Single cell transcriptomes of macrophages with HIV 2024 - comparative analysis
Burnet Bioinformatics group
2025-04-01
Introduction
We are interested in comparing DEGs between the mock (ctrl) and productively-infected (case).
Here are the general steps:
We will obtain the list of top pathways.
Get the list of genes that are driving the enrichment.
Make a network diagram using the gs2net function I made previously
Modify it so that the colours represent the direction of regulation, and size represents the FDR.
suppressPackageStartupMessages({
library("gplots")
library("kableExtra")
library("ggplot2")
library("network")
library("eulerr")
library("mitch")
library("dplyr")
library("reshape2")
})
knitr::opts_chunk$set(dev = 'svg') # set output device to svg
load("../scanalyse.Rdata")
go <- gmt_import("go_2024-11.gmt")Functions.
map2color <- function(x,pal,limits=NULL){
if (is.null(limits)) limits <- range(x)
pal[findInterval(x,seq(limits[1],limits[2],length.out=length(pal)+1), all.inside=TRUE)]
}
gs2net <- function(gset,em,colfunc=colorRampPalette(c("blue", "white","red"))(n=100)){
gset <- gset[order(names(gset))]
mydf <- dplyr::bind_rows(lapply(gset, as.data.frame.list))
rownames(mydf) <- names(gset)
j <- apply(mydf,1,function(x) {
apply(mydf,1,function(y) {
length(intersect(x,y) ) / length(union(x,y))
})
})
j[lower.tri(j)] <- NA
j[lower.tri(j,diag=TRUE)] <- 0
jl <- reshape2::melt(j)
jl <- jl[which(jl$Var1 != jl$Var2),]
jl <- jl[which(jl$value != 1),]
jl <- jl[order(-jl$value),]
jl <- head(jl,length(gset)*2)
jl$edgeSize = jl$value/sum(jl$value)
nodes <- sort(union(jl[,1],jl[,2]))
lengths <- unlist(lapply(gset,length))
lengths <- lengths[names(lengths) %in% nodes]
nodes <- data.frame("nodes"=nodes,"lengths"=lengths)
nodes$vertexsize <- sqrt(nodes$lengths/sum(nodes$lengths) * 100)
nodes$es <- em[match(nodes$nodes,em$set),"s.dist"]
nodes$colours <- map2color(nodes$es,colfunc)
jl2 <- apply(jl[,1:2],2,as.character)
jlnet <- network(jl2)
jlnet$val <- lapply(jlnet$val, function(x) {
vn <- x[[2]]
vn <- substr(vn, 1, 60)
if (nchar(vn) == 60 ) {
vn <- paste(vn,"...",sep="")
}
x[[2]] <- vn
return(x)
} )
plot(jlnet, displaylabels = TRUE, label.col = "steelblue",
edge.lwd = c(jl$edgeSize) * 100,
arrowhead.cex = 0,
label.cex = 0.8, vertex.border = "white",vertex.cex = nodes$vertexsize,
vertex.col = nodes$colours, edge.col = "black")
E1 <- min(nodes$es)
E5 <- max(nodes$es)
E3 <- mean(c(E1,E5))
EE <- c(E1,E3,E5)
legcols <- map2color(EE,colfunc)
legend("topleft", legend=signif(EE,2) ,title="ES",box.lty=0,
fill=legcols, cex=0.8)
S1 <- min(nodes$vertexsize)
FRAG <- S1/10
S5 <- max(nodes$vertexsize)
S3 <- mean(c(S1,S5))
SS <- c(S1-FRAG,0,S5-FRAG)
L1 <- min(nodes$lengths)
L5 <- max(nodes$lengths)
LL <- paste(" ",c(L1,"",L5))
legend("topright", legend=LL ,title="no. genes",box.lty=0,
pt.cex=SS*1, cex=0.9 , pch=19,col="darkgray")
J1 <- min(jl$edgeSize)
FRAG <- J1*3
J5 <- max(jl$edgeSize)
J3 <- mean(c(J1,J5))
JJ <- c(J1,J3,J5)
JL <- JJ+FRAG
JJ <- c( min(jl$value), mean(c(min(jl$value),max(jl$value))),max(jl$value) )
legend("bottomleft", legend=signif(JJ,2) , lwd=JL*50, title="Jaccard",
box.lty=0, cex=0.9 , lty=1, col="black")
}
networkplot <- function(eres,FDR=0.05,n_sets=20) {
scores <- eres[[1]][,1]
names(scores) <- rownames(eres[[1]])
gs <- eres[[2]]
eres <- eres[[4]]
up <- head(eres[eres$p.adjustANOVA < FDR & eres$s.dist > 0,],n_sets)
n_up <- nrow(up)
if (n_up >= 5) {
up_gs <- up[,1]
up_gs <- gs[which(names(gs) %in% up_gs)]
topgs_up <- lapply(seq(from=1,to=length(up_gs)),function(i) {
gsname <- names(up_gs)[i]
genes <- up_gs[[i]]
gene_scores <- scores[which(names(scores) %in% genes)]
top_genes <- names(which(gene_scores > quantile(gene_scores,c(2/3))))
return(top_genes)
})
names(topgs_up) <- names(up_gs)
gs2net(gset=topgs_up,em=eres,colfunc=colorRampPalette(c("pink","darkred"))(n=100))
} else {
message("Can't plot upregulated sets. Fewer than 5 found.")
}
dn <- head(eres[eres$p.adjustANOVA < FDR & eres$s.dist < 0,],n_sets)
n_dn <- nrow(dn)
if (n_dn >= 5) {
dn_gs <- dn[,1]
dn_gs <- gs[which(names(gs) %in% dn_gs)]
topgs_dn <- lapply(seq(from=1,to=length(dn_gs)),function(i) {
gsname <- names(dn_gs)[i]
genes <- dn_gs[[i]]
gene_scores <- scores[which(names(scores) %in% genes)]
top_genes <- names(which(gene_scores < quantile(gene_scores,c(1/3))))
return(top_genes)
})
names(topgs_dn) <- names(dn_gs)
gs2net(gset=topgs_dn,em=eres,colfunc=colorRampPalette(c("darkblue","lightblue"))(n=100))
} else {
message("Can't plot downregulated sets. Fewer than 5 found.")
}
}
network_genes <- function(eres,FDR=0.05,n_sets=20) {
scores <- eres[[1]][,1]
names(scores) <- rownames(eres[[1]])
gs <- eres[[2]]
eres <- eres[[4]]
up <- head(eres[eres$p.adjustANOVA < FDR & eres$s.dist > 0,],n_sets)
n_up <- nrow(up)
if (n_up > 0) {
up_gs <- up[,1]
up_gs <- gs[which(names(gs) %in% up_gs)]
topgs_up <- lapply(seq(from=1,to=length(up_gs)),function(i) {
gsname <- names(up_gs)[i]
genes <- up_gs[[i]]
gene_scores <- scores[which(names(scores) %in% genes)]
top_genes <- names(which(gene_scores>2))
return(top_genes)
})
names(topgs_up) <- names(up_gs)
} else {
topgs_up <- NULL
message("No significant upregulated sets to show.")
}
dn <- head(eres[eres$p.adjustANOVA < FDR & eres$s.dist < 0,],n_sets)
n_dn <- nrow(dn)
if (n_dn > 0) {
dn_gs <- dn[,1]
dn_gs <- gs[which(names(gs) %in% dn_gs)]
topgs_dn <- lapply(seq(from=1,to=length(dn_gs)),function(i) {
gsname <- names(dn_gs)[i]
genes <- dn_gs[[i]]
gene_scores <- scores[which(names(scores) %in% genes)]
top_genes <- names(which(gene_scores<2))
return(top_genes)
})
names(topgs_dn) <- names(dn_gs)
} else {
topgs_dn <- NULL
message("No significant upregulated sets to show.")
}
return(list(c("UP genesets"=topgs_up,"DOWN genesets"=topgs_dn)))
}DE3 AlvMDM
We are interested in comparing DEGs between the mock (ctrl) and productively-infected (case) in Alv cells. Read in the key data.
N_SETS=20 and 30
x <- read.table("de3af.tsv")
m3af <- mitch_import(x,DEtype="DESeq2")## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 15728## Note: no. genes in output = 15728## Note: estimated proportion of input genes in output = 1mres3af <- mitch_calc(m3af,genesets=go,cores=8,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.networkplot(mres3af,FDR=0.05,n_sets=20)
network_genes(mres3af,FDR=0.05,n_sets=20)## [[1]]
## [[1]]$`UP genesets.GO:0001836 release of cytochrome c from mitochondria`
## [1] "IFI27L2" "IFI6" "BID" "BCL2L1" "BAD" "BCL2" "SOD2"
## [8] "CLU"
##
## [[1]]$`UP genesets.GO:0002230 positive regulation of defense response to virus by host`
## [1] "TRIM22" "LILRB1" "PARP9" "CREB3" "SELENOK" "STAT1" "TRIM6"
## [8] "DTX3L" "EIF2AK4"
##
## [[1]]$`UP genesets.GO:0005179 hormone activity`
## [1] "METRN" "HAMP" "POMC" "ENHO" "NMB" "UTS2" "FNDC5" "GDF15" "APLN"
##
## [[1]]$`UP genesets.GO:0005758 mitochondrial intermembrane space`
## [1] "TRIAP1" "TIMM8A" "UQCC2" "TIMM10B" "BLOC1S1" "CHCHD7" "THEM4"
## [8] "REXO2" "HAX1" "CMC4" "ARL2BP" "COX17" "CYCS" "COX6C"
## [15] "ALPL" "TIMM9" "THOP1" "GFER" "SDHAF3" "CHCHD4" "PRELID2"
## [22] "NDUFA8"
##
## [[1]]$`UP genesets.GO:0005762 mitochondrial large ribosomal subunit`
## [1] "MRPL42" "MRPL52" "MRPL41" "MRPL18" "MRPS30" "MRPL40" "MRPL33" "MRPL57"
## [9] "MRPL43" "MRPL15"
##
## [[1]]$`UP genesets.GO:0005763 mitochondrial small ribosomal subunit`
## [1] "MRPS33" "MRPS18C" "MRPS16" "MRPS6" "MRPL42" "AURKAIP1"
## [7] "MRPS17" "MRPS28" "MRPS10" "MRPS15" "MRPS12" "CHCHD1"
##
## [[1]]$`UP genesets.GO:0006091 generation of precursor metabolites and energy`
## [1] "FDXR" "POMC" "ATP5IF1" "PPP1R2" "CROT" "GIPR" "COX7C"
## [8] "COX17" "COX6C" "SLC25A4"
##
## [[1]]$`UP genesets.GO:0006626 protein targeting to mitochondrion`
## [1] "BID" "TOMM5" "GDAP1" "PITRM1" "TIMM17A" "TIMM9"
##
## [[1]]$`UP genesets.GO:0006826 iron ion transport`
## [1] "SFXN1" "FTL" "SLC11A2" "TFRC" "FXN"
##
## [[1]]$`UP genesets.GO:0008429 phosphatidylethanolamine binding`
## [1] "GABARAPL2" "CD300A" "MAP1LC3B" "MAP1LC3A" "GABARAP"
##
## [[1]]$`UP genesets.GO:0016226 iron-sulfur cluster assembly`
## [1] "BOLA3" "CIAO1" "XDH" "LYRM4" "FDX2" "ISCA1" "NUBPL" "FXN" "HSPA9"
## [10] "GLRX3"
##
## [[1]]$`UP genesets.GO:0032402 melanosome transport`
## [1] "BBS7" "MLPH" "RAB1A"
##
## [[1]]$`UP genesets.GO:0032543 mitochondrial translation`
## [1] "MRPS33" "MRPS18C" "MRPS16" "MRPS6" "MRPL42" "MRPL52"
## [7] "MRPL41" "MRPL18" "MRPS30" "MRPL40" "MRPL33" "MRPL57"
## [13] "AURKAIP1" "MRPS17" "MRPL43" "MRPS28" "MRPS10" "MRPS15"
## [19] "MRPL15" "MRPS12" "CHCHD1"
##
## [[1]]$`UP genesets.GO:0033617 mitochondrial cytochrome c oxidase assembly`
## [1] "COX14" "COX17" "COA3" "COA1"
##
## [[1]]$`UP genesets.GO:0044571 [2Fe-2S] cluster assembly`
## [1] "LYRM4" "FDX2" "FXN" "GLRX3"
##
## [[1]]$`UP genesets.GO:0045039 protein insertion into mitochondrial inner membrane`
## [1] "TIMM8A" "TIMM10B" "NDUFA13" "ROMO1" "TIMM9"
##
## [[1]]$`UP genesets.GO:0045071 negative regulation of viral genome replication`
## [1] "ISG15" "IFIT1" "OASL" "OAS1" "BST2" "RSAD2"
## [7] "OAS3" "TNIP1" "OAS2" "ISG20" "PLSCR1" "ZC3HAV1"
## [13] "IFIH1" "EIF2AK2" "IFITM3" "TRIM6" "APOBEC3C" "APOBEC3A"
##
## [[1]]$`UP genesets.GO:0051537 2 iron, 2 sulfur cluster binding`
## [1] "SLC25A39" "XDH" "GLRX2" "CISD3" "FDX2" "ISCA1" "FXN"
