• Data Setup
    • Import DGElist Data
  • Reactome
  • Export Data

Last updated: 2023-01-20

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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=1
reactome=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)
}
 
kable(x = reactome_sig[[p]]) %>%
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 0.1744548 0.0000000 0.0000023 5.646701 0.0000019 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 0.1904762 0.0000000 0.0000040 5.400249 0.0000034 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 0.1451943 0.0000001 0.0000176 4.754163 0.0000150 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 0.2676056 0.0000010 0.0001715 3.765660 0.0001464 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 0.2727273 0.0000014 0.0001956 3.708584 0.0001670 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 0.1758794 0.0000026 0.0002986 3.524891 0.0002549 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 0.3636364 0.0000030 0.0002986 3.524891 0.0002549 Adamts20/Sema5b/Adamts16/Adamts19/Thsd7b/Thsd1/Adamts1/Adamts10/Adamts7/Adamtsl1/Sbspon/Adamts17 12
R-MMU-5173105 O-linked glycosylation 0.2187500 0.0000090 0.0007894 3.102709 0.0006737 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 0.1838235 0.0000325 0.0025359 2.595874 0.0021643 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 0.2285714 0.0000592 0.0041624 2.380653 0.0035526 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 0.3225806 0.0000665 0.0042502 2.371590 0.0036275 Rgs16/Adcy3/Gngt2/Adcy4/Adcy7/Gng11/Gng2/Gnaz/Gnb5/Gnb4 10
R-MMU-6794362 Protein-protein interactions at synapses 0.2272727 0.0001074 0.0062930 2.201141 0.0053710 Gria4/Ptprd/Nlgn1/Epb41l3/Lrrc4b/Grin2b/Shank2/Ppfia2/Slitrk3/Ppfia4/Dlg2/Nlgn3/Lrfn2/Dlg4/Nlgn2 15
R-MMU-1650814 Collagen biosynthesis and modifying enzymes 0.2333333 0.0001343 0.0068857 2.162050 0.0058769 Col11a1/Col26a1/P3h3/Col14a1/Col4a6/Col16a1/Col13a1/Col5a2/Col15a1/P3h1/Crtap/Col23a1/Col18a1/Col4a5 14
R-MMU-977444 GABA B receptor activation 0.2750000 0.0001469 0.0068857 2.162050 0.0058769 Kcnj3/Gnai1/Adcy3/Gngt2/Adcy4/Adcy7/Gng11/Gng2/Gnb5/Gnb4/Gabbr1 11
R-MMU-991365 Activation of GABAB receptors 0.2750000 0.0001469 0.0068857 2.162050 0.0058769 Kcnj3/Gnai1/Adcy3/Gngt2/Adcy4/Adcy7/Gng11/Gng2/Gnb5/Gnb4/Gabbr1 11
R-MMU-76002 Platelet activation, signaling and aggregation 0.1440329 0.0002003 0.0087992 2.055556 0.0075100 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 0.2321429 0.0002447 0.0101197 1.994832 0.0086370 Kcnj3/Gnai1/Adcy3/Gngt2/Adcy4/Adcy7/Gabra4/Gng11/Gng2/Gnb5/Arhgef9/Gnb4/Gabbr1 13
