth1r/Gng11/Adcyap1r1/Gng2/Calcrl/Gnb5/Gnb4 | 10 |
| R-MMU-1500931 | Cell-Cell communication | 0.157 | 0.00322 | 0.0486 | 1.31 | 0.0411 | Sdk2/Fermt2/Cdh2/Cdh6/Cdh13/Cdh10/Cdh5/Cdh11/Pard6g/Parvb/Flnc/Fyn/Itgb4 | 13 |
| R-MMU-1971475 | A tetrasaccharide linker sequence is required for GAG synthesis | 0.261 | 0.00329 | 0.0486 | 1.31 | 0.0411 | Gpc6/Cspg4/Gpc3/Bgn/Xylt1/Gpc2 | 6 |
| R-MMU-975576 | N-glycan antennae elongation in the medial/trans-Golgi | 0.261 | 0.00329 | 0.0486 | 1.31 | 0.0411 | St8sia2/Man2a2/Chst10/B4galt2/St8sia6/St3gal4 | 6 |
react_dot[[p]]
upset[[p]]
p=p+1reactome_sig[[p]] %>%
dplyr::mutate_if(is.numeric, funs(as.character(signif(., 3)))) %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Description | GeneRatio | pvalue | p.adjust | logFDR | qvalue | geneID | Count | |
|---|---|---|---|---|---|---|---|---|
| R-MMU-112316 | Neuronal System | 0.0623 | 8.08e-07 | 0.00026 | 3.58 | 0.000223 | Kcnk3/Kcnb2/Syn2/Kcnj3/Slc1a3/Kcnd2/Gria4/Kcna6/Kcnd3/Lrrc7/Nlgn1/Ptprd/Abat/Epb41l3/Lrrc4b/Gnai1/Kcnq5/Ppfia2/Grin2b/Gabra4 | 20 |
| R-MMU-6794362 | Protein-protein interactions at synapses | 0.106 | 0.000151 | 0.0244 | 1.61 | 0.0209 | Gria4/Nlgn1/Ptprd/Epb41l3/Lrrc4b/Ppfia2/Grin2b | 7 |
| R-MMU-5173214 | O-glycosylation of TSR domain-containing proteins | 0.152 | 0.000255 | 0.0258 | 1.59 | 0.0221 | Adamts20/Sema5b/Adamts16/Thsd7b/Adamts19 | 5 |
| R-MMU-422475 | Axon guidance | 0.0522 | 0.000443 | 0.0258 | 1.59 | 0.0221 | Gap43/Epha8/Efnb3/Dcc/St8sia2/Plxnb1/St8sia4/Dab1/Evl/Grin2b/Sema7a/Mmp2/Cxcl12 | 13 |
| R-MMU-9675108 | Nervous system development | 0.052 | 0.000461 | 0.0258 | 1.59 | 0.0221 | Gap43/Epha8/Efnb3/Dcc/St8sia2/Plxnb1/St8sia4/Dab1/Evl/Grin2b/Sema7a/Mmp2/Cxcl12 | 13 |
| R-MMU-1474228 | Degradation of the extracellular matrix | 0.0748 | 0.000583 | 0.0258 | 1.59 | 0.0221 | Col11a1/Mmp16/Col26a1/Capn6/Col4a6/Cd44/Mmp2/Nid1 | 8 |
| R-MMU-3000157 | Laminin interactions | 0.3 | 0.000591 | 0.0258 | 1.59 | 0.0221 | Col4a6/Lama4/Nid1 | 3 |
| R-MMU-1296072 | Voltage gated Potassium channels | 0.125 | 0.000641 | 0.0258 | 1.59 | 0.0221 | Kcnb2/Kcnd2/Kcna6/Kcnd3/Kcnq5 | 5 |
| R-MMU-1474244 | Extracellular matrix organization | 0.0519 | 0.000771 | 0.0259 | 1.59 | 0.0222 | Col11a1/Mmp16/Col26a1/Col14a1/Capn6/Col4a6/Itga4/P3h3/Cd44/Mmp2/Lama4/Nid1 | 12 |
| R-MMU-975634 | Retinoid metabolism and transport | 0.119 | 0.000806 | 0.0259 | 1.59 | 0.0222 | Gpc6/Apob/Ttr/Gpc3/Lrp2 | 5 |