##
## [[1]]$`UP genesets.GO:0090201 negative regulation of release of cytochrome c from mitochondria`
## [1] "TRIAP1" "IFI6" "PPIF" "GHITM" "BCL2L1" "PRKN" "CLU" "FXN"
##
## [[1]]$`UP genesets.GO:1990229 iron-sulfur cluster assembly complex`
## [1] "BOLA3" "LYRM4" "FDX2" "FXN" "GLRX3"
##
## [[1]]$`DOWN genesets.GO:0000727 double-strand break repair via break-induced replication`
## [1] "MCM3" "MCM7" "GINS2" "CDC45" "GINS4" "MCM4" "MCM2" "MCM6"
## [9] "MCM5" "CDC7" "MUS81" "MCMDC2"
##
## [[1]]$`DOWN genesets.GO:0002437 inflammatory response to antigenic stimulus`
## [1] "RBPJ" "HMGB2" "KDM6B" "NOTCH1" "HLA-DRB1" "PNMA1"
## [7] "HMGB1" "FOSL2" "NOTCH2" "CYSLTR1" "IL20RB" "CD68"
## [13] "RASGRP1"
##
## [[1]]$`DOWN genesets.GO:0006265 DNA topological change`
## [1] "HMGB2" "TDRD3" "TOP2B" "HMGB1" "TOP3A" "TOP1MT" "TOP1" "TOP2A"
## [9] "ERCC3" "TOP3B"
##
## [[1]]$`DOWN genesets.GO:0006270 DNA replication initiation`
## [1] "MCM3" "MCM10" "MCM7" "PURA" "CDC45" "CCNE1" "CCNE2" "MCM2"
## [9] "POLA1" "POLA2" "ORC6" "MCM6" "TOPBP1" "CDC6" "PRIM2" "ORC1"
## [17] "LRWD1" "MCM5" "NOC3L" "ORC4" "ORC5" "PRIM1" "ORC3" "ORC2"
##
## [[1]]$`DOWN genesets.GO:0006346 DNA methylation-dependent constitutive heterochromatin formation`
## [1] "DNMT1" "ATF7IP" "HELLS" "BAZ2A" "SETDB1" "CTCF" "DNMT3A"
## [8] "HDAC1" "EHMT1" "TRIM28" "SIRT1" "MBD1" "EZH2" "PPM1D"
## [15] "MBD2" "EHMT2" "BMI1" "MBD3" "ZNF304" "SMARCA5" "BEND3"
##
## [[1]]$`DOWN genesets.GO:0006353 DNA-templated transcription termination`
## [1] "SETX" "WDR82" "SMN1" "DHX9" "ZC3H4" "POLR2A" "TTF2" "TTF1"
## [9] "MTERF1" "PRMT5"
##
## [[1]]$`DOWN genesets.GO:0022625 cytosolic large ribosomal subunit`
## [1] "RPL10A" "RPL3" "RPL5" "RPL7A" "RPL36A" "RPL26" "RPL32"
## [8] "RPL4" "RPL22" "RPL10" "RPL23" "RPL11" "RPL7" "RPL34"
## [15] "RPL31" "RPL6" "RPL13" "RPL35A" "RPL12" "RPL27A" "RPL37A"
## [22] "RPL24" "RPL14" "RPL21" "RPL30" "RPL15" "RPL37" "RPL17"
## [29] "RPL23A" "RPL18" "RPLP1" "RPL13A" "RPL41" "RPL28" "RPL29"
## [36] "RPL26L1" "RPL18A" "RPL38" "RPLP2" "RPL27" "RPL19" "RPL36AL"
## [43] "RPL39" "RPL35" "RPL9" "RPL8" "RPL36" "RPL7L1" "RPL39L"
## [50] "UBA52"
##
## [[1]]$`DOWN genesets.GO:0030174 regulation of DNA-templated DNA replication initiation`
## [1] "MCM3" "MCM7" "CDT1" "MCM4" "MCM2" "KAT7" "MCM6" "NBN"
## [9] "GMNN" "MCM5" "WRNIP1"
##
## [[1]]$`DOWN genesets.GO:0032454 histone H3K9 demethylase activity`
## [1] "JMJD1C" "KDM3B" "KDM4B" "KDM3A" "PHF2" "PHF8" "KDM4C" "KDM7A"
## [9] "KDM1A" "KDM4A" "KDM4D"
##
## [[1]]$`DOWN genesets.GO:0034501 protein localization to kinetochore`
## [1] "CDK1" "TTK" "ZWILCH" "SPDL1" "IK" "KNL1" "CHAMP1" "BUB3"
## [9] "AURKB" "ZW10" "MTBP"
##
## [[1]]$`DOWN genesets.GO:0035196 miRNA processing`
## [1] "AGO3" "DICER1" "PUM2" "PUM1" "AGO2" "AGO4" "AGO1" "SNIP1"
## [9] "ZC3H7A" "PRKRA" "TARBP2" "ZC3H7B" "SPOUT1" "NUP155"
##
## [[1]]$`DOWN genesets.GO:0036002 pre-mRNA binding`
## [1] "TRA2B" "HNRNPU" "HNRNPA1" "ARGLU1" "DDX5" "SRSF3" "SRSF2"
## [8] "CELF2" "CELF1" "RBM22" "PTBP1" "TARBP2" "SRSF6"
##
## [[1]]$`DOWN genesets.GO:0042555 MCM complex`
## [1] "MCM3" "MCM7" "MCM9" "MMS22L" "MCMBP" "MCM4" "MCM2" "MCM6"
## [9] "MCM8" "MCM5" "TONSL"
##
## [[1]]$`DOWN genesets.GO:0042800 histone H3K4 methyltransferase activity`
## [1] "KMT2C" "SETD3" "ASH1L" "SETD1B" "KMT2D" "KMT2B" "KMT2A" "SETD1A"
## [9] "SETD4" "SETBP1" "SETMAR" "WDR5"
##
## [[1]]$`DOWN genesets.GO:0044027 negative regulation of gene expression via chromosomal CpG island methylation`
## [1] "DNMT1" "MYC" "HELLS" "BRCA1" "UHRF1" "CTCF"
## [7] "DNMT3A" "MECP2" "UHRF2" "ZNF445" "MPHOSPH8" "EHMT2"
## [13] "PRMT5" "USP7"
##
## [[1]]$`DOWN genesets.GO:0044849 estrous cycle`
## [1] "IGF1R" "NCOA1" "OPRL1" "ADNP" "NCOR2" "SLC26A6" "EGR1"
## [8] "PCNA" "MDK" "CYP1B1"
##
## [[1]]$`DOWN genesets.GO:0061158 3'-UTR-mediated mRNA destabilization`
## [1] "CPEB3" "ZFP36L1" "PUM2" "HNRNPD" "ZFP36" "PUM1" "KHSRP"
## [8] "ZC3H12D" "RC3H1" "TARDBP" "UPF1" "ZFP36L2" "DHX36" "ZC3H12A"
## [15] "MOV10"
##
## [[1]]$`DOWN genesets.GO:0071162 CMG complex`
## [1] "MCM3" "MCM7" "GINS2" "CDC45" "GINS4" "MCM4" "MCM2" "MCM6" "GINS3"
## [10] "MCM5" "GINS1"
##
## [[1]]$`DOWN genesets.GO:0071168 protein localization to chromatin`
## [1] "ZMYND8" "BRD2" "MCM9" "MMS22L" "RAD21" "BRD3" "ESR1" "MCM8"
## [9] "MSH2" "PARP1" "CHMP7" "SPIN1" "EZH2" "ESCO2" "FAM47E" "TONSL"
## [17] "PLK1" "APLF" "WAPL" "MRNIP" "LEMD2"
##
## [[1]]$`DOWN genesets.GO:0106222 lncRNA binding`
## [1] "DNMT1" "HADHB" "HNRNPU" "ATP2A2" "PCBP2" "DNMT3A" "RAD21" "PUM2"
## [9] "BRD3" "STAT3" "EZH2" "RBM33" "SUZ12" "CSDE1" "ELAVL1" "SUGT1"networkplot(mres3af,FDR=0.05,n_sets=30)
network_genes(mres3af,FDR=0.05,n_sets=30)## [[1]]
## [[1]]$`UP genesets.GO:0001836 release of cytochrome c from mitochondria`
## [1] "IFI27L2" "IFI6" "BID" "BCL2L1" "BAD" "BCL2" "SOD2"
## [8] "CLU"
##
## [[1]]$`UP genesets.GO:0002230 positive regulation of defense response to virus by host`
## [1] "TRIM22" "LILRB1" "PARP9" "CREB3" "SELENOK" "STAT1" "TRIM6"
## [8] "DTX3L" "EIF2AK4"
##
## [[1]]$`UP genesets.GO:0003925 G protein activity`
## [1] "GNA13" "RALA" "MRAS" "HRAS" "SAR1A" "RAB1A"
##
## [[1]]$`UP genesets.GO:0005179 hormone activity`
## [1] "METRN" "HAMP" "POMC" "ENHO" "NMB" "UTS2" "FNDC5" "GDF15" "APLN"
##
## [[1]]$`UP genesets.GO:0005743 mitochondrial inner membrane`
## [1] "MRPS33" "IFI6" "FDXR" "MRPS18C" "UQCRQ" "COX7A2"
## [7] "MRPS16" "TIMM8A" "SFXN1" "UQCC2" "TIMM10B" "TMEM70"
## [13] "SLC41A3" "NDUFA13" "MCUB" "MRPS6" "MRPL42" "MRPL52"
## [19] "MRPL41" "DNAJC15" "RSAD2" "PPIF" "GCAT" "SLC25A19"
## [25] "DMAC1" "THEM4" "NDUFB3" "PTPMT1" "SLC25A39" "MRPL18"
## [31] "MRPS30" "NDUFV1" "LETM1" "HCCS" "UQCRH" "NDUFB8"
## [37] "MRPL40" "ATP5PF" "GHITM" "MRPL33" "NDUFA7" "COX7B"
## [43] "COX14" "NDUFAF1" "BCL2L1" "COX7C" "MRPL57" "IMMP1L"
## [49] "CHCHD6" "FLVCR1" "CYCS" "TIMM17A" "AURKAIP1" "COX6C"
## [55] "SLC25A4" "NDUFA11" "ROMO1" "COA3" "COA1" "SLC25A1"
## [61] "TIMM9" "NDUFA5" "COQ3" "NDUFB10" "COQ10B" "YME1L1"
## [67] "NDUFAF6" "MRPS17" "SLC25A27" "MRPL43" "MRPS28" "MRPS10"
## [73] "MRPS15" "SRC" "NDUFA6" "NDUFB2" "CLU" "MRPL15"
## [79] "MRPS12" "NDUFA8" "HSPA9" "CHCHD1" "ATP5MC1"
##
## [[1]]$`UP genesets.GO:0005758 mitochondrial intermembrane space`
## [1] "TRIAP1" "TIMM8A" "UQCC2" "TIMM10B" "BLOC1S1" "CHCHD7" "THEM4"
## [8] "REXO2" "HAX1" "CMC4" "ARL2BP" "COX17" "CYCS" "COX6C"
## [15] "ALPL" "TIMM9" "THOP1" "GFER" "SDHAF3" "CHCHD4" "PRELID2"
## [22] "NDUFA8"
##
## [[1]]$`UP genesets.GO:0005762 mitochondrial large ribosomal subunit`
## [1] "MRPL42" "MRPL52" "MRPL41" "MRPL18" "MRPS30" "MRPL40" "MRPL33" "MRPL57"
## [9] "MRPL43" "MRPL15"
##
## [[1]]$`UP genesets.GO:0005763 mitochondrial small ribosomal subunit`
## [1] "MRPS33" "MRPS18C" "MRPS16" "MRPS6" "MRPL42" "AURKAIP1"
## [7] "MRPS17" "MRPS28" "MRPS10" "MRPS15" "MRPS12" "CHCHD1"
##
## [[1]]$`UP genesets.GO:0006091 generation of precursor metabolites and energy`
## [1] "FDXR" "POMC" "ATP5IF1" "PPP1R2" "CROT" "GIPR" "COX7C"
## [8] "COX17" "COX6C" "SLC25A4"
##
## [[1]]$`UP genesets.GO:0006626 protein targeting to mitochondrion`
## [1] "BID" "TOMM5" "GDAP1" "PITRM1" "TIMM17A" "TIMM9"
##
## [[1]]$`UP genesets.GO:0006826 iron ion transport`
## [1] "SFXN1" "FTL" "SLC11A2" "TFRC" "FXN"
##
## [[1]]$`UP genesets.GO:0008429 phosphatidylethanolamine binding`
## [1] "GABARAPL2" "CD300A" "MAP1LC3B" "MAP1LC3A" "GABARAP"
##
## [[1]]$`UP genesets.GO:0009615 response to virus`
## [1] "CCL22" "ISG15" "ACTA2" "TRIM22" "IRF7" "LILRB1" "IFIT1"
## [8] "OASL" "LAMTOR5" "OAS1" "IFIT2" "BST2" "RSAD2" "OAS3"
## [15] "DDX60" "IFIT3" "OAS2" "FOSL1" "ISG20" "AP1S1" "ZC3HAV1"
## [22] "IFIH1" "BATF3" "EIF2AK2" "IFI44" "IFITM3" "SMPD1" "AUP1"
## [29] "CLU"
##
## [[1]]$`UP genesets.GO:0016226 iron-sulfur cluster assembly`
## [1] "BOLA3" "CIAO1" "XDH" "LYRM4" "FDX2" "ISCA1" "NUBPL" "FXN" "HSPA9"
## [10] "GLRX3"
##
## [[1]]$`UP genesets.GO:0019003 GDP binding`
## [1] "GEM" "RHEB" "RAB8A" "RALA" "RAB18" "MRAS" "HRAS" "RRAS2" "RRAGD"
##
## [[1]]$`UP genesets.GO:0030133 transport vesicle`
## [1] "ATP13A2" "YKT6" "COPZ2" "ERG28" "LAPTM5" "IGF2R" "CAV2"
## [8] "GOLGA5" "BET1"
##
## [[1]]$`UP genesets.GO:0031966 mitochondrial membrane`
## [1] "IFI27L2" "ABCG2" "IFI6" "COX7A2" "TMEM70" "BNIP3"
## [7] "NDUFA13" "REEP1" "MAP1LC3B" "GHITM" "COX7B" "ELK1"
## [13] "COX7C" "COX6C" "SLC25A4" "ALPL" "TMEM135" "SMIM30"
## [19] "TMEM14B" "SLC25A27" "NDUFA6" "SLC22A4"
##
## [[1]]$`UP genesets.GO:0032402 melanosome transport`
## [1] "BBS7" "MLPH" "RAB1A"
##
## [[1]]$`UP genesets.GO:0032418 lysosome localization`
## [1] "BLOC1S1" "BLOC1S2" "DEF8" "RAB34" "PLEKHM1" "RNF167" "SPAG9"
## [8] "KLC2"
##
## [[1]]$`UP genesets.GO:0032543 mitochondrial translation`
## [1] "MRPS33" "MRPS18C" "MRPS16" "MRPS6" "MRPL42" "MRPL52"
## [7] "MRPL41" "MRPL18" "MRPS30" "MRPL40" "MRPL33" "MRPL57"
## [13] "AURKAIP1" "MRPS17" "MRPL43" "MRPS28" "MRPS10" "MRPS15"
## [19] "MRPL15" "MRPS12" "CHCHD1"
##
## [[1]]$`UP genesets.GO:0032981 mitochondrial respiratory chain complex I assembly`
## [1] "NDUFA13" "DMAC1" "NDUFB3" "NDUFAF8" "NDUFB8" "NDUFAF1" "LYRM2"
## [8] "NDUFA11" "COA1" "NDUFA5" "NDUFB10" "NDUFAF6" "NUBPL" "NDUFA6"
## [15] "NDUFB2" "NDUFA8"
##
## [[1]]$`UP genesets.GO:0033116 endoplasmic