R-MMU-397795 G-protein beta:gamma signalling 0.3000000 0.0002876 0.0111282 1.953575 0.0094978 Gngt2/Pik3r6/Plcb1/Gng11/Gng2/Plcb2/Akt3/Gnb5/Gnb4 9
R-MMU-1296071 Potassium Channels 0.1875000 0.0003137 0.0111282 1.953575 0.0094978 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 0.3684211 0.0003372 0.0111282 1.953575 0.0094978 Itk/Cd3g/Zap70/Lat/Lcp2/Grap2/Cd4 7
R-MMU-418217 G beta:gamma signalling through PLC beta 0.3684211 0.0003372 0.0111282 1.953575 0.0094978 Gngt2/Plcb1/Gng11/Gng2/Plcb2/Gnb5/Gnb4 7
R-MMU-1474290 Collagen formation 0.2054795 0.0003519 0.0111282 1.953575 0.0094978 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 0.1910112 0.0003641 0.0111282 1.953575 0.0094978 Apob/Angpt1/Itga4/Cd44/Fn1/Jam3/Tek/Procr/Itgal/Esam/Sele/Pecam1/Pros1/Fyn/Cd84/Spn/Jam2 17
R-MMU-3000157 Laminin interactions 0.5000000 0.0004767 0.0136328 1.865417 0.0116353 Col4a6/Lama4/Nid1/Nid2/Col4a5 5
R-MMU-500657 Presynaptic function of Kainate receptors 0.3500000 0.0004848 0.0136328 1.865417 0.0116353 Gngt2/Plcb1/Gng11/Gng2/Plcb2/Gnb5/Gnb4 7
R-MMU-111885 Opioid Signalling 0.2028986 0.0006283 0.0163874 1.785490 0.0139864 Gnai1/Pde1b/Adcy3/Gngt2/Plcb1/Adcy4/Adcy7/Gng11/Pde1a/Gng2/Plcb2/Gnb5/Gnb4/Prkar1b 14
R-MMU-4085001 Sialic acid metabolism 0.2727273 0.0006294 0.0163874 1.785490 0.0139864 St6gal2/St8sia2/St8sia4/Npl/St3gal2/St6galnac4/St8sia6/St6galnac6/St3gal4 9
R-MMU-8948216 Collagen chain trimerization 0.2571429 0.0010032 0.0251865 1.598832 0.0214963 Col11a1/Col26a1/Col14a1/Col16a1/Col13a1/Col5a2/Col15a1/Col23a1/Col18a1 9
R-MMU-451326 Activation of kainate receptors upon glutamate binding 0.2758621 0.0011595 0.0281070 1.551185 0.0239889 Gngt2/Plcb1/Gng11/Gng2/Plcb2/Dlg4/Gnb5/Gnb4 8
R-MMU-4086398 Ca2+ pathway 0.2325581 0.0012401 0.0290608 1.536692 0.0248030 Lef1/Wnt11/Gngt2/Plcb1/Gng11/Gng2/Plcb2/Fzd2/Gnb5/Gnb4 10
R-MMU-9013149 RAC1 GTPase cycle 0.1481481 0.0013126 0.0290804 1.536399 0.0248197 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 0.1198980 0.0013237 0.0290804 1.536399 0.0248197 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 0.1623932 0.0013730 0.0292500 1.533874 0.0249644 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 0.1807229 0.0014375 0.0297233 1.526903 0.0253684 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 0.2916667 0.0016515 0.0331723 1.479225 0.0283120 Gngt2/Pik3r6/Gng11/Gng2/Akt3/Gnb5/Gnb4 7
R-MMU-456926 Thrombin signalling through proteinase activated receptors (PARs) 0.2580645 0.0018586 0.0362946 1.440157 0.0309769 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+1
kable(x = reactome_sig[[p]]) %>%