| R-MMU-6806667 | Metabolism of fat-soluble vitamins | 0.109 | 0.00123 | 0.0359 | 1.44 | 0.0308 | Gpc6/Apob/Ttr/Gpc3/Lrp2 | 5 |
| R-MMU-1296071 | Potassium Channels | 0.0729 | 0.00149 | 0.04 | 1.4 | 0.0343 | Kcnk3/Kcnb2/Kcnj3/Kcnd2/Kcna6/Kcnd3/Kcnq5 | 7 |
react_dot[[p]]
upset[[p]]
Export Data
# save to csv
writexl::write_xlsx(x = reactome_all, here::here("3_output/reactome_all.xlsx"))
writexl::write_xlsx(x = reactome_sig, here::here("3_output/reactome_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] ReactomePA_1.40.0 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 pheatmap_1.0.12 cowplot_1.1.1
[19] pander_0.6.5 kableExtra_1.3.4 forcats_0.5.2
[22] stringr_1.4.1 purrr_0.3.5 tidyr_1.2.1
[25] ggplot2_3.3.6 tidyverse_1.3.2 reshape2_1.4.4
[28] tibble_3.1.8 readr_2.1.3 magrittr_2.0.3
[31] 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 DOSE_3.22.1
[17] labeling_0.4.2 MatrixGenerics_1.8.1
[19] git2r_0.30.1 GenomeInfoDbData_1.2.8
[21] polyclip_1.10-0 bit64_4.0.5
[23] farver_2.1.1 rprojroot_2.0.3
[25] downloader_0.4 treeio_1.20.2
[27] vctrs_0.4.2 generics_0.1.3
[29] xfun_0.33 R6_2.5.1
[31] GenomeInfoDb_1.32.4 graphlayouts_0.8.2
[33] locfit_1.5-9.6 bitops_1.0-7
[35] cachem_1.0.6 fgsea_1.22.0
[37] gridGraphics_0.5-1 DelayedArray_0.22.0
[39] assertthat_0.2.1 promises_1.2.0.1
[41] ggraph_2.1.0 googlesheets4_1.0.1
[43] gtable_0.3.1 tidygraph_1.2.2
[45] workflowr_1.7.0 rlang_1.0.6
[47] genefilter_1.78.0 systemfonts_1.0.4
[49] splines_4.2.1 lazyeval_0.2.2
[51] gargle_1.2.1 broom_1.0.1
[53] yaml_2.3.5 modelr_0.1.9
[55] backports_1.4.1 httpuv_1.6.6
[57] qvalue_2.28.0 tools_4.2.1
[59] ggplotify_0.1.0 ellipsis_0.3.2
[61] jquerylib_0.1.4 RColorBrewer_1.1-3
[63] Rcpp_1.0.9 zlibbioc_1.42.0
[65] RCurl_1.98-1.9 viridis_0.6.2
[67] SummarizedExperiment_1.26.1 haven_2.5.1
[69] fs_1.5.2 here_1.0.1
[71] data.table_1.14.2 DO.db_2.9
[73] reactome.db_1.81.0 reprex_2.0.2
[75] googledrive_2.0.0 whisker_0.4
[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 rappdirs_0.3.3
[101] MASS_7.3-57 Matrix_1.5-1
[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 graphite_1.42.0
[125] lifecycle_1.0.3 nlme_3.1-157
[127] jsonlite_1.8.2 viridisLite_0.4.1
[129] fansi_1.0.3 pillar_1.8.1
[131] lattice_0.20-45 KEGGREST_1.36.3
[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] 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] DESeq2_1.36.0 memoise_2.0.1
[147] ape_5.6-2