reticulum-Golgi intermediate compartment membrane`
## [1] "DCSTAMP" "YKT6" "TAP1" "COPZ2" "ERGIC1" "VMA21" "GOSR2"
## [8] "TAPBP" "TAP2" "GOLGA2" "YIF1A" "BET1"
##
## [[1]]$`UP genesets.GO:0033617 mitochondrial cytochrome c oxidase assembly`
## [1] "COX14" "COX17" "COA3" "COA1"
##
## [[1]]$`UP genesets.GO:0044571 [2Fe-2S] cluster assembly`
## [1] "LYRM4" "FDX2" "FXN" "GLRX3"
##
## [[1]]$`UP genesets.GO:0045039 protein insertion into mitochondrial inner membrane`
## [1] "TIMM8A" "TIMM10B" "NDUFA13" "ROMO1" "TIMM9"
##
## [[1]]$`UP genesets.GO:0045071 negative regulation of viral genome replication`
## [1] "ISG15" "IFIT1" "OASL" "OAS1" "BST2" "RSAD2"
## [7] "OAS3" "TNIP1" "OAS2" "ISG20" "PLSCR1" "ZC3HAV1"
## [13] "IFIH1" "EIF2AK2" "IFITM3" "TRIM6" "APOBEC3C" "APOBEC3A"
##
## [[1]]$`UP genesets.GO:0051537 2 iron, 2 sulfur cluster binding`
## [1] "SLC25A39" "XDH" "GLRX2" "CISD3" "FDX2" "ISCA1" "FXN"
##
## [[1]]$`UP genesets.GO:0090201 negative regulation of release of cytochrome c from mitochondria`
## [1] "TRIAP1" "IFI6" "PPIF" "GHITM" "BCL2L1" "PRKN" "CLU" "FXN"
##
## [[1]]$`UP genesets.GO:1902600 proton transmembrane transport`
## [1] "ATP6V1D" "ATP6V0E1" "SLC15A3" "NDUFB3" "SLC11A2" "NDUFV1"
## [7] "LETM1" "UQCRH" "NDUFB8" "ATP5PF" "GHITM" "NDUFA7"
## [13] "COX7B" "SLC15A4" "SLC25A4" "ATP6V0D2" "NDUFA5" "NDUFB10"
## [19] "SLC25A27" "SLC9A2" "NDUFA6" "NDUFB2" "ATP6V0E2" "NDUFA8"
## [25] "ATP5MC1"
##
## [[1]]$`UP genesets.GO:1990229 iron-sulfur cluster assembly complex`
## [1] "BOLA3" "LYRM4" "FDX2" "FXN" "GLRX3"
##
## [[1]]$`DOWN genesets.GO:0000727 double-strand break repair via break-induced replication`
## [1] "MCM3" "MCM7" "GINS2" "CDC45" "GINS4" "MCM4" "MCM2" "MCM6"
## [9] "MCM5" "CDC7" "MUS81" "MCMDC2"
##
## [[1]]$`DOWN genesets.GO:0002181 cytoplasmic translation`
## [1] "RPL10A" "RPL3" "RPL5" "RPL7A" "RPL36A" "RPL26" "RPS9"
## [8] "RPS24" "RPL22L1" "RPL32" "RPS8" "RPL4" "RPS14" "RPS15A"
## [15] "RPS18" "RPL22" "RPL10" "RPL23" "RPL11" "RPL7" "RPL34"
## [22] "RPL31" "RPL6" "RPS3" "RPL13" "RACK1" "RPS3A" "RPL35A"
## [29] "RPS23" "RPL12" "RPL27A" "RPL37A" "RPL24" "RPS13" "RPS6"
## [36] "RPS7" "RPL14" "RPL21" "RPS25" "RPL30" "RPL15" "RPL37"
## [43] "RPL17" "RPL23A" "RPS2" "RPS4X" "RPL18" "RPLP1" "RPS20"
## [50] "RPL13A" "RPS11" "RPL41" "RPS16" "RPS27" "FTSJ1" "DRG2"
## [57] "RPL28" "RPS21" "RPL29" "RPL26L1" "RPL18A" "RWDD1" "RPL38"
## [64] "RPLP2" "RPL27" "RPL19" "GTPBP1" "RPL39" "RPS29" "RPS26"
## [71] "RPL35" "RPL9" "RPL8" "RPS12" "RPS15" "FAU" "RPS10"
## [78] "RPL36" "DRG1" "RPS17" "RPS27A" "RPS5" "UBA52"
##
## [[1]]$`DOWN genesets.GO:0002437 inflammatory response to antigenic stimulus`
## [1] "RBPJ" "HMGB2" "KDM6B" "NOTCH1" "HLA-DRB1" "PNMA1"
## [7] "HMGB1" "FOSL2" "NOTCH2" "CYSLTR1" "IL20RB" "CD68"
## [13] "RASGRP1"
##
## [[1]]$`DOWN genesets.GO:0006265 DNA topological change`
## [1] "HMGB2" "TDRD3" "TOP2B" "HMGB1" "TOP3A" "TOP1MT" "TOP1" "TOP2A"
## [9] "ERCC3" "TOP3B"
##
## [[1]]$`DOWN genesets.GO:0006270 DNA replication initiation`
## [1] "MCM3" "MCM10" "MCM7" "PURA" "CDC45" "CCNE1" "CCNE2" "MCM2"
## [9] "POLA1" "POLA2" "ORC6" "MCM6" "TOPBP1" "CDC6" "PRIM2" "ORC1"
## [17] "LRWD1" "MCM5" "NOC3L" "ORC4" "ORC5" "PRIM1" "ORC3" "ORC2"
##
## [[1]]$`DOWN genesets.GO:0006346 DNA methylation-dependent constitutive heterochromatin formation`
## [1] "DNMT1" "ATF7IP" "HELLS" "BAZ2A" "SETDB1" "CTCF" "DNMT3A"
## [8] "HDAC1" "EHMT1" "TRIM28" "SIRT1" "MBD1" "EZH2" "PPM1D"
## [15] "MBD2" "EHMT2" "BMI1" "MBD3" "ZNF304" "SMARCA5" "BEND3"
##
## [[1]]$`DOWN genesets.GO:0006353 DNA-templated transcription termination`
## [1] "SETX" "WDR82" "SMN1" "DHX9" "ZC3H4" "POLR2A" "TTF2" "TTF1"
## [9] "MTERF1" "PRMT5"
##
## [[1]]$`DOWN genesets.GO:0006376 mRNA splice site recognition`
## [1] "SETX" "LUC7L" "CELF6" "PTBP2" "LUC7L2" "CELF2" "LUC7L3" "CELF1"
## [9] "SRSF10" "NOL3" "PUF60" "SRSF5" "YTHDC1" "SRSF1" "KHDC4" "SRSF6"
## [17] "SRSF9"
##
## [[1]]$`DOWN genesets.GO:0008608 attachment of spindle microtubules to kinetochore`
## [1] "DSN1" "EML4" "TEX14" "ZNF207" "SGO1" "SPC25"
## [7] "KNL1" "NDC80" "ABRAXAS1" "BUB3" "PMF1" "MIS12"
## [13] "ABRAXAS2" "NUF2" "AURKC" "NSL1"
##
## [[1]]$`DOWN genesets.GO:0022625 cytosolic large ribosomal subunit`
## [1] "RPL10A" "RPL3" "RPL5" "RPL7A" "RPL36A" "RPL26" "RPL32"
## [8] "RPL4" "RPL22" "RPL10" "RPL23" "RPL11" "RPL7" "RPL34"
## [15] "RPL31" "RPL6" "RPL13" "RPL35A" "RPL12" "RPL27A" "RPL37A"
## [22] "RPL24" "RPL14" "RPL21" "RPL30" "RPL15" "RPL37" "RPL17"
## [29] "RPL23A" "RPL18" "RPLP1" "RPL13A" "RPL41" "RPL28" "RPL29"
## [36] "RPL26L1" "RPL18A" "RPL38" "RPLP2" "RPL27" "RPL19" "RPL36AL"
## [43] "RPL39" "RPL35" "RPL9" "RPL8" "RPL36" "RPL7L1" "RPL39L"
## [50] "UBA52"
##
## [[1]]$`DOWN genesets.GO:0030174 regulation of DNA-templated DNA replication initiation`
## [1] "MCM3" "MCM7" "CDT1" "MCM4" "MCM2" "KAT7" "MCM6" "NBN"
## [9] "GMNN" "MCM5" "WRNIP1"
##
## [[1]]$`DOWN genesets.GO:0032454 histone H3K9 demethylase activity`
## [1] "JMJD1C" "KDM3B" "KDM4B" "KDM3A" "PHF2" "PHF8" "KDM4C" "KDM7A"
## [9] "KDM1A" "KDM4A" "KDM4D"
##
## [[1]]$`DOWN genesets.GO:0032993 protein-DNA complex`
## [1] "HHEX" "SP3" "FOS" "SP1" "EP300" "TCF7L2" "XRCC5" "PRKDC"
## [9] "NFE2L2" "NUPR1" "MAX" "NPM1" "KDM5A" "NFYC" "RAD52" "ST18"
## [17] "PARP1" "SOX12" "JUP" "ATF6B" "SUZ12" "TOP1" "MED1" "GTF2B"
## [25] "XRCC6" "POLR2H" "NFYA" "CTNNB1" "NFYB" "DDIT3" "ZBTB17"
##
## [[1]]$`DOWN genesets.GO:0034501 protein localization to kinetochore`
## [1] "CDK1" "TTK" "ZWILCH" "SPDL1" "IK" "KNL1" "CHAMP1" "BUB3"
## [9] "AURKB" "ZW10" "MTBP"
##
## [[1]]$`DOWN genesets.GO:0035196 miRNA processing`
## [1] "AGO3" "DICER1" "PUM2" "PUM1" "AGO2" "AGO4" "AGO1" "SNIP1"
## [9] "ZC3H7A" "PRKRA" "TARBP2" "ZC3H7B" "SPOUT1" "NUP155"
##
## [[1]]$`DOWN genesets.GO:0036002 pre-mRNA binding`
## [1] "TRA2B" "HNRNPU" "HNRNPA1" "ARGLU1" "DDX5" "SRSF3" "SRSF2"
## [8] "CELF2" "CELF1" "RBM22" "PTBP1" "TARBP2" "SRSF6"
##
## [[1]]$`DOWN genesets.GO:0042555 MCM complex`
## [1] "MCM3" "MCM7" "MCM9" "MMS22L" "MCMBP" "MCM4" "MCM2" "MCM6"
## [9] "MCM8" "MCM5" "TONSL"
##
## [[1]]$`DOWN genesets.GO:0042800 histone H3K4 methyltransferase activity`
## [1] "KMT2C" "SETD3" "ASH1L" "SETD1B" "KMT2D" "KMT2B" "KMT2A" "SETD1A"
## [9] "SETD4" "SETBP1" "SETMAR" "WDR5"
##
## [[1]]$`DOWN genesets.GO:0043923 positive regulation by host of viral transcription`
## [1] "SP1" "EP300" "NUCKS1" "TFAP4" "SNW1" "CTDP1" "CCNT2"
## [8] "CCNT1" "TAF11" "SMARCB1" "CDK9" "CHD1" "SMARCA4" "ZNF639"
## [15] "RRP1B" "JUN"
##
## [[1]]$`DOWN genesets.GO:0043995 histone H4K5 acetyltransferase activity`
## [1] "JADE1" "KAT6B" "NCOA1" "BRPF1" "EP300" "KAT6A" "KAT8" "CREBBP"
## [9] "BRD1" "KAT7" "ING4" "TAF1" "HAT1" "BRPF3" "NAA60" "ING3"
## [17] "GTF2B" "MCM3AP" "KAT2B" "JADE2" "NCOA3" "CLOCK" "MEAF6" "GTF3C4"
## [25] "KAT5" "KAT2A"
##
## [[1]]$`DOWN genesets.GO:0043996 histone H4K8 acetyltransferase activity`
## [1] "JADE1" "KAT6B" "NCOA1" "BRPF1" "EP300" "KAT6A" "KAT8" "CREBBP"
## [9] "BRD1" "KAT7" "ING4" "TAF1" "HAT1" "BRPF3" "NAA60" "ING3"
## [17] "GTF2B" "MCM3AP" "KAT2B" "JADE2" "NCOA3" "CLOCK" "MEAF6" "GTF3C4"
## [25] "KAT5" "KAT2A"
##
## [[1]]$`DOWN genesets.GO:0043997 histone H4K12 acetyltransferase activity`
## [1] "JADE1" "KAT6B" "NCOA1" "BRPF1" "EP300" "KAT6A" "KAT8" "CREBBP"
## [9] "BRD1" "KAT7" "ING4" "TAF1" "HAT1" "BRPF3" "NAA60" "ING3"
## [17] "GTF2B" "MCM3AP" "KAT2B" "JADE2" "NCOA3" "CLOCK" "MEAF6" "GTF3C4"
## [25] "KAT5" "KAT2A"
##
## [[1]]$`DOWN genesets.GO:0044027 negative regulation of gene expression via chromosomal CpG island methylation`
## [1] "DNMT1" "MYC" "HELLS" "BRCA1" "UHRF1" "CTCF"
## [7] "DNMT3A" "MECP2" "UHRF2" "ZNF445" "MPHOSPH8" "EHMT2"
## [13] "PRMT5" "USP7"
##
## [[1]]$`DOWN genesets.GO:0044849 estrous cycle`
## [1] "IGF1R" "NCOA1" "OPRL1" "ADNP" "NCOR2" "SLC26A6" "EGR1"
## [8] "PCNA" "MDK" "CYP1B1"
##
## [[1]]$`DOWN genesets.GO:0046972 histone H4K16 acetyltransferase activity`
## [1] "JADE1" "KAT6B" "NCOA1" "EP300" "KAT6A" "KAT8" "CREBBP" "KAT7"
## [9] "ING4" "TAF1" "HAT1" "NAA60" "ING3" "GTF2B" "MCM3AP" "KAT2B"
## [17] "JADE2" "NCOA3" "CLOCK" "GTF3C4" "KAT5" "KAT2A"
##
## [[1]]$`DOWN genesets.GO:0048706 embryonic skeletal system development`
## [1] "MBTD1" "SP3" "PCSK5" "XYLT1" "DLX3" "TAPT1" "DEAF1" "RBP4"
## [9] "ACVR2A" "SCX" "DLX4" "MOSMO" "MKS1"
##
## [[1]]$`DOWN genesets.GO:0061158 3'-UTR-mediated mRNA destabilization`
## [1] "CPEB3" "ZFP36L1" "PUM2" "HNRNPD" "ZFP36" "PUM1" "KHSRP"
## [8] "ZC3H12D" "RC3H1" "TARDBP" "UPF1" "ZFP36L2" "DHX36" "ZC3H12A"
## [15] "MOV10"
##
## [[1]]$`DOWN genesets.GO:0071162 CMG complex`
## [1] "MCM3" "MCM7" "GINS2" "CDC45" "GINS4" "MCM4" "MCM2" "MCM6" "GINS3"
## [10] "MCM5" "GINS1"
##
## [[1]]$`DOWN genesets.GO:0071168 protein localization to chromatin`
## [1] "ZMYND8" "BRD2" "MCM9" "MMS22L" "RAD21" "BRD3" "ESR1" "MCM8"
## [9] "MSH2" "PARP1" "CHMP7" "SPIN1" "EZH2" "ESCO2" "FAM47E" "TONSL"
## [17] "PLK1" "APLF" "WAPL" "MRNIP" "LEMD2"
##
## [[1]]$`DOWN genesets.GO:0106222 lncRNA binding`
## [1] "DNMT1" "HADHB" "HNRNPU" "ATP2A2" "PCBP2" "DNMT3A" "RAD21" "PUM2"
## [9] "BRD3" "STAT3" "EZH2" "RBM33" "SUZ12" "CSDE1" "ELAVL1" "SUGT1"DE3 MDM
We are interested in comparing DEGs between the mock (ctrl) and productively-infected (case) in MDM cells. Read in the key data.