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 0.1619938 0.0000000 0.0000009 6.027692 0.0000008 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 0.1645022 0.0000002 0.0000561 4.251364 0.0000474 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 0.3636364 0.0000007 0.0001520 3.818039 0.0001285 Adamts20/Sema5b/Adamts16/Adamts19/Thsd7b/Thsd1/Adamts1/Adamts10/Adamts7/Adamtsl1/Sbspon/Adamts17 12
R-MMU-112315 Transmission across Chemical Synapses 0.1658291 0.0000009 0.0001533 3.814372 0.0001296 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 0.1226994 0.0000024 0.0003200 3.494859 0.0002705 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 0.2394366 0.0000029 0.0003220 3.492147 0.0002722 Apob/Nos3/Slc8a1/P2rx2/Pde1b/Gngt2/Slc8a3/Trpc6/Gng11/Pde1a/Pecam1/Gng2/Pde5a/Fgr/Atp2b4/Gnb5/Gnb4 17
R-MMU-5173105 O-linked glycosylation 0.1979167 0.0000153 0.0014582 2.836168 0.0012326 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 0.3225806 0.0000202 0.0016123 2.792544 0.0013629 Rgs16/Adcy3/Gngt2/Adcy4/Gng11/Adcy7/Gng2/Gnaz/Gnb5/Gnb4 10
R-MMU-216083 Integrin cell surface interactions 0.2272727 0.0000218 0.0016123 2.792544 0.0013629 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 0.1691176 0.0000302 0.0020055 2.697778 0.0016952 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 0.2750000 0.0000420 0.0023266 2.633279 0.0019666 Kcnj3/Gnai1/Adcy3/Gngt2/Adcy4/Gng11/Adcy7/Gng2/Gnb5/Gnb4/Gabbr1 11
R-MMU-991365 Activation of GABAB receptors 0.2750000 0.0000420 0.0023266 2.633279 0.0019666 Kcnj3/Gnai1/Adcy3/Gngt2/Adcy4/Gng11/Adcy7/Gng2/Gnb5/Gnb4/Gabbr1 11
R-MMU-977443 GABA receptor activation 0.2321429 0.0000606 0.0031021 2.508347 0.0026221 Kcnj3/Gnai1/Adcy3/Gngt2/Gabra4/Adcy4/Gng11/Adcy7/Gng2/Gnb5/Arhgef9/Gnb4/Gabbr1 13
R-MMU-6794362 Protein-protein interactions at synapses 0.2121212 0.0000917 0.0043570 2.360809 0.0036829 Gria4/Ptprd/Nlgn1/Epb41l3/Lrrc4b/Grin2b/Shank2/Ppfia2/Slitrk3/Dlg2/Ppfia4/Nlgn3/Lrfn2/Dlg4 14
R-MMU-397795 G-protein beta:gamma signalling 0.3000000 0.0001003 0.0044487 2.351765 0.0037604 Gngt2/Pik3r6/Plcb1/Gng11/Gng2/Plcb2/Akt3/Gnb5/Gnb4 9
R-MMU-1650814 Collagen biosynthesis and modifying enzymes 0.2166667 0.0001295 0.0053807 2.269160 0.0045482 Col11a1/Col26a1/P3h3/Col14a1/Col4a6/Col16a1/Col13a1/Col5a2/Col15a1/P3h1/Crtap/Col23a1/Col18a1 13
R-MMU-418217 G beta:gamma signalling through PLC beta 0.3684211 0.0001426 0.0055776 2.253554 0.0047146 Gngt2/Plcb1/Gng11/Gng2/Plcb2/Gnb5/Gnb4 7
R-MMU-416482 G alpha (12/13) signalling events 0.2000000 0.0001787 0.0063804 2.195151 0.0053932 Plxnb1/Adra1a/Arhgef25/Gngt2/Gng11/Arhgef15/Gng2/Arhgef26/Net1/Fgd1/Gnb5/Ngef/Arhgef9/Gnb4 14
R-MMU-1296071 Potassium Channels 0.1770833 0.0001823 0.0063804 2.195151 0.0053932 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 0.3500000 0.0002068 0.0068768 2.162615 0.0058127 Gngt2/Plcb1/Gng11/Gng2/Plcb2/Gnb5/Gnb4 7
R-MMU-4085001 Sialic acid metabolism 0.2727273 0.0002258 0.0071491 2.145752 0.0060429 St6gal2/St8sia2/St8sia4/Npl/St6galnac4/St3gal2/St8sia6/St6galnac6/St3gal4 9
R-MMU-1474290 Collagen formation 0.1917808 0.0002839 0.0085803 2.066500 0.0072526 Col11a1/Col26a1/P3h3/Col14a1/Col4a6/Col16a1/Col13a1/Loxl3/Col5a2/Col15a1/P3h1/Crtap/Col23a1/Col18a1 14
R-MMU-76002 Platelet activation, signaling and aggregation 0.1275720 0.0003594 0.0101540 1.993364 0.0085829 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 0.2571429 0.0003665 0.0101540 1.993364 0.0085829 Col11a1/Col26a1/Col14a1/Col16a1/Col13a1/Col5a2/Col15a1/Col23a1/Col18a1 9
R-MMU-4086398 Ca2+ pathway 0.2325581 0.0004216 0.0112147 1.950213 0.0094794 Lef1/Wnt11/Gngt2/Plcb1/Gng11/Gng2/Plcb2/Fzd2/Gnb5/Gnb4 10
R-MMU-9013149 RAC1 GTPase cycle 0.1419753 0.0004551 0.0114220 1.942257 0.0096547 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 0.2758621 0.0004638 0.0114220 1.942257 0.0096547 Gngt2/Plcb1/Gng11/Gng2/Plcb2/Dlg4/Gnb5/Gnb4 8
R-MMU-111885 Opioid Signalling 0.1884058 0.0005559 0.0132027 1.879337 0.0111599 Gnai1/Pde1b/Adcy3/Gngt2/Plcb1/Adcy4/Gng11/Adcy7/Pde1a/Gng2/Plcb2/Gnb5/Gnb4 13
R-MMU-392451 G beta:gamma signalling through PI3Kgamma 0.2916667 0.0007301 0.0164497 1.783841 0.0139045 Gngt2/Pik3r6/Gng11/Gng2/Akt3/Gnb5/Gnb4 7
R-MMU-202733 Cell surface interactions at the vascular wall 0.1685393 0.0007421 0.0164497 1.783841 0.0139045 Apob/Angpt1/Itga4/Cd44/Fn1/Tek/Jam3/Procr/Esam/Itgal/Sele/Pecam1/Pros1/Cd84/Fyn 15
R-MMU-446728 Cell junction organization 0.1875000 0.0009405 0.0201758 1.695169 0.0170540 Sdk2/Fermt2/Cdh2/Cdh6/Cdh13/Cdh10/Cdh5/Cdh11/Pard6g/Parvb/Flnc/Itgb4 12
R-MMU-9013148 CDC42 GTPase cycle 0.1686747 0.0010945 0.0227450 1.643114 0.0192257 Arhgap45/Arhgef25/Dock10/Arhgef15/Arap3/Prex2/Arhgef26/Arhgap10/Dlc1/Fgd1/Arhgap31/Ngef/Arhgef9/Cav1 14
R-MMU-397014 Muscle contraction 0.1372549 0.0012365 0.0249183 1.603481 0.0210627 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 0.2592593 0.0015718 0.0290350 1.537078 0.0245425 Kcnj3/Gngt2/Gng11/Gng2/Gnb5/Gnb4/Gabbr1 7
R-MMU-1296059 G protein gated Potassium channels 0.2592593 0.0015718 0.0290350 1.537078 0.0245425 Kcnj3/Gngt2/Gng11/Gng2/Gnb5/Gnb4/Gabbr1 7
R-MMU-997272 Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits 0.2592593 0.0015718 0.0290350 1.537078 0.0245425 Kcnj3/Gngt2/Gng11/Gng2/Gnb5/Gnb4/Gabbr1 7
R-MMU-1630316 Glycosaminoglycan metabolism 0.1452991 0.0018891 0.0339521 1.469134 0.0286987 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 0.2857143 0.0019821 0.0346868 1.459836 0.0293197 Gnai1/Gngt2/Gng11/Gng2/Gnb5/Gnb4 6