x <- read.table("de3mf.tsv")
m3mf <- mitch_import(x,DEtype="DESeq2")## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 14556## Note: no. genes in output = 14556## Note: estimated proportion of input genes in output = 1mres3mf <- mitch_calc(m3mf,genesets=go,cores=8,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.networkplot(mres3mf,FDR=0.05,n_sets=20)
network_genes(mres3mf,FDR=0.05,n_sets=20)## [[1]]
## [[1]]$`UP genesets.GO:0000176 nuclear exosome (RNase complex)`
## [1] "EXOSC1"
##
## [[1]]$`UP genesets.GO:0000266 mitochondrial fission`
## character(0)
##
## [[1]]$`UP genesets.GO:0000502 proteasome complex`
## [1] "PSMD8" "PSMB2" "RAD23A" "RAD23B" "PSMC4" "PSMA7" "PSMD3" "PSMC5"
## [9] "PSMB1"
##
## [[1]]$`UP genesets.GO:0004532 RNA exonuclease activity`
## [1] "EXOSC1"
##
## [[1]]$`UP genesets.GO:0005744 TIM23 mitochondrial import inner membrane translocase complex`
## character(0)
##
## [[1]]$`UP genesets.GO:0005761 mitochondrial ribosome`
## [1] "MRPL18" "MRPS22" "MRPL43"
##
## [[1]]$`UP genesets.GO:0005762 mitochondrial large ribosomal subunit`
## [1] "MRPL18" "MRPL42" "MRPL43"
##
## [[1]]$`UP genesets.GO:0005763 mitochondrial small ribosomal subunit`
## [1] "MRPS16" "MRPL42" "MRPS15" "MRPS22" "MRPS10"
##
## [[1]]$`UP genesets.GO:0005839 proteasome core complex`
## [1] "PSMB2" "PSMA7" "PSMB1"
##
## [[1]]$`UP genesets.GO:0008540 proteasome regulatory particle, base subcomplex`
## [1] "PSMC4" "PSMC5"
##
## [[1]]$`UP genesets.GO:0016226 iron-sulfur cluster assembly`
## [1] "CIAO2B" "BOLA1" "NUBPL"
##
## [[1]]$`UP genesets.GO:0016559 peroxisome fission`
## character(0)
##
## [[1]]$`UP genesets.GO:0022624 proteasome accessory complex`
## [1] "PSMD8" "PSMC4" "PSMD3" "PSMC5"
##
## [[1]]$`UP genesets.GO:0030150 protein import into mitochondrial matrix`
## character(0)
##
## [[1]]$`UP genesets.GO:0031083 BLOC-1 complex`
## [1] "BLOC1S5"
##
## [[1]]$`UP genesets.GO:0032543 mitochondrial translation`
## [1] "MRPS16" "MRPL18" "MRPL42" "MRPS15" "MRPS22" "MRPL43" "MRPS10"
##
## [[1]]$`UP genesets.GO:0042176 regulation of protein catabolic process`
## [1] "MDM2" "SNF8" "PSMD3" "TMEM9"
##
## [[1]]$`UP genesets.GO:0101019 nucleolar exosome (RNase complex)`
## [1] "EXOSC1"
##
## [[1]]$`UP genesets.GO:0101031 protein folding chaperone complex`
## [1] "PSMG1" "DNAJC9" "SPAG1" "UXT" "CCDC47"
##
## [[1]]$`UP genesets.GO:1990229 iron-sulfur cluster assembly complex`
## [1] "BOLA1"
##
## [[1]]$`DOWN genesets.GO:0000727 double-strand break repair via break-induced replication`
## [1] "GINS2" "MCM7" "MCM5" "MCM6" "MCM3" "MCM2" "MCM4" "MUS81"
## [9] "GINS4" "MCMDC2" "CDC7"
##
## [[1]]$`DOWN genesets.GO:0000940 outer kinetochore`
## [1] "SPC25" "CENPF" "CCNB1" "PLK1" "KNL1" "BUB1" "NDC80" "ZWINT" "DSN1"
## [10] "BUB1B" "NUF2" "SKA2" "PMF1" "MIS12" "BOD1" "SPDL1" "NSL1"
##
## [[1]]$`DOWN genesets.GO:0002503 peptide antigen assembly with MHC class II protein complex`
## [1] "HLA-DMA" "HLA-DPB1" "HLA-DMB" "HLA-DRA" "HLA-DPA1" "HLA-DOA"
## [7] "HLA-DRB1" "HLA-DQA1" "HLA-DQA2" "HLA-DRB5" "HLA-DQB1" "B2M"
##
## [[1]]$`DOWN genesets.GO:0007019 microtubule depolymerization`
## [1] "KIF14" "BMERB1" "KIF2C" "NCKAP5L" "CKAP5" "STMN1" "KIF18A"
## [8] "KIF24" "KIF2A" "KATNB1"
##
## [[1]]$`DOWN genesets.GO:0007094 mitotic spindle assembly checkpoint signaling`
## [1] "SPC25" "CENPF" "BIRC5" "TEX14" "TTK" "PLK1" "BUB1" "NDC80"
## [9] "ZWINT" "KNTC1" "BUB1B" "ATM" "NUF2" "ZNF207" "MAD2L2" "MAD2L1"
## [17] "APC" "MAD1L1" "TPR" "ZWILCH" "ZW10" "PSMG2" "IK" "KLHL22"
## [25] "SPDL1" "BUB3" "CDC20"
##
## [[1]]$`DOWN genesets.GO:0007275 multicellular organism development`
## [1] "IGF1R" "LEPR" "TIE1" "CSF1R" "GCNT2" "FGFR1" "PDGFRA" "MERTK"
## [9] "FLT1" "RYK" "ALK" "ERBB2" "INSR" "RET" "ROR1"
##
## [[1]]$`DOWN genesets.GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II`
## [1] "HLA-DMA" "HLA-DPB1" "HLA-DMB" "CTSS" "HLA-DRA" "HLA-DPA1"
## [7] "IFI30" "FCGR2B" "CD74" "HLA-DOA" "CTSV" "HLA-DRB1"
## [13] "CTSF" "UNC93B1" "DNM2" "PIKFYVE" "HLA-DQA1" "HLA-DQA2"
## [19] "CTSD" "HLA-DRB5" "FCER1G" "CTSL" "HLA-DQB1" "B2M"
## [25] "LGMN" "TRAF6"
##
## [[1]]$`DOWN genesets.GO:0030174 regulation of DNA-templated DNA replication initiation`
## [1] "CDT1" "MCM7" "MCM5" "MCM6" "MCM3" "MCM2" "MCM4" "KAT7"
## [9] "NBN" "WRNIP1" "GMNN"
##
## [[1]]$`DOWN genesets.GO:0032870 cellular response to hormone stimulus`
## [1] "RAMP1" "IGFBP7" "IGFBP2" "RAMP2" "NCOA2" "GPR150" "ROBO2" "NCOA1"
## [9] "STAT5B" "SLIT3" "INPP5K" "STAT3" "NCOA3" "FOSB"
##
## [[1]]$`DOWN genesets.GO:0035904 aorta development`
## [1] "GAA" "EGR2" "PRDM1" "TAB1" "PKD2" "PLXND1" "SUFU"
## [8] "HECTD1" "ROBO2" "CNTRL" "ADAMTS6" "AP2B1" "DCTN5" "NDST1"
## [15] "SMAD6" "PDE2A" "MEGF8" "SNX17"
##
## [[1]]$`DOWN genesets.GO:0042555 MCM complex`
## [1] "MCM7" "MCM5" "MCM6" "MCM3" "TONSL" "MCM2" "MCM4" "MCM9"
## [9] "MCM8" "MCMBP" "MMS22L"
##
## [[1]]$`DOWN genesets.GO:0042613 MHC class II protein complex`
## [1] "HLA-DMA" "HLA-DPB1" "HLA-DMB" "HLA-DRA" "HLA-DPA1" "CD74"
## [7] "HLA-DOA" "HLA-DRB1" "HLA-DQA1" "HLA-DQA2" "HLA-DRB5" "HLA-DQB1"
## [13] "B2M"
##
## [[1]]$`DOWN genesets.GO:0044027 negative regulation of gene expression via chromosomal CpG island methylation`
## [1] "BRCA1" "HELLS" "UHRF2" "UHRF1" "MPHOSPH8" "MYC"
## [7] "DNMT1" "MECP2" "DNMT3A" "USP7" "ZNF445" "CTCF"
## [13] "EHMT2" "PRMT5"
##
## [[1]]$`DOWN genesets.GO:0044849 estrous cycle`
## [1] "IGF1R" "EGR1" "NCOR2" "OPRL1" "CYP1B1" "PCNA" "NCOA1"
## [8] "MDK" "SLC26A6" "ADNP"
##
## [[1]]$`DOWN genesets.GO:0050769 positive regulation of neurogenesis`
## [1] "NAP1L1" "GPER1" "XRCC5" "SERPINF1" "ACE" "SPEN"
## [7] "XRCC2" "NUMBL" "RGS14" "MAN2A1" "TRIM32" "MME"
## [13] "ZNF335" "SRRT" "TGM2" "SNW1" "LIG4" "NUMB"
##
## [[1]]$`DOWN genesets.GO:0051256 mitotic spindle midzone assembly`
## [1] "BIRC5" "KIF4A" "PRC1" "KIF23" "AURKB" "CDCA8" "RACGAP1"
## [8] "MAP10" "INCENP"
##
## [[1]]$`DOWN genesets.GO:0051983 regulation of chromosome segregation`
## [1] "MKI67" "CDCA2" "BUB1" "KIF2C" "AURKB" "ZNF207" "PUM1"
## [8] "PUM2" "PPP2R2D" "PPP2R2A"
##
## [[1]]$`DOWN genesets.GO:0051984 positive regulation of chromosome segregation`
## [1] "NCAPG" "NCAPH" "CDC6" "NCAPG2" "SMC4" "SMC2" "RAD18" "SMC6"
## [9] "NUMA1" "SMC5" "NCAPH2" "NCAPD3" "NCAPD2"
##
## [[1]]$`DOWN genesets.GO:0071162 CMG complex`
## [1] "GINS2" "MCM7" "MCM5" "MCM6" "MCM3" "MCM2" "MCM4" "GINS4" "GINS3"
## [10] "GINS1"
##
## [[1]]$`DOWN genesets.GO:0090267 positive regulation of mitotic cell cycle spindle assembly checkpoint`
## [1] "BIRC5" "NDC80" "AURKB" "GEN1" "CDCA8" "MAD2L1"
## [7] "XRCC3" "PCID2" "DYNC1LI1" "MAD1L1" "TPR" "INCENP"networkplot(mres3mf,FDR=0.05,n_sets=30)
network_genes(mres3mf,FDR=0.05,n_sets=30)## [[1]]
## [[1]]$`UP genesets.GO:0000176 nuclear exosome (RNase complex)`
## [1] "EXOSC1"
##
## [[1]]$`UP genesets.GO:0000266 mitochondrial fission`
## character(0)
##
## [[1]]$`UP genesets.GO:0000502 proteasome complex`
## [1] "PSMD8" "PSMB2" "RAD23A" "RAD23B" "PSMC4" "PSMA7" "PSMD3" "PSMC5"
## [9] "PSMB1"
##
## [[1]]$`UP genesets.GO:0003925 G protein activity`
## [1] "RAB10"
##
## [[1]]$`UP genesets.GO:0004532 RNA exonuclease activity`
## [1] "EXOSC1"
##
## [[1]]$`UP genesets.GO:0005179 hormone activity`
## [1] "CCN3" "GDF15" "EDN1"
##
## [[1]]$`UP genesets.GO:0005484 SNAP receptor activity`
## [1] "YKT6" "VTI1B" "STX3"
##
## [[1]]$`UP genesets.GO:0005669 transcription factor TFIID complex`
## [1] "GTF2A2"
##
## [[1]]$`UP genesets.GO:0005744 TIM23 mitochondrial import inner membrane translocase complex`
## character(0)
##
## [[1]]$`UP genesets.GO:0005758 mitochondrial intermembrane space`
## [1] "PRELID3B" "STOML2" "TRIAP1" "HAX1" "TIMM8A" "TIMM29" "SDHAF3"
##
## [[1]]$`UP genesets.GO:0005761 mitochondrial ribosome`
## [1] "MRPL18" "MRPS22" "MRPL43"
##
## [[1]]$`UP genesets.GO:0005762 mitochondrial large ribosomal subunit`
## [1] "MRPL18" "MRPL42" "MRPL43"
##
## [[1]]$`UP genesets.GO:0005763 mitochondrial small ribosomal subunit`
## [1] "MRPS16" "MRPL42" "MRPS15" "MRPS22" "MRPS10"
##
## [[1]]$`UP genesets.GO:0005839 proteasome core complex`
## [1] "PSMB2" "PSMA7" "PSMB1"
##
## [[1]]$`UP genesets.GO:0008540 proteasome regulatory particle, base subcomplex`
## [1] "PSMC4" "PSMC5"
##
## [[1]]$`UP genesets.GO:0016226 iron-sulfur cluster assembly`
## [1] "CIAO2B" "BOLA1" "NUBPL"
##
## [[1]]$`UP genesets.GO:0016559 peroxisome fission`
## character(0)
##
## [[1]]$`UP genesets.GO:0019003 GDP binding`
## [1] "RRAGD" "RAB10" "RHEBL1"
##
## [[1]]$`UP genesets.GO:0022624 proteasome accessory complex`
## [1] "PSMD8" "PSMC4" "PSMD3" "PSMC5"
##
## [[1]]$`UP genesets.GO:0030150 protein import into mitochondrial matrix`
## character(0)
##
## [[1]]$`UP genesets.GO:0031083 BLOC-1 complex`
## [1] "BLOC1S5"
##
## [[1]]$`UP genesets.GO:0031201 SNARE complex`
## [1] "YKT6" "VTI1B" "STX3"
##
## [[1]]$`UP genesets.GO:0032543 mitochondrial translation`
## [1] "MRPS16" "MRPL18" "MRPL42" "MRPS15" "MRPS22" "MRPL43" "MRPS10"
##
## [[1]]$`UP genesets.GO:0033617 mitochondrial cytochrome c oxidase assembly`
## [1] "COA1"
##
## [[1]]$`UP genesets.GO:0042176 regulation of protein catabolic process`
## [1] "MDM2" "SNF8" "PSMD3" "TMEM9"
##
## [[1]]$`UP genesets.GO:0051537 2 iron, 2 sulfur cluster binding`
## [1] "GLRX2"
##
## [[1]]$`UP genesets.GO:0061025 membrane fusion`
## [1] "YKT6" "VTI1B" "DPP4"
##
## [[1]]$`UP genesets.GO:0101019 nucleolar exosome (RNase complex)`
## [1] "EXOSC1"
##
## [[1]]$`UP genesets.GO:0101031 protein folding chaperone complex`
## [1] "PSMG1" "DNAJC9" "SPAG1" "UXT" "CCDC47"
##
## [[1]]$`UP genesets.GO:1990229 iron-sulfur cluster assembly complex`
## [1] "BOLA1"
##
## [[1]]$`DOWN genesets.GO:0000727 double-strand break repair via break-induced replication`
## [1] "GINS2" "MCM7" "MCM5" "MCM6" "MCM3" "MCM2" "MCM4" "MUS81"
## [9] "GINS4" "MCMDC2" "CDC7"
##
## [[1]]$`DOWN genesets.GO:0000940 outer kinetochore`
## [1] "SPC25" "CENPF" "CCNB1" "PLK1" "KNL1" "BUB1" "NDC80" "ZWINT" "DSN1"
## [10] "BUB1B" "NUF2" "SKA2" "PMF1" "MIS12" "BOD1" "SPDL1" "NSL1"
##
## [[1]]$`DOWN genesets.GO:0002503 peptide antigen assembly with MHC class II protein complex`
## [1] "HLA-DMA" "HLA-DPB1" "HLA-DMB" "HLA-DRA" "HLA-DPA1" "HLA-DOA"
## [7] "HLA-DRB1" "HLA-DQA1" "HLA-DQA2" "HLA-DRB5" "HLA-DQB1" "B2M"
##
## [[1]]$`DOWN genesets.GO:0007019 microtubule depolymerization`
## [1] "KIF14" "BMERB1" "KIF2C" "NCKAP5L" "CKAP5" "STMN1" "KIF18A"
## [8] "KIF24" "KIF2A" "KATNB1"
##
## [[1]]$`DOWN genesets.GO:0007076 mitotic chromosome condensation`
## [1] "NCAPG" "PLK1" "NCAPH" "PHF13" "TENT4A" "SMC4" "CDCA5" "SMC2"
## [9] "NUSAP1" "KMT5A" "AKAP8" "AKAP8L" "NCAPH2" "CHMP1A" "TTN" "NCAPD3"
## [17] "NCAPD2"
##
## [[1]]$`DOWN genesets.GO:0007094 mitotic spindle assembly checkpoint signaling`
## [1] "SPC25" "CENPF" "BIRC5" "TEX14" "TTK" "PLK1" "BUB1" "NDC80"
## [9] "ZWINT" "KNTC1" "BUB1B" "ATM" "NUF2" "ZNF207" "MAD2L2" "MAD2L1"
## [17] "APC" "MAD1L1" "TPR" "ZWILCH" "ZW10" "PSMG2" "IK" "KLHL22"
## [25] "SPDL1" "BUB3" "CDC20"
##
## [[1]]$`DOWN genesets.GO:0007275 multicellular organism development`
## [1] "IGF1R" "LEPR" "TIE1" "CSF1R" "GCNT2" "FGFR1" "PDGFRA" "MERTK"
## [9] "FLT1" "RYK" "ALK" "ERBB2" "INSR" "RET" "ROR1"
##
## [[1]]$`DOWN genesets.GO:0017116 single-stranded DNA helicase activity`
## [1] "MCM7" "MCM5" "POLQ" "HELB" "MCM3" "RFC3" "MCM2" "MCM4"
## [9] "DSCC1" "RFC5" "MCM9" "MCM8" "CHTF8" "DNA2" "WRNIP1" "RAD51"
## [17] "RFC2" "PIF1" "RFC4"
##
## [[1]]$`DOWN genesets.GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II`
## [1] "HLA-DMA" "HLA-DPB1" "HLA-DMB" "CTSS" "HLA-DRA" "HLA-DPA1"
## [7] "IFI30" "FCGR2B" "CD74" "HLA-DOA" "CTSV" "HLA-DRB1"
## [13] "CTSF" "UNC93B1" "DNM2" "PIKFYVE" "HLA-DQA1" "HLA-DQA2"
## [19] "CTSD" "HLA-DRB5" "FCER1G" "CTSL" "HLA-DQB1" "B2M"
## [25] "LGMN" "TRAF6"
##
## [[1]]$`DOWN genesets.GO:0021772 olfactory bulb development`
## [1] "KIF14" "CSF1R" "TTC8" "SEMA3A" "LRRK2" "ID2"
## [7] "SKI" "RPGRIP1L" "MECP2" "CHD7" "EXT1" "AGTPBP1"
##
## [[1]]$`DOWN genesets.GO:0023026 MHC class II protein complex binding`
## [1] "HLA-DMA" "CD4" "HLA-DPB1" "HLA-DMB" "HLA-DRA" "HLA-DPA1"
## [7] "CD74" "HLA-DOA" "HLA-DRB1" "HLA-DQA1" "HLA-DQA2" "HLA-DRB5"
## [13] "HSP90AA1" "CD81" "HLA-DQB1" "HSP90AB1" "YWHAE" "B2M"
## [19] "HSPA8" "ANXA11" "PKM"
##
## [[1]]$`DOWN genesets.GO:0030174 regulation of DNA-templated DNA replication initiation`
## [1] "CDT1" "MCM7" "MCM5" "MCM6" "MCM3" "MCM2" "MCM4" "KAT7"
## [9] "NBN" "WRNIP1" "GMNN"
##
## [[1]]$`DOWN genesets.GO:0030325 adrenal gland development`
## [1] "CDKN1C" "SMAD3" "ARID5B" "PDGFRA" "CYP1B1" "MDK" "NR3C1" "INSR"
## [9] "SMAD4" "NF1" "TSPO" "SMAD2"
##
## [[1]]$`DOWN genesets.GO:0031904 endosome lumen`
## [1] "AP4E1" "JAK2" "PRLR" "PTPN2" "AP4B1" "AP4M1" "CTSD" "PTPN1"
## [9] "CD63" "LRPAP1" "APP" "AP4S1"
##
## [[1]]$`DOWN genesets.GO:0032870 cellular response to hormone stimulus`
## [1] "RAMP1" "IGFBP7" "IGFBP2" "RAMP2" "NCOA2" "GPR150" "ROBO2" "NCOA1"
## [9] "STAT5B" "SLIT3" "INPP5K" "STAT3" "NCOA3" "FOSB"
##
## [[1]]$`DOWN genesets.GO:0035790 platelet-derived growth factor receptor-alpha signaling pathway`
## [1] "IGF1R" "TIE1" "CSF1R" "FGFR1" "PDGFRA" "MERTK" "FLT1" "PDGFA"
## [9] "ALK" "ERBB2" "INSR" "RET" "EPHB1" "EPHB2"
##
## [[1]]$`DOWN genesets.GO:0035791 platelet-derived growth factor receptor-beta signaling pathway`
## [1] "IGF1R" "TIE1" "CSF1R" "ABL1" "FGFR1" "PDGFRA" "MERTK" "FLT1"
## [9] "CLASP2" "ALK" "ERBB2" "INSR" "RET" "EPHB1" "PTPN1" "EPHB2"
##
## [[1]]$`DOWN genesets.GO:0035904 aorta development`
## [1] "GAA" "EGR2" "PRDM1" "TAB1" "PKD2" "PLXND1" "SUFU"
## [8] "HECTD1" "ROBO2" "CNTRL" "ADAMTS6" "AP2B1" "DCTN5" "NDST1"
## [15] "SMAD6" "PDE2A" "MEGF8" "SNX17"
##
## [[1]]$`DOWN genesets.GO:0042555 MCM complex`
## [1] "MCM7" "MCM5" "MCM6" "MCM3" "TONSL" "MCM2" "MCM4" "MCM9"
## [9] "MCM8" "MCMBP" "MMS22L"
##
## [[1]]$`DOWN genesets.GO:0042613 MHC class II protein complex`
## [1] "HLA-DMA" "HLA-DPB1" "HLA-DMB" "HLA-DRA" "HLA-DPA1" "CD74"
## [7] "HLA-DOA" "HLA-DRB1" "HLA-DQA1" "HLA-DQA2" "HLA-DRB5" "HLA-DQB1"
## [13] "B2M"
##
## [[1]]$`DOWN genesets.GO:0044027 negative regulation of gene expression via chromosomal CpG island methylation`
## [1] "BRCA1" "HELLS" "UHRF2" "UHRF1" "MPHOSPH8" "MYC"
## [7] "DNMT1" "MECP2" "DNMT3A" "USP7" "ZNF445" "CTCF"
## [13] "EHMT2" "PRMT5"
##
## [[1]]$`DOWN genesets.GO:0044849 estrous cycle`
## [1] "IGF1R" "EGR1" "NCOR2" "OPRL1" "CYP1B1" "PCNA" "NCOA1"
## [8] "MDK" "SLC26A6" "ADNP"
##
## [[1]]$`DOWN genesets.GO:0050769 positive regulation of neurogenesis`
## [1] "NAP1L1" "GPER1" "XRCC5" "SERPINF1" "ACE" "SPEN"
## [7] "XRCC2" "NUMBL" "RGS14" "MAN2A1" "TRIM32" "MME"
## [13] "ZNF335" "SRRT" "TGM2" "SNW1" "LIG4" "NUMB"
##
## [[1]]$`DOWN genesets.GO:0050778 positive regulation of immune response`
## [1] "HLA-DMA" "HLA-DPB1" "HLA-DMB" "HLA-DRA" "HLA-DPA1" "RSAD2"
## [7] "CFP" "HLA-DOA" "HLA-DRB1" "HLA-DQA1" "HLA-DQA2" "IL15"
## [13] "HLA-DRB5" "HLA-DQB1" "TGFB2" "C9" "B2M"
##
## [[1]]$`DOWN genesets.GO:0051256 mitotic spindle midzone assembly`
## [1] "BIRC5" "KIF4A" "PRC1" "KIF23" "AURKB" "CDCA8" "RACGAP1"
## [8] "MAP10" "INCENP"
##
## [[1]]$`DOWN genesets.GO:0051983 regulation of chromosome segregation`
## [1] "MKI67" "CDCA2" "BUB1" "KIF2C" "AURKB" "ZNF207" "PUM1"
## [8] "PUM2" "PPP2R2D" "PPP2R2A"
##
## [[1]]$`DOWN genesets.GO:0051984 positive regulation of chromosome segregation`
## [1] "NCAPG" "NCAPH" "CDC6" "NCAPG2" "SMC4" "SMC2" "RAD18" "SMC6"
## [9] "NUMA1" "SMC5" "NCAPH2" "NCAPD3" "NCAPD2"
##
## [[1]]$`DOWN genesets.GO:0071162 CMG complex`
## [1] "GINS2" "MCM7" "MCM5" "MCM6" "MCM3" "MCM2" "MCM4" "GINS4" "GINS3"
## [10] "GINS1"
##
## [[1]]$`DOWN genesets.GO:0090267 positive regulation of mitotic cell cycle spindle assembly checkpoint`
## [1] "BIRC5" "NDC80" "AURKB" "GEN1" "CDCA8" "MAD2L1"
## [7] "XRCC3" "PCID2" "DYNC1LI1" "MAD1L1" "TPR" "INCENP"
##
## [[1]]$`DOWN genesets.GO:1904385 cellular response to angiotensin`
## [1] "IGF1R" "CDC6" "BRIP1" "MAP3K7" "PRKCD" "HSF1" "NFE2L2" "ARID1B"
## [9] "NFKB1" "PTPN1" "RELA"DE5 Mock MDM vs Mock AlvMDM
We are interested in comparing DEGs between the mock MDM (ctrl) and the mock Alv (case).
x <- read.table("demockf.tsv")
m5f <- mitch_import(x,DEtype="DESeq2")## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 15053## Note: no. genes in output = 15053## Note: estimated proportion of input genes in output = 1mres5f <- mitch_calc(m5f,genesets=go,cores=8,priority="effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.networkplot(mres5f,FDR=0.05,n_sets=20)
network_genes(mres5f,FDR=0.05,n_sets=20)## [[1]]
## [[1]]$`UP genesets.GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding`
## [1] "PPARD" "PITX1" "NFATC3" "ZNF366" "SKI" "RBPJ"
## [7] "TCF7L2" "EGR2" "DLX3" "STAT6" "ESR1" "RARA"
## [13] "ZBTB7B" "HIVEP3" "AR" "MAF" "VDR" "KLF9"
## [19] "VAX2" "CALCOCO1" "SNAI3" "TEAD3" "CEBPA" "HDAC4"
## [25] "NACC2" "HIC2" "POU3F1" "KLF16" "ZBTB8A" "IKZF2"
## [31] "NR2F6" "ZNF362" "DNMT3A" "E2F3" "TFCP2" "MXD4"
## [37] "ZNF678" "ZNF76" "MITF" "NLRC5" "KLF4" "SREBF2"
## [43] "ZNF711" "ZNF808" "MEF2A" "TEF" "POU2F2" "NFYC"
## [49] "ZFHX3" "ZBTB7C" "RXRA" "NFATC1" "RREB1" "KDM2B"
## [55] "MLXIPL" "BCL6" "DMTF1" "MED1" "ZNF692" "GFI1"
## [61] "TFE3" "FOXK2" "IKZF5" "TP63" "NR3C1" "ZNF646"
## [67] "SKIL" "GRHL1" "ZNF585A" "MZF1" "ZNF347" "TFEB"
## [73] "ZNF573" "ZNF514" "ZNF761" "TARDBP" "IKZF1" "ZFAT"
## [79] "ZNF623" "ZNF470" "CHD7" "JUND" "ZNF121" "MAFK"
##
## [[1]]$`UP genesets.GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific`
## [1] "PPARD" "PITX1" "GTF2I" "NFATC3" "SKI" "RBPJ" "TCF7L2" "EGR2"
## [9] "DLX3" "STAT6" "ESR1" "RARA" "ZBTB7B" "HIVEP3" "AR" "MAF"
## [17] "VDR" "KLF9" "VAX2" "SNAI3" "TEAD3" "CEBPA" "NACC2" "POU3F1"
## [25] "KLF16" "ZBTB8A" "NR2F6" "NPAS1" "E2F3" "TFCP2" "MXD4" "ZBTB46"
## [33] "ZNF678" "ZNF76" "MITF" "ERF" "MYRF" "KLF4" "SREBF2" "ZNF711"
## [41] "ZNF79" "PKNOX1" "MEF2A" "TEF" "POU2F2" "NFYC" "ZFHX3" "ZBTB7C"
## [49] "RXRA" "NFATC1" "MLXIPL" "ZBTB40" "DMTF1" "ZNF768" "SCX" "TFE3"
## [57] "FOXK2" "TP63" "NR3C1" "ZNF646" "SKIL" "GRHL1" "ZGLP1" "ZNF316"
## [65] "MZF1" "CASZ1" "ESRRA" "ZNF347" "TFEB" "ZNF573" "ZNF514" "ZNF440"
## [73] "ZNF672" "ELF5" "CREB5" "ZNF761" "ZBTB42" "ZFAT" "ZNF623" "ZNF470"
## [81] "JUND" "CUX1" "ZNF121" "MAFK"
##
## [[1]]$`UP genesets.GO:0005096 GTPase activator activity`
## [1] "RGS16" "ABR" "RAP1GAP" "FAM13B" "ASAP1" "TBC1D1"
## [7] "RGS12" "RANGAP1" "ARHGAP31" "ACAP3" "RANBP2" "ARHGAP25"
## [13] "SGSM2" "ARAP1" "RASAL2" "RGS18" "ARHGAP10" "ARHGAP18"
## [19] "ARHGEF1" "DEPDC5" "RASGRP3" "LLGL1" "VPS9D1" "SH3BP1"
## [25] "TBC1D12" "RGS3" "TBC1D9B" "AGAP1" "RACGAP1" "TBC1D22B"
## [31] "SRGAP3" "TBCD" "TBC1D2B" "RASA4B" "SIPA1" "ARRB1"
## [37] "TBC1D4" "AGAP2" "ARHGAP44" "RIN2" "RABEP2" "ARHGAP1"
## [43] "ARHGAP22" "RASA4" "TBC1D10C" "RAP1GAP2" "ARHGAP20" "SGSM3"
## [49] "TBC1D14" "AGFG2"
##
## [[1]]$`UP genesets.GO:0005524 ATP binding`
## [1] "NEK6" "TRPV1" "ABCB9" "ABCA6" "TGFBR1" "SHPK"
## [7] "VWA8" "MYO1F" "ENTPD1" "MERTK" "DCLK3" "MAP3K5"
## [13] "ATP2B2" "ABCA2" "MYO1E" "PDK2" "MINK1" "GCLC"
## [19] "CAMK1" "CHD9" "MARK2" "TTLL12" "ADCY7" "NOD1"
## [25] "PIK3CD" "MARK3" "FGFR1" "ATP2A3" "ITPKB" "KCNJ1"
## [31] "PRKACB" "PRKCA" "PRAG1" "ABCD1" "AKT1" "TAP2"
## [37] "MAP3K11" "MTHFD1" "PRKCD" "EEF2K" "MYO6" "DGKH"
## [43] "PI4KA" "DDX6" "COQ8A" "DMPK" "IKBKE" "NPR1"
## [49] "KIF17" "SNRK" "TRIB1" "TOP2B" "TTLL11" "KIFC2"
## [55] "GRK2" "PEX6" "PIKFYVE" "IPPK" "ATP2B3" "ITPK1"
## [61] "TTL" "DCLK2" "ADCK1" "CHKA" "NLRC5" "NWD1"
## [67] "ALPK1" "PI4K2A" "ACSS2" "PIK3CG" "ABCB8" "KIF1B"
## [73] "EIF4G1" "DAPK1" "HK3" "CLCN7" "CSNK1G2" "PTK2B"
## [79] "ABCA9" "RPS6KL1" "GAK" "ACSF3" "MLKL" "ADK"
## [85] "SMG1" "MYLK" "TPK1" "SLC12A4" "CDK17" "HSPA14"
## [91] "DCAF1" "ULK2" "XYLB" "DGKZ" "CARNS1" "TGFBR2"
## [97] "MCM3" "LMTK2" "QRSL1" "ATR" "GATC" "ADCY10"
## [103] "DYRK1A" "PTK6" "AGAP2" "AFG3L2" "CHEK2" "ACTR3B"
## [109] "KATNAL2" "MYO19" "MCM5" "ROR1" "ABCC1" "NLK"
## [115] "ABL2" "RNF213" "MAPKAPK3" "FARSA" "PMVK" "IGF1R"
## [121] "CSK" "PIK3C2B" "ABCC4" "LRRK1" "IP6K1" "DHX38"
## [127] "MKKS" "DSTYK" "CAMK2B" "DHX34" "MOV10" "ABCC10"
## [133] "CAMKK1" "BBS10" "BMPR2" "MYO1C" "PFKL" "LIG1"
## [139] "AKT2" "OPLAH" "LRGUK" "BTK" "ASCC3" "FARS2"
## [145] "AAK1" "NLRP2" "MYH11" "ADCK2" "PSKH1" "PDPK1"
## [151] "MYO15A" "PIK3R4" "PIK3C3" "DDX10" "CHD7" "MAP3K14"
## [157] "IKBKB" "CDK6" "MAP3K3" "ARAF"
##
## [[1]]$`UP genesets.GO:0006338 chromatin remodeling`
## [1] "NEK6" "ENTPD1" "MERTK" "DPF3" "DCLK3" "ESR1"
## [7] "PTPRA" "MINK1" "CHD9" "MARK2" "RB1" "DUSP2"
## [13] "DUSP7" "MARK3" "FGFR1" "PWWP2A" "PRKCA" "HDAC4"
## [19] "AKT1" "BCOR" "PRKCD" "KAT2B" "DDX6" "DMPK"
## [25] "SNRK" "BAP1" "PHLPP1" "PTPRC" "SETD3" "BRPF1"
## [31] "PIKFYVE" "PTPN13" "PTPN22" "DUSP19" "DCLK2" "CHKA"
## [37] "ALPK1" "CDC25B" "PIK3CG" "MBD3" "DAPK1" "UBASH3B"
## [43] "CSNK1G2" "PTK2B" "RPS6KL1" "GAK" "PPM1M" "SMG1"
## [49] "PADI2" "PTPRO" "PER2" "DCAF1" "ULK2" "PTPN7"
## [55] "KDM2B" "MCM3" "LMTK2" "ATR" "DYRK1A" "PPP3CA"
## [61] "PTK6" "AFG3L2" "CHEK2" "ALPL" "EPM2A" "MCM5"
## [67] "TP63" "ABL2" "RNF213" "MAPKAPK3" "IGF1R" "CSK"
## [73] "LRRK1" "DHX38" "DSTYK" "DHX34" "YEATS2" "MYO1C"
## [79] "PPM1N" "PTPN18" "GATAD2A" "AKT2" "BTK" "ASCC3"
## [85] "KDM4B" "AAK1" "PSKH1" "KDM4C" "PDPK1" "PTPRM"
## [91] "PIK3R4" "HCFC2" "DDX10" "CHD7" "IKBKB" "ARAF"
##
## [[1]]$`UP genesets.GO:0032012 regulation of ARF protein signal transduction`
## [1] "CYTH4" "GBF1" "PSD4"
##
## [[1]]$`UP genesets.GO:0046872 metal ion binding`
## [1] "STAC" "TRPV1" "ADAM12" "CBFA2T3" "TGFBR1"
## [6] "SMAD6" "ASAP1" "FGD5" "PDLIM7" "ZNF366"
## [11] "STAC2" "MICAL3" "KCNC3" "CSGALNACT1" "EGR2"
## [16] "RNF128" "SLC30A3" "SPON2" "ATP2B2" "ZBTB7B"
## [21] "HIVEP3" "PARP12" "LONRF3" "SH3RF2" "VAV1"
## [26] "WTIP" "KLF9" "ACAP3" "CALCOCO1" "CHSY3"
## [31] "ADCY7" "HDAC7" "ZC3H7B" "NTHL1" "ATP2A3"
## [36] "RANBP2" "TRIP6" "SOBP" "FURIN" "TAP2"
## [41] "PRKCD" "CLEC7A" "ZC3H12B" "GALNT12" "DGKH"
## [46] "ZNF618" "TRERF1" "HIC2" "TATDN2" "DPYD"
## [51] "ARAP1" "ZNF804A" "MICALL2" "SMAD7" "PHOSPHO1"
## [56] "KLF16" "ZBTB8A" "IKZF2" "F13A1" "OVCH1"
## [61] "KCNK6" "DMPK" "FRRS1" "MBNL1" "TOP2B"
## [66] "CHFR" "TTLL11" "ZNF362" "PHLPP1" "SLC30A1"
## [71] "XYLT1" "DNMT3A" "BRPF1" "TNFRSF11A" "PLEKHF1"
## [76] "ABAT" "RNF40" "ATP2B3" "ZNF592" "ADARB1"
## [81] "ZBTB46" "ZNF678" "KAT6B" "ZNF76" "MSL2"
## [86] "LIN54" "RNF166" "PHYHD1" "ZNF711" "MGRN1"
## [91] "FGD6" "ZNF79" "FHL3" "B4GALT2" "KCNK13"
## [96] "IRF2BPL" "SMPD4" "GNA11" "ZNF808" "NDUFS1"
## [101] "ASXL2" "ZC3H4" "TNS1" "AGAP1" "ITGA11"
## [106] "RACGAP1" "EXT1" "ADK" "PDE4A" "SMG1"
## [111] "MYLK" "PDSS1" "ANKFY1" "FYCO1" "USP4"
## [116] "ZBTB7C" "SLC12A6" "STAC3" "RASA4B" "TMEM129"
## [121] "ITGAM" "MT1F" "NLN" "DAGLA" "OGDH"
## [126] "CYB561D1" "RREB1" "BCL6" "CNOT6" "LNPK"
## [131] "DGKZ" "PDE8B" "DBR1" "GTF2E1" "LIMD2"
## [136] "USP2" "CARNS1" "TGFBR2" "ZBTB40" "CEPT1"
## [141] "ADAM15" "ZNF768" "ZNF692" "POLD1" "AGAP2"
## [146] "CHEK2" "MIPEP" "GALNT18" "GFI1" "ZNF41"
## [151] "PAN2" "FLYWCH1" "TP63" "ZNF646" "HMOX1"
## [156] "PHRF1" "RNF213" "BAK1" "ADAM17" "CSK"
## [161] "UNC13D" "ZNF585A" "ZNF316" "MZF1" "RASA4"
## [166] "LRRK1" "CASZ1" "CYBB" "RAPSN" "ZNF347"
## [171] "CYB561A3" "PDLIM2" "ZNF573" "ZNF514" "ZNF440"
## [176] "RNF121" "BMPR2" "THOP1" "ZNF672" "TCF20"
## [181] "PFKL" "ALKBH5" "MAN2C1" "LIG1" "GATAD2A"
## [186] "AKT2" "RNF168" "BTK" "KDM4B" "CREB5"
## [191] "PPM1D" "PRORP" "MBNL3" "ZNF761" "ZBTB42"
## [196] "LPP" "CARD9" "NUDT22" "IKZF1" "ZFAT"
## [201] "ZNF623" "ZNF470" "AGFG2" "ZNF121" "MAP3K3"
## [206] "ARAF" "ABLIM1"
##
## [[1]]$`UP genesets.GO:0051056 regulation of small GTPase mediated signal transduction`
## [1] "ABR" "RAP1GAP" "FAM13B" "FGD5" "ARHGEF3" "VAV1"
## [7] "ARHGAP31" "ARHGEF17" "ARAP1" "ARHGAP10" "ARHGAP18" "ARHGEF1"
## [13] "TIAM1" "SH3BP1" "RACGAP1" "SRGAP3" "SIPA1" "ARHGAP44"
## [19] "ARHGAP1" "ARHGAP22" "ARHGEF40" "RAP1GAP2" "ARHGAP20"
##
## [[1]]$`UP genesets.GO:0061003 positive regulation of dendritic spine morphogenesis`
## [1] "DBN1" "EEF2K" "SLC30A1" "TIAM1" "BAIAP2" "CAMK2B"
##
## [[1]]$`DOWN genesets.GO:0000028 ribosomal small subunit assembly`
## [1] "RPS19" "RPS27L" "RPS14" "RPS5" "RPS15" "FAU" "RPS27" "RPS28"
## [9] "RPSA" "RRP7A" "MRPS7" "ERAL1"
##
## [[1]]$`DOWN genesets.GO:0002181 cytoplasmic translation`
## [1] "RPL7A" "RPL17" "RPS27A" "RPL8" "RPS7" "RPL28" "RPL6"
## [8] "RPL18" "RPL5" "RPL9" "RPL24" "RPS3A" "RPS3" "RACK1"
## [15] "RPL11" "RPL14" "RPS19" "RPS25" "RPL15" "RPL22" "RPL35A"
## [22] "RPS10" "RPL13" "RPS15A" "RPS8" "RPL26" "RPL19" "RPLP1"