R-MMU-400042 Adrenaline,noradrenaline inhibits insulin secretion 0.2727273 0.0025737 0.0437866 1.358659 0.0370115 Gnai1/Gngt2/Gng11/Gng2/Gnb5/Gnb4 6
R-MMU-9012999 RHO GTPase cycle 0.1045918 0.0026338 0.0437866 1.358659 0.0370115 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 0.1218274 0.0030033 0.0485967 1.313393 0.0410774 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) 0.1818182 0.0031179 0.0485967 1.313393 0.0410774 Vipr2/Gngt2/Calca/Pth1r/Gng11/Adcyap1r1/Gng2/Calcrl/Gnb5/Gnb4 10
R-MMU-1500931 Cell-Cell communication 0.1566265 0.0032224 0.0485967 1.313393 0.0410774 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 0.2608696 0.0032885 0.0485967 1.313393 0.0410774 Gpc6/Cspg4/Gpc3/Bgn/Xylt1/Gpc2 6
R-MMU-975576 N-glycan antennae elongation in the medial/trans-Golgi 0.2608696 0.0032885 0.0485967 1.313393 0.0410774 St8sia2/Man2a2/Chst10/B4galt2/St8sia6/St3gal4 6 
react_dot[[p]]

upset[[p]]

p=p+1
kable(x = reactome_sig[[p]]) %>%
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 0.0623053 0.0000008 0.0002601 3.584822 0.0002228 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 0.1060606 0.0001513 0.0243552 1.613409 0.0208599 Gria4/Nlgn1/Ptprd/Epb41l3/Lrrc4b/Ppfia2/Grin2b 7
R-MMU-5173214 O-glycosylation of TSR domain-containing proteins 0.1515152 0.0002554 0.0258090 1.588229 0.0221051 Adamts20/Sema5b/Adamts16/Thsd7b/Adamts19 5
R-MMU-422475 Axon guidance 0.0522088 0.0004433 0.0258090 1.588229 0.0221051 Gap43/Epha8/Efnb3/Dcc/St8sia2/Plxnb1/St8sia4/Dab1/Evl/Grin2b/Sema7a/Mmp2/Cxcl12 13
R-MMU-9675108 Nervous system development 0.0520000 0.0004606 0.0258090 1.588229 0.0221051 Gap43/Epha8/Efnb3/Dcc/St8sia2/Plxnb1/St8sia4/Dab1/Evl/Grin2b/Sema7a/Mmp2/Cxcl12 13
R-MMU-1474228 Degradation of the extracellular matrix 0.0747664 0.0005833 0.0258090 1.588229 0.0221051 Col11a1/Mmp16/Col26a1/Capn6/Col4a6/Cd44/Mmp2/Nid1 8
R-MMU-3000157 Laminin interactions 0.3000000 0.0005908 0.0258090 1.588229 0.0221051 Col4a6/Lama4/Nid1 3
R-MMU-1296072 Voltage gated Potassium channels 0.1250000 0.0006412 0.0258090 1.588229 0.0221051 Kcnb2/Kcnd2/Kcna6/Kcnd3/Kcnq5 5
R-MMU-1474244 Extracellular matrix organization 0.0519481 0.0007709 0.0259472 1.585909 0.0222235 Col11a1/Mmp16/Col26a1/Col14a1/Capn6/Col4a6/Itga4/P3h3/Cd44/Mmp2/Lama4/Nid1 12
R-MMU-975634 Retinoid metabolism and transport 0.1190476 0.0008058 0.0259472 1.585909 0.0222235 Gpc6/Apob/Ttr/Gpc3/Lrp2 5
R-MMU-6806667 Metabolism of fat-soluble vitamins 0.1086957 0.0012271 0.0359194 1.444671 0.0307646 Gpc6/Apob/Ttr/Gpc3/Lrp2 5
R-MMU-1296071 Potassium Channels 0.0729167 0.0014909 0.0400069 1.397865 0.0342655 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