## [29] "RPL10" "RPL27" "RPL12" "RPS13" "RPS14" "RPL29" "RPL21"
## [36] "RPLP0" "RPL7" "RPS23" "RPS5" "RPL3" "RPS12" "RPS11"
## [43] "RPL37" "RPS15" "RPL39" "RPS6" "RPL30" "RPL18A" "RPL13A"
## [50] "RPL23" "RPS4X" "RPL23A" "RPS20" "RPL34" "RPL32" "DRG1"
## [57] "FAU" "RPS9" "UBA52" "RPS24" "RPL36A" "RPL4" "RPL35"
## [64] "RPL41" "RPS17" "RPL31" "RPS2" "RPS16" "RPS18" "RPS27"
## [71] "FTSJ1" "RPL27A" "RPL36" "RPS28" "RPLP2" "RWDD1" "RPL22L1"
## [78] "RPSA" "RPL37A" "RPS29" "RPL38" "RPL26L1" "ZC3H15" "RPS21"
## [85] "RPS26" "DRG2" "RPL10A"
##
## [[1]]$`DOWN genesets.GO:0002503 peptide antigen assembly with MHC class II protein complex`
## [1] "HLA-DQA2" "HLA-DOA" "HLA-DMB" "HLA-DMA" "HLA-DQA1" "HLA-DPB1"
## [7] "B2M" "HLA-DRA" "HLA-DQB1" "HLA-DPA1" "HLA-DRB5" "HLA-DRB1"
##
## [[1]]$`DOWN genesets.GO:0003735 structural constituent of ribosome`
## [1] "RPL7A" "RPL17" "RPS27A" "RPL8" "RPS7" "RPL28" "RPL6"
## [8] "RPL18" "RPL5" "RPL9" "RPL24" "RPS3A" "RPS3" "RPL11"
## [15] "RPL14" "MRPL9" "RPS19" "RPS25" "RPL15" "RPL22" "RPL35A"
## [22] "RPS10" "RPL13" "RPS15A" "RPS8" "RPL26" "RPL19" "RPS27L"
## [29] "RPLP1" "RPL10" "RPL27" "MRPL18" "MRPL43" "RPL12" "RPS13"
## [36] "RPS14" "RPL29" "RPL21" "RPLP0" "RPL7" "RPS23" "RSL24D1"
## [43] "RPS5" "RPL3" "RPS12" "MRPL17" "RPS11" "RPL37" "RPS15"
## [50] "MRPS16" "RPL39" "RPS6" "RPL30" "MRPS18C" "RPL18A" "RPL13A"
## [57] "RPL23" "RPS4X" "RPL23A" "MRPS23" "RPS20" "MRPS2" "RPL34"
## [64] "RPL32" "FAU" "RPS9" "MRPS6" "MRPS22" "MRPS15" "UBA52"
## [71] "RPS24" "RPL36AL" "SRBD1" "RPL36A" "RPL4" "RPL39L" "MRPL36"
## [78] "RPL35" "MRPS21" "RPL41" "MRPS30" "MRPS14" "RPS17" "RPL31"
## [85] "MRPL13" "RPS2" "MRPL10" "RPS16" "MRPL46" "RPS18" "RPS27"
## [92] "MRPL51" "MRPL52" "MRPL30" "MRPL21" "MRPS18B" "RPL27A" "MRPL22"
## [99] "MRPL24" "MRPL12" "MRPS31" "MRPL3" "RPL36" "MRPL23" "RPL7L1"
## [106] "MRPL49" "MRPS12" "MRPL28" "RPS28" "RPLP2" "MRPS24" "MRPS18A"
## [113] "MRPL2" "RPL22L1" "MRPL1" "RPSA" "MRPL41" "MRPL55" "MRPL54"
## [120] "MRPS35" "RPL37A" "RPS29" "MRPL16" "MRPL47" "MRPL27" "MRPS33"
## [127] "MRPS34" "MRPL20" "MRPL14" "RPL38" "RPL26L1" "MRPS9" "MRPL42"
## [134] "MRPS11" "MRPS25" "MRPL4" "MRPL33" "RPS21" "MRPL35" "MRPL19"
## [141] "MRPS7" "MRPL57" "MRPL15" "RPS26" "MRPL34" "MRPL32" "MRPS5"
## [148] "RPS4Y1" "MRPL45" "MRPL11" "RPL10A" "MRPS17" "DAP3"
##
## [[1]]$`DOWN genesets.GO:0005687 U4 snRNP`
## [1] "SNRPD3" "SNRPD2" "SNRPG" "SNRPE" "PRPF31" "SNRPN" "DDX39B" "SNRPD1"
## [9] "SNRPF" "SNRPB"
##
## [[1]]$`DOWN genesets.GO:0005839 proteasome core complex`
## [1] "PSMB2" "PSMA2" "PSMA6" "PSMB1" "PSMA3" "PSMB3" "PSMA7" "PSMA4"
## [9] "PSMA1" "PSMB4" "PSMF1" "PSMB5" "PSMB7" "PSMA5" "PSMB10" "PSMB8"
## [17] "PSMB9" "PSMB6"
##
## [[1]]$`DOWN genesets.GO:0005840 ribosome`
## [1] "RPL7A" "RPS7" "RPL9" "RPS3" "RPS19" "SERP1" "RPS25"
## [8] "RPL15" "RPS10" "EEF1A1" "PSMA6" "RPL27" "APEX1" "RPS13"
## [15] "OAS1" "RPS23" "RSL24D1" "RPS5" "RPS11" "RPL13A" "RPL23"
## [22] "RPS4X" "EEF2" "FXR1" "RPS9" "RPL36A" "RPS17" "MRPL13"
## [29] "RPS18" "RPS27" "PNPT1" "ELAVL4" "CALR" "DNAJC21" "MRPS12"
## [36] "RPS28" "FUBP3" "EIF2AK2" "NUFIP2" "RPL22L1" "RPS29" "NCK1"
## [43] "RRBP1" "SF1" "MRPS7" "RPS26" "RPS4Y1" "SRP68"
##
## [[1]]$`DOWN genesets.GO:0006412 translation`
## [1] "RPL7A" "RPL17" "RPS27A" "RPL8" "RPS7" "RPL28"
## [7] "RPL6" "RPL18" "RPL5" "NACA" "RPL9" "RPL24"
## [13] "RPS3A" "RPS3" "RPL11" "RPL14" "MRPL9" "RPS19"
## [19] "RPS25" "RPL15" "RPL22" "RPL35A" "RPS10" "RPL13"
## [25] "RPS15A" "EEF1A1" "RPS8" "RPL26" "RPL19" "RPS27L"
## [31] "RPLP1" "RPL10" "RPL27" "MRPL18" "MRPL43" "RPL12"
## [37] "RPS13" "RPS14" "RPL29" "RPL21" "RPLP0" "RPL7"
## [43] "GSPT2" "RPS23" "RSL24D1" "RPS5" "RPL3" "RPS12"
## [49] "RPS11" "RPL37" "RPS15" "PABPC4" "MRPS16" "RPL39"
## [55] "RPS6" "RPL30" "MRPS18C" "RPL18A" "RPL13A" "RPL23"
## [61] "RPS4X" "RPL23A" "PSTK" "RPS20" "RPL34" "RPL32"
## [67] "FAU" "EIF4EBP2" "RPS9" "MRPS6" "MRPS15" "UBA52"
## [73] "RPS24" "EEF1E1" "RPL36AL" "SRBD1" "RPL36A" "RPL4"
## [79] "RPL39L" "MRPL36" "RPL35" "MRPS21" "YARS2" "RPL41"
## [85] "MRPS14" "RPS6KB2" "RPS17" "RPL31" "MRPL13" "RPS2"
## [91] "MRPL10" "COPS5" "RPS16" "RPS18" "RPS27" "MRPL51"
## [97] "FARSB" "METTL17" "RMND1" "MRPL52" "MRPS18B" "AIMP1"
## [103] "RPL27A" "MRPL22" "MRPL24" "MRPL12" "MRPL3" "RPL36"
## [109] "MRPL23" "MRPS12" "MRPL28" "RPS28" "RPLP2" "MRRF"
## [115] "DHPS" "MRPS18A" "EIF2AK2" "EIF4ENIF1" "RPSA" "MRPL41"
## [121] "MRPL55" "AGO2" "RPL37A" "RPS29" "ABCF1" "MRPL27"
## [127] "MRPS33" "CPEB4" "RPL38" "GEMIN5" "MRPL42" "MRPS11"
## [133] "CPEB1" "LARP4" "RPS21" "RRBP1" "MRPL35" "GUF1"
## [139] "MRPS7" "RPS26" "IGF2BP3" "MRPL34" "MRPL32" "MRPS5"
## [145] "HBS1L" "GSPT1" "RPS4Y1" "MRPL11" "AIMP2" "HARS2"
## [151] "PAIP2" "RPL10A" "MRPS17"
##
## [[1]]$`DOWN genesets.GO:0015935 small ribosomal subunit`
## [1] "RPS27A" "RACK1" "RPS25" "RPS6" "RPS4X" "FAU" "MRPS6" "RPS24"
## [9] "RPS16" "RPS18" "RPS28" "RPS29" "RPS21" "RPS26"
##
## [[1]]$`DOWN genesets.GO:0019731 antibacterial humoral response`
## [1] "DEFB1" "CAMP" "ANG" "BPI" "RNASE4" "B2M" "RPL39" "FAU"
## [9] "HLA-A" "RNASE6" "APP" "ADM" "PLA2G6" "HLA-E" "WFDC2" "WFDC3"
##
## [[1]]$`DOWN genesets.GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II`
## [1] "IFI30" "CTSL" "HLA-DQA2" "HLA-DOA" "HLA-DMB" "HLA-DMA"
## [7] "FCGR2B" "LGMN" "HLA-DQA1" "HLA-DPB1" "B2M" "FCER1G"
## [13] "CTSS" "HLA-DRA" "HLA-DQB1" "CD74" "HLA-DPA1" "UNC93B1"
## [19] "CTSF" "CTSD" "TRAF6" "CTSV" "HLA-DRB5" "HLA-DRB1"
##
## [[1]]$`DOWN genesets.GO:0022624 proteasome accessory complex`
## [1] "PSMD6" "PSMD8" "PSMC4" "PSMD11" "PSMC6" "PSMD12" "PSMD4" "PSMD14"
## [9] "PSMD3" "PSMC1" "PSMC3" "PSMC5" "PSMD2" "PSMC2" "PSMD13" "PSMD1"
## [17] "PSMD5"
##
## [[1]]$`DOWN genesets.GO:0022625 cytosolic large ribosomal subunit`
## [1] "RPL7A" "RPL17" "RPL8" "RPL28" "RPL6" "RPL18" "RPL5"
## [8] "RPL9" "RPL24" "RPL11" "RPL14" "RPL15" "RPL22" "RPL35A"
## [15] "RPL13" "RPL26" "RPL19" "RPLP1" "RPL10" "RPL27" "RPL12"
## [22] "RPL29" "RPL21" "RPLP0" "RPL7" "RPL3" "RPL37" "RPL39"
## [29] "ZCCHC17" "RPL30" "RPL18A" "RPL13A" "RPL23" "RPL23A" "RPL34"
## [36] "RPL32" "UBA52" "RPL36AL" "RPL36A" "RPL4" "RPL39L" "RPL35"
## [43] "RPL41" "RPL31" "RPL27A" "RPL36" "RPL7L1" "RPLP2" "RPL37A"
## [50] "RPL38" "RPL26L1" "RPL10A"
##
## [[1]]$`DOWN genesets.GO:0022626 cytosolic ribosome`
## [1] "RPL7A" "RPL17" "RPS27A" "RPL8" "RPS7" "RPL28" "RPL6"
## [8] "RPL18" "RPL5" "RPL9" "RPL24" "RPS3A" "RPS3" "RPL11"
## [15] "RPL14" "RPS19" "RPS25" "RPL15" "RPL22" "RPL35A" "RPS10"
## [22] "PELO" "RPL13" "RPS15A" "EEF1A1" "RPS8" "RPL26" "RPL19"
## [29] "RPLP1" "RPL10" "RPL27" "RPL12" "RPS13" "RPS14" "RPL29"
## [36] "RPL21" "RPLP0" "RPL7" "RPS23" "RPS5" "RPL3" "RPS12"
## [43] "RPS11" "RPL37" "RPS15" "RPL39" "RPS6" "RPL30" "RPL18A"
## [50] "EIF2AK4" "RPL13A" "RPL23" "RPS4X" "RPL23A" "RPS20" "RPL34"
## [57] "RPL32" "FAU" "RPS9" "UBA52" "RPS24" "RPL36A" "RPL4"
## [64] "RPL35" "ABCE1" "RPS17" "RPL31" "RNF10" "RPS2" "RPS16"
## [71] "RPS18" "METAP1" "RPS27" "NEMF" "ZNF598" "RPL27A" "RPL36"
## [78] "LTN1" "USP10" "RPSA" "RPL37A" "APOD" "ETF1" "ASCC2"
## [85] "RPL38" "RNF25" "RPS21" "RNF14" "HBS1L" "GSPT1" "RPL10A"
##
## [[1]]$`DOWN genesets.GO:0022627 cytosolic small ribosomal subunit`
## [1] "RPS27A" "RPS7" "RPS3A" "RPS3" "RACK1" "RPS19" "RPS25" "RPS10"
## [9] "RPS15A" "RPS8" "RPS27L" "RPS13" "RPS14" "RPS23" "RPS5" "RPS12"
## [17] "RPS11" "RPS15" "RPS6" "RPS4X" "RPS20" "FAU" "RPS9" "RPS24"
## [25] "RPS17" "RPS2" "RPS16" "RPS18" "RPS27" "RPS28" "RPSA" "RPS29"
## [33] "DHX29" "DDX3X" "EIF2A" "LARP4" "RPS21" "RPS26" "RPS4Y1"
##
## [[1]]$`DOWN genesets.GO:0042605 peptide antigen binding`
## [1] "HLA-DQA2" "HLA-DOA" "FCGRT" "HLA-DMB" "HLA-DMA" "HFE"
## [7] "SLC7A5" "HLA-B" "HLA-DQA1" "HLA-DPB1" "B2M" "HLA-DRA"
## [13] "HLA-F" "HLA-DQB1" "HLA-A" "HLA-DPA1" "TAPBP" "HLA-C"
## [19] "HLA-E" "HLA-DRB5" "HLA-G" "TAP1" "MAML1" "HLA-DRB1"
## [25] "CD209" "DHCR24" "SLC7A8"
##
## [[1]]$`DOWN genesets.GO:0042613 MHC class II protein complex`
## [1] "HLA-DQA2" "HLA-DOA" "HLA-DMB" "HLA-DMA" "HLA-DQA1" "HLA-DPB1"
## [7] "B2M" "HLA-DRA" "HLA-DQB1" "CD74" "HLA-DPA1" "HLA-DRB5"
## [13] "HLA-DRB1"
##
## [[1]]$`DOWN genesets.GO:0071011 precatalytic spliceosome`
## [1] "SNRPD3" "SNRPD2" "SF3B4" "RBMX2" "SF3B2" "SNRPG" "SNRPE"
## [8] "PRPF31" "LSM8" "WBP4" "SMU1" "SNRPD1" "SF3B5" "LSM2"
## [15] "LSM3" "PHF5A" "SNU13" "PRPF38A" "PRPF38B"
##
## [[1]]$`DOWN genesets.GO:0097435 supramolecular fiber organization`
## [1] "SNCA" "MFAP4" "BID" "FKBP1A" "MFAP5" "BASP1"
## [7] "HSP90AB1" "B4GALT7" "CST3" "BAX"
##
## [[1]]$`DOWN genesets.GO:0097542 ciliary tip`
## [1] "KIF3A" "IFT22" "ARMC9" "DYNLRB1" "WDR19" "IFT20"
## [7] "KIF3C" "WDR35" "IFT43" "DYNLL1" "DYNLRB2" "KIFAP3"
## [13] "DYNC2LI1" "IFT57" "DYNC2H1" "CLUAP1" "TRAF3IP1" "TTC21B"
## [19] "IFT52" "IFT88" "CYLD" "IFT81" "IFT140" "DYNLL2"
## [25] "IFT172" "IFT27" "CDKL5" "SUFU" "IFT80" "IFT74"
## [31] "IFT46" "ULK3" "KIF3B"networkplot(mres5f,FDR=0.05,n_sets=30)
network_genes(mres5f,FDR=0.05,n_sets=30)## [[1]]
## [[1]]$`UP genesets.GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding`
## [1] "PPARD" "PITX1" "NFATC3" "ZNF366" "SKI" "RBPJ"
## [7] "TCF7L2" "EGR2" "DLX3" "STAT6" "ESR1" "RARA"
## [13] "ZBTB7B" "HIVEP3" "AR" "MAF" "VDR" "KLF9"
## [19] "VAX2" "CALCOCO1" "SNAI3" "TEAD3" "CEBPA" "HDAC4"
## [25] "NACC2" "HIC2" "POU3F1" "KLF16" "ZBTB8A" "IKZF2"
## [31] "NR2F6" "ZNF362" "DNMT3A" "E2F3" "TFCP2" "MXD4"
## [37] "ZNF678" "ZNF76" "MITF" "NLRC5" "KLF4" "SREBF2"
## [43] "ZNF711" "ZNF808" "MEF2A" "TEF" "POU2F2" "NFYC"
## [49] "ZFHX3" "ZBTB7C" "RXRA" "NFATC1" "RREB1" "KDM2B"
## [55] "MLXIPL" "BCL6" "DMTF1" "MED1" "ZNF692" "GFI1"
## [61] "TFE3" "FOXK2" "IKZF5" "TP63" "NR3C1" "ZNF646"
## [67] "SKIL" "GRHL1" "ZNF585A" "MZF1" "ZNF347" "TFEB"
## [73] "ZNF573" "ZNF514" "ZNF761" "TARDBP" "IKZF1" "ZFAT"
## [79] "ZNF623" "ZNF470" "CHD7" "JUND" "ZNF121" "MAFK"
##
## [[1]]$`UP genesets.GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific`
## [1] "PPARD" "PITX1" "GTF2I" "NFATC3" "SKI" "RBPJ" "TCF7L2" "EGR2"
## [9] "DLX3" "STAT6" "ESR1" "RARA" "ZBTB7B" "HIVEP3" "AR" "MAF"
## [17] "VDR" "KLF9" "VAX2" "SNAI3" "TEAD3" "CEBPA" "NACC2" "POU3F1"
## [25] "KLF16" "ZBTB8A" "NR2F6" "NPAS1" "E2F3" "TFCP2" "MXD4" "ZBTB46"
## [33] "ZNF678" "ZNF76" "MITF" "ERF" "MYRF" "KLF4" "SREBF2" "ZNF711"
## [41] "ZNF79" "PKNOX1" "MEF2A" "TEF" "POU2F2" "NFYC" "ZFHX3" "ZBTB7C"
## [49] "RXRA" "NFATC1" "MLXIPL" "ZBTB40" "DMTF1" "ZNF768" "SCX" "TFE3"
## [57] "FOXK2" "TP63" "NR3C1" "ZNF646" "SKIL" "GRHL1" "ZGLP1" "ZNF316"
## [65] "MZF1" "CASZ1" "ESRRA" "ZNF347" "TFEB" "ZNF573" "ZNF514" "ZNF440"
## [73] "ZNF672" "ELF5" "CREB5" "ZNF761" "ZBTB42" "ZFAT" "ZNF623" "ZNF470"
## [81] "JUND" "CUX1" "ZNF121" "MAFK"
##
## [[1]]$`UP genesets.GO:0005096 GTPase activator activity`
## [1] "RGS16" "ABR" "RAP1GAP" "FAM13B" "ASAP1" "TBC1D1"
## [7] "RGS12" "RANGAP1" "ARHGAP31" "ACAP3" "RANBP2" "ARHGAP25"
## [13] "SGSM2" "ARAP1" "RASAL2" "RGS18" "ARHGAP10" "ARHGAP18"
## [19] "ARHGEF1" "DEPDC5" "RASGRP3" "LLGL1" "VPS9D1" "SH3BP1"
## [25] "TBC1D12" "RGS3" "TBC1D9B" "AGAP1" "RACGAP1" "TBC1D22B"
## [31] "SRGAP3" "TBCD" "TBC1D2B" "RASA4B" "SIPA1" "ARRB1"
## [37] "TBC1D4" "AGAP2" "ARHGAP44" "RIN2" "RABEP2" "ARHGAP1"
## [43] "ARHGAP22" "RASA4" "TBC1D10C" "RAP1GAP2" "ARHGAP20" "SGSM3"
## [49] "TBC1D14" "AGFG2"
##
## [[1]]$`UP genesets.GO:0005524 ATP binding`
## [1] "NEK6" "TRPV1" "ABCB9" "ABCA6" "TGFBR1" "SHPK"
## [7] "VWA8" "MYO1F" "ENTPD1" "MERTK" "DCLK3" "MAP3K5"
## [13] "ATP2B2" "ABCA2" "MYO1E" "PDK2" "MINK1" "GCLC"
## [19] "CAMK1" "CHD9" "MARK2" "TTLL12" "ADCY7" "NOD1"
## [25] "PIK3CD" "MARK3" "FGFR1" "ATP2A3" "ITPKB" "KCNJ1"
## [31] "PRKACB" "PRKCA" "PRAG1" "ABCD1" "AKT1" "TAP2"
## [37] "MAP3K11" "MTHFD1" "PRKCD" "EEF2K" "MYO6" "DGKH"
## [43] "PI4KA" "DDX6" "COQ8A" "DMPK" "IKBKE" "NPR1"
## [49] "KIF17" "SNRK" "TRIB1" "TOP2B" "TTLL11" "KIFC2"
## [55] "GRK2" "PEX6" "PIKFYVE" "IPPK" "ATP2B3" "ITPK1"
## [61] "TTL" "DCLK2" "ADCK1" "CHKA" "NLRC5" "NWD1"
## [67] "ALPK1" "PI4K2A" "ACSS2" "PIK3CG" "ABCB8" "KIF1B"
## [73] "EIF4G1" "DAPK1" "HK3" "CLCN7" "CSNK1G2" "PTK2B"
## [79] "ABCA9" "RPS6KL1" "GAK" "ACSF3" "MLKL" "ADK"
## [85] "SMG1" "MYLK" "TPK1" "SLC12A4" "CDK17" "HSPA14"
## [91] "DCAF1" "ULK2" "XYLB" "DGKZ" "CARNS1" "TGFBR2"
## [97] "MCM3" "LMTK2" "QRSL1" "ATR" "GATC" "ADCY10"
## [103] "DYRK1A" "PTK6" "AGAP2" "AFG3L2" "CHEK2" "ACTR3B"
## [109] "KATNAL2" "MYO19" "MCM5" "ROR1" "ABCC1" "NLK"
## [115] "ABL2" "RNF213" "MAPKAPK3" "FARSA" "PMVK" "IGF1R"
## [121] "CSK" "PIK3C2B" "ABCC4" "LRRK1" "IP6K1" "DHX38"
## [127] "MKKS" "DSTYK" "CAMK2B" "DHX34" "MOV10" "ABCC10"
## [133] "CAMKK1" "BBS10" "BMPR2" "MYO1C" "PFKL" "LIG1"
## [139] "AKT2" "OPLAH" "LRGUK" "BTK" "ASCC3" "FARS2"
## [145] "AAK1" "NLRP2" "MYH11" "ADCK2" "PSKH1" "PDPK1"
## [151] "MYO15A" "PIK3R4" "PIK3C3" "DDX10" "CHD7" "MAP3K14"
## [157] "IKBKB" "CDK6" "MAP3K3" "ARAF"
##
## [[1]]$`UP genesets.GO:0006338 chromatin remodeling`
## [1] "NEK6" "ENTPD1" "MERTK" "DPF3" "DCLK3" "ESR1"
## [7] "PTPRA" "MINK1" "CHD9" "MARK2" "RB1" "DUSP2"
## [13] "DUSP7" "MARK3" "FGFR1" "PWWP2A" "PRKCA" "HDAC4"
## [19] "AKT1" "BCOR" "PRKCD" "KAT2B" "DDX6" "DMPK"
## [25] "SNRK" "BAP1" "PHLPP1" "PTPRC" "SETD3" "BRPF1"
## [31] "PIKFYVE" "PTPN13" "PTPN22" "DUSP19" "DCLK2" "CHKA"
## [37] "ALPK1" "CDC25B" "PIK3CG" "MBD3" "DAPK1" "UBASH3B"
## [43] "CSNK1G2" "PTK2B" "RPS6KL1" "GAK" "PPM1M" "SMG1"
## [49] "PADI2" "PTPRO" "PER2" "DCAF1" "ULK2" "PTPN7"
## [55] "KDM2B" "MCM3" "LMTK2" "ATR" "DYRK1A" "PPP3CA"
## [61] "PTK6" "AFG3L2" "CHEK2" "ALPL" "EPM2A" "MCM5"
## [67] "TP63" "ABL2" "RNF213" "MAPKAPK3" "IGF1R" "CSK"
## [73] "LRRK1" "DHX38" "DSTYK" "DHX34" "YEATS2" "MYO1C"
## [79] "PPM1N" "PTPN18" "GATAD2A" "AKT2" "BTK" "ASCC3"
## [85] "KDM4B" "AAK1" "PSKH1" "KDM4C" "PDPK1" "PTPRM"
## [91] "PIK3R4" "HCFC2" "DDX10" "CHD7" "IKBKB" "ARAF"
##
## [[1]]$`UP genesets.GO:0032012 regulation of ARF protein signal transduction`
## [1] "CYTH4" "GBF1" "PSD4"
##
## [[1]]$`UP genesets.GO:0046872 metal ion binding`
## [1] "STAC" "TRPV1" "ADAM12" "CBFA2T3" "TGFBR1"
## [6] "SMAD6" "ASAP1" "FGD5" "PDLIM7" "ZNF366"
## [11] "STAC2" "MICAL3" "KCNC3" "CSGALNACT1" "EGR2"
## [16] "RNF128" "SLC30A3" "SPON2" "ATP2B2" "ZBTB7B"
## [21] "HIVEP3" "PARP12" "LONRF3" "SH3RF2" "VAV1"
## [26] "WTIP" "KLF9" "ACAP3" "CALCOCO1" "CHSY3"
## [31] "ADCY7" "HDAC7" "ZC3H7B" "NTHL1" "ATP2A3"
## [36] "RANBP2" "TRIP6" "SOBP" "FURIN" "TAP2"
## [41] "PRKCD" "CLEC7A" "ZC3H12B" "GALNT12" "DGKH"
## [46] "ZNF618" "TRERF1" "HIC2" "TATDN2" "DPYD"
## [51] "ARAP1" "ZNF804A" "MICALL2" "SMAD7" "PHOSPHO1"
## [56] "KLF16" "ZBTB8A" "IKZF2" "F13A1" "OVCH1"
## [61] "KCNK6" "DMPK" "FRRS1" "MBNL1" "TOP2B"
## [66] "CHFR" "TTLL11" "ZNF362" "PHLPP1" "SLC30A1"
## [71] "XYLT1" "DNMT3A" "BRPF1" "TNFRSF11A" "PLEKHF1"
## [76] "ABAT" "RNF40" "ATP2B3" "ZNF592" "ADARB1"
## [81] "ZBTB46" "ZNF678" "KAT6B" "ZNF76" "MSL2"
## [86] "LIN54" "RNF166" "PHYHD1" "ZNF711" "MGRN1"
## [91] "FGD6" "ZNF79" "FHL3" "B4GALT2" "KCNK13"
## [96] "IRF2BPL" "SMPD4" "GNA11" "ZNF808" "NDUFS1"
## [101] "ASXL2" "ZC3H4" "TNS1" "AGAP1" "ITGA11"
## [106] "RACGAP1" "EXT1" "ADK" "PDE4A" "SMG1"
## [111] "MYLK" "PDSS1" "ANKFY1" "FYCO1" "USP4"
## [116] "ZBTB7C" "SLC12A6" "STAC3" "RASA4B" "TMEM129"
## [121] "ITGAM" "MT1F" "NLN" "DAGLA" "OGDH"
## [126] "CYB561D1" "RREB1" "BCL6" "CNOT6" "LNPK"
## [131] "DGKZ" "PDE8B" "DBR1" "GTF2E1" "LIMD2"
## [136] "USP2" "CARNS1" "TGFBR2" "ZBTB40" "CEPT1"
## [141] "ADAM15" "ZNF768" "ZNF692" "POLD1" "AGAP2"
## [146] "CHEK2" "MIPEP" "GALNT18" "GFI1" "ZNF41"
## [151] "PAN2" "FLYWCH1" "TP63" "ZNF646" "HMOX1"
## [156] "PHRF1" "RNF213" "BAK1" "ADAM17" "CSK"
## [161] "UNC13D" "ZNF585A" "ZNF316" "MZF1" "RASA4"
## [166] "LRRK1" "CASZ1" "CYBB" "RAPSN" "ZNF347"
## [171] "CYB561A3" "PDLIM2" "ZNF573" "ZNF514" "ZNF440"
## [176] "RNF121" "BMPR2" "THOP1" "ZNF672" "TCF20"
## [181] "PFKL" "ALKBH5" "MAN2C1" "LIG1" "GATAD2A"
## [186] "AKT2" "RNF168" "BTK" "KDM4B" "CREB5"
## [191] "PPM1D" "PRORP" "MBNL3" "ZNF761" "ZBTB42"
## [196] "LPP" "CARD9" "NUDT22" "IKZF1" "ZFAT"
## [201] "ZNF623" "ZNF470" "AGFG2" "ZNF121" "MAP3K3"
## [206] "ARAF" "ABLIM1"
##
## [[1]]$`UP genesets.GO:0051056 regulation of small GTPase mediated signal transduction`
## [1] "ABR" "RAP1GAP" "FAM13B" "FGD5" "ARHGEF3" "VAV1"
## [7] "ARHGAP31" "ARHGEF17" "ARAP1" "ARHGAP10" "ARHGAP18" "ARHGEF1"
## [13] "TIAM1" "SH3BP1" "RACGAP1" "SRGAP3" "SIPA1" "ARHGAP44"
## [19] "ARHGAP1" "ARHGAP22" "ARHGEF40" "RAP1GAP2" "ARHGAP20"
##
## [[1]]$`UP genesets.GO:0061003 positive regulation of dendritic spine morphogenesis`
## [1] "DBN1" "EEF2K" "SLC30A1" "TIAM1" "BAIAP2" "CAMK2B"
##
## [[1]]$`DOWN genesets.GO:0000028 ribosomal small subunit assembly`
## [1] "RPS19" "RPS27L" "RPS14" "RPS5" "RPS15" "FAU" "RPS27" "RPS28"
## [9] "RPSA" "RRP7A" "MRPS7" "ERAL1"
##
## [[1]]$`DOWN genesets.GO:0000502 proteasome complex`
## [1] "HSPB1" "PSMB2" "PSMD6" "PSMA2" "TXNL1" "PSMA6" "PSMB1"
## [8] "PSMA3" "PSMD8" "PSMB3" "ADRM1" "PSMA7" "PSMC4" "PSMA4"
## [15] "PSMA1" "PSMB4" "PSMD11" "PSMB5" "SEM1" "PSME2" "PSMB7"
## [22] "PSMC6" "PSMD7" "UBE3C" "PSMA5" "RAD23A" "PSMD12" "PSMD4"
## [29] "PSME3" "VCP" "UBE3A" "PAAF1" "PSMD14" "PSMB10" "PSMD3"
## [36] "PSMC1" "PSME1" "ZFAND2A" "RAD23B" "PSMC3" "PSMD10" "PSMB8"
## [43] "PSMC5" "PSMD2" "PSMC2" "PSMD13" "PSMD1" "ECPAS" "PSMB9"
## [50] "PSMD5" "UBQLN1" "USP14" "ZFAND2B" "PSMB6" "UBR1" "DNAJB2"
##
## [[1]]$`DOWN genesets.GO:0002181 cytoplasmic translation`
## [1] "RPL7A" "RPL17" "RPS27A" "RPL8" "RPS7" "RPL28" "RPL6"
## [8] "RPL18" "RPL5" "RPL9" "RPL24" "RPS3A" "RPS3" "RACK1"
## [15] "RPL11" "RPL14" "RPS19" "RPS25" "RPL15" "RPL22" "RPL35A"
## [22] "RPS10" "RPL13" "RPS15A" "RPS8" "RPL26" "RPL19" "RPLP1"
## [29] "RPL10" "RPL27" "RPL12" "RPS13" "RPS14" "RPL29" "RPL21"
## [36] "RPLP0" "RPL7" "RPS23" "RPS5" "RPL3" "RPS12" "RPS11"
## [43] "RPL37" "RPS15" "RPL39" "RPS6" "RPL30" "RPL18A" "RPL13A"
## [50] "RPL23" "RPS4X" "RPL23A" "RPS20" "RPL34" "RPL32" "DRG1"
## [57] "FAU" "RPS9" "UBA52" "RPS24" "RPL36A" "RPL4" "RPL35"
## [64] "RPL41" "RPS17" "RPL31" "RPS2" "RPS16" "RPS18" "RPS27"
## [71] "FTSJ1" "RPL27A" "RPL36" "RPS28" "RPLP2" "RWDD1" "RPL22L1"
## [78] "RPSA" "RPL37A" "RPS29" "RPL38" "RPL26L1" "ZC3H15" "RPS21"
## [85] "RPS26" "DRG2" "RPL10A"
##
## [[1]]$`DOWN genesets.GO:0002503 peptide antigen assembly with MHC class II protein complex`
## [1] "HLA-DQA2" "HLA-DOA" "HLA-DMB" "HLA-DMA" "HLA-DQA1" "HLA-DPB1"
## [7] "B2M" "HLA-DRA" "HLA-DQB1" "HLA-DPA1" "HLA-DRB5" "HLA-DRB1"
##
## [[1]]$`DOWN genesets.GO:0003735 structural constituent of ribosome`
## [1] "RPL7A" "RPL17" "RPS27A" "RPL8" "RPS7" "RPL28" "RPL6"
## [8] "RPL18" "RPL5" "RPL9" "RPL24" "RPS3A" "RPS3" "RPL11"
## [15] "RPL14" "MRPL9" "RPS19" "RPS25" "RPL15" "RPL22" "RPL35A"
## [22] "RPS10" "RPL13" "RPS15A" "RPS8" "RPL26" "RPL19" "RPS27L"
## [29] "RPLP1" "RPL10" "RPL27" "MRPL18" "MRPL43" "RPL12" "RPS13"
## [36] "RPS14" "RPL29" "RPL21" "RPLP0" "RPL7" "RPS23" "RSL24D1"
## [43] "RPS5" "RPL3" "RPS12" "MRPL17" "RPS11" "RPL37" "RPS15"
## [50] "MRPS16" "RPL39" "RPS6" "RPL30" "MRPS18C" "RPL18A" "RPL13A"
## [57] "RPL23" "RPS4X" "RPL23A" "MRPS23" "RPS20" "MRPS2" "RPL34"
## [64] "RPL32" "FAU" "RPS9" "MRPS6" "MRPS22" "MRPS15" "UBA52"
## [71] "RPS24" "RPL36AL" "SRBD1" "RPL36A" "RPL4" "RPL39L" "MRPL36"
## [78] "RPL35" "MRPS21" "RPL41" "MRPS30" "MRPS14" "RPS17" "RPL31"
## [85] "MRPL13" "RPS2" "MRPL10" "RPS16" "MRPL46" "RPS18" "RPS27"
## [92] "MRPL51" "MRPL52" "MRPL30" "MRPL21" "MRPS18B" "RPL27A" "MRPL22"
## [99] "MRPL24" "MRPL12" "MRPS31" "MRPL3" "RPL36" "MRPL23" "RPL7L1"
## [106] "MRPL49" "MRPS12" "MRPL28" "RPS28" "RPLP2" "MRPS24" "MRPS18A"
## [113] "MRPL2" "RPL22L1" "MRPL1" "RPSA" "MRPL41" "MRPL55" "MRPL54"
## [120] "MRPS35" "RPL37A" "RPS29" "MRPL16" "MRPL47" "MRPL27" "MRPS33"
## [127] "MRPS34" "MRPL20" "MRPL14" "RPL38" "RPL26L1" "MRPS9" "MRPL42"
## [134] "MRPS11" "MRPS25" "MRPL4" "MRPL33" "RPS21" "MRPL35" "MRPL19"
## [141] "MRPS7" "MRPL57" "MRPL15" "RPS26" "MRPL34" "MRPL32" "MRPS5"
## [148] "RPS4Y1" "MRPL45" "MRPL11" "RPL10A" "MRPS17" "DAP3"
##
## [[1]]$`DOWN genesets.GO:0005687 U4 snRNP`
## [1] "SNRPD3" "SNRPD2" "SNRPG" "SNRPE" "PRPF31" "SNRPN" "DDX39B" "SNRPD1"
## [9] "SNRPF" "SNRPB"
##
## [[1]]$`DOWN genesets.GO:0005839 proteasome core complex`
## [1] "PSMB2" "PSMA2" "PSMA6" "PSMB1" "PSMA3" "PSMB3" "PSMA7" "PSMA4"
## [9] "PSMA1" "PSMB4" "PSMF1" "PSMB5" "PSMB7" "PSMA5" "PSMB10" "PSMB8"
## [17] "PSMB9" "PSMB6"
##
## [[1]]$`DOWN genesets.GO:0005840 ribosome`
## [1] "RPL7A" "RPS7" "RPL9" "RPS3" "RPS19" "SERP1" "RPS25"
## [8] "RPL15" "RPS10" "EEF1A1" "PSMA6" "RPL27" "APEX1" "RPS13"
## [15] "OAS1" "RPS23" "RSL24D1" "RPS5" "RPS11" "RPL13A" "RPL23"
## [22] "RPS4X" "EEF2" "FXR1" "RPS9" "RPL36A" "RPS17" "MRPL13"
## [29] "RPS18" "RPS27" "PNPT1" "ELAVL4" "CALR" "DNAJC21" "MRPS12"
## [36] "RPS28" "FUBP3" "EIF2AK2" "NUFIP2" "RPL22L1" "RPS29" "NCK1"
## [43] "RRBP1" "SF1" "MRPS7" "RPS26" "RPS4Y1" "SRP68"
##
## [[1]]$`DOWN genesets.GO:0006412 translation`
## [1] "RPL7A" "RPL17" "RPS27A" "RPL8" "RPS7" "RPL28"
## [7] "RPL6" "RPL18" "RPL5" "NACA" "RPL9" "RPL24"
## [13] "RPS3A" "RPS3" "RPL11" "RPL14" "MRPL9" "RPS19"
## [19] "RPS25" "RPL15" "RPL22" "RPL35A" "RPS10" "RPL13"
## [25] "RPS15A" "EEF1A1" "RPS8" "RPL26" "RPL19" "RPS27L"
## [31] "RPLP1" "RPL10" "RPL27" "MRPL18" "MRPL43" "RPL12"
## [37] "RPS13" "RPS14" "RPL29" "RPL21" "RPLP0" "RPL7"
## [43] "GSPT2" "RPS23" "RSL24D1" "RPS5" "RPL3" "RPS12"
## [49] "RPS11" "RPL37" "RPS15" "PABPC4" "MRPS16" "RPL39"
## [55] "RPS6" "RPL30" "MRPS18C" "RPL18A" "RPL13A" "RPL23"
## [61] "RPS4X" "RPL23A" "PSTK" "RPS20" "RPL34" "RPL32"
## [67] "FAU" "EIF4EBP2" "RPS9" "MRPS6" "MRPS15" "UBA52"
## [73] "RPS24" "EEF1E1" "RPL36AL" "SRBD1" "RPL36A" "RPL4"
## [79] "RPL39L" "MRPL36" "RPL35" "MRPS21" "YARS2" "RPL41"
## [85] "MRPS14" "RPS6KB2" "RPS17" "RPL31" "MRPL13" "RPS2"
## [91] "MRPL10" "COPS5" "RPS16" "RPS18" "RPS27" "MRPL51"
## [97] "FARSB" "METTL17" "RMND1" "MRPL52" "MRPS18B" "AIMP1"
## [103] "RPL27A" "MRPL22" "MRPL24" "MRPL12" "MRPL3" "RPL36"
## [109] "MRPL23" "MRPS12" "MRPL28" "RPS28" "RPLP2" "MRRF"
## [115] "DHPS" "MRPS18A" "EIF2AK2" "EIF4ENIF1" "RPSA" "MRPL41"
## [121] "MRPL55" "AGO2" "RPL37A" "RPS29" "ABCF1" "MRPL27"
## [127] "MRPS33" "CPEB4" "RPL38" "GEMIN5" "MRPL42" "MRPS11"
## [133] "CPEB1" "LARP4" "RPS21" "RRBP1" "MRPL35" "GUF1"
## [139] "MRPS7" "RPS26" "IGF2BP3" "MRPL34" "MRPL32" "MRPS5"
## [145] "HBS1L" "GSPT1" "RPS4Y1" "MRPL11" "AIMP2" "HARS2"
## [151] "PAIP2" "RPL10A" "MRPS17"
##
## [[1]]$`DOWN genesets.GO:0006413 translational initiation`
## [1] "RPS3A" "RPS3" "EIF3F" "EIF3G" "EIF4A1" "EIF2S2" "EIF2S3" "EIF3H"
## [9] "EIF1B" "RPS5" "EIF3I" "EIF3M" "EIF3E" "EIF1" "EIF3L" "EIF2B5"
## [17] "PAIP1" "ABCE1" "EIF2B2" "EIF4A2" "RPS17" "EIF4B" "COPS5" "EIF1AD"
## [25] "EIF1AX" "EIF2B1" "EIF3K" "EIF4E2" "EIF4G2" "EIF4G3" "EIF2B4" "AGO2"
## [33] "LARP1" "EIF3C" "MTFMT" "ABCF1" "DHX33" "EIF4H" "EIF3J" "DDX3X"
## [41] "EIF2A" "EIF2B3" "EIF6" "EIF5B" "EIF3A" "EIF4E" "LTO1" "EIF2S1"
## [49] "EIF1AY" "EIF3D"
##
## [[1]]$`DOWN genesets.GO:0015935 small ribosomal subunit`
## [1] "RPS27A" "RACK1" "RPS25" "RPS6" "RPS4X" "FAU" "MRPS6" "RPS24"
## [9] "RPS16" "RPS18" "RPS28" "RPS29" "RPS21" "RPS26"
##
## [[1]]$`DOWN genesets.GO:0019731 antibacterial humoral response`
## [1] "DEFB1" "CAMP" "ANG" "BPI" "RNASE4" "B2M" "RPL39" "FAU"
## [9] "HLA-A" "RNASE6" "APP" "ADM" "PLA2G6" "HLA-E" "WFDC2" "WFDC3"
##
## [[1]]$`DOWN genesets.GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II`
## [1] "IFI30" "CTSL" "HLA-DQA2" "HLA-DOA" "HLA-DMB" "HLA-DMA"
## [7] "FCGR2B" "LGMN" "HLA-DQA1" "HLA-DPB1" "B2M" "FCER1G"
## [13] "CTSS" "HLA-DRA" "HLA-DQB1" "CD74" "HLA-DPA1" "UNC93B1"
## [19] "CTSF" "CTSD" "TRAF6" "CTSV" "HLA-DRB5" "HLA-DRB1"
##
## [[1]]$`DOWN genesets.GO:0022624 proteasome accessory complex`
## [1] "PSMD6" "PSMD8" "PSMC4" "PSMD11" "PSMC6" "PSMD12" "PSMD4" "PSMD14"
## [9] "PSMD3" "PSMC1" "PSMC3" "PSMC5" "PSMD2" "PSMC2" "PSMD13" "PSMD1"
## [17] "PSMD5"
##
## [[1]]$`DOWN genesets.GO:0022625 cytosolic large ribosomal subunit`
## [1] "RPL7A" "RPL17" "RPL8" "RPL28" "RPL6" "RPL18" "RPL5"
## [8] "RPL9" "RPL24" "RPL11" "RPL14" "RPL15" "RPL22" "RPL35A"
## [15] "RPL13" "RPL26" "RPL19" "RPLP1" "RPL10" "RPL27" "RPL12"
## [22] "RPL29" "RPL21" "RPLP0" "RPL7" "RPL3" "RPL37" "RPL39"
## [29] "ZCCHC17" "RPL30" "RPL18A" "RPL13A" "RPL23" "RPL23A" "RPL34"
## [36] "RPL32" "UBA52" "RPL36AL" "RPL36A" "RPL4" "RPL39L" "RPL35"
## [43] "RPL41" "RPL31" "RPL27A" "RPL36" "RPL7L1" "RPLP2" "RPL37A"
## [50] "RPL38" "RPL26L1" "RPL10A"
##
## [[1]]$`DOWN genesets.GO:0022626 cytosolic ribosome`
## [1] "RPL7A" "RPL17" "RPS27A" "RPL8" "RPS7" "RPL28" "RPL6"
## [8] "RPL18" "RPL5" "RPL9" "RPL24" "RPS3A" "RPS3" "RPL11"
## [15] "RPL14" "RPS19" "RPS25" "RPL15" "RPL22" "RPL35A" "RPS10"
## [22] "PELO" "RPL13" "RPS15A" "EEF1A1" "RPS8" "RPL26" "RPL19"
## [29] "RPLP1" "RPL10" "RPL27" "RPL12" "RPS13" "RPS14" "RPL29"
## [36] "RPL21" "RPLP0" "RPL7" "RPS23" "RPS5" "RPL3" "RPS12"
## [43] "RPS11" "RPL37" "RPS15" "RPL39" "RPS6" "RPL30" "RPL18A"
## [50] "EIF2AK4" "RPL13A" "RPL23" "RPS4X" "RPL23A" "RPS20" "RPL34"
## [57] "RPL32" "FAU" "RPS9" "UBA52" "RPS24" "RPL36A" "RPL4"
## [64] "RPL35" "ABCE1" "RPS17" "RPL31" "RNF10" "RPS2" "RPS16"
## [71] "RPS18" "METAP1" "RPS27" "NEMF" "ZNF598" "RPL27A" "RPL36"
## [78] "LTN1" "USP10" "RPSA" "RPL37A" "APOD" "ETF1" "ASCC2"
## [85] "RPL38" "RNF25" "RPS21" "RNF14" "HBS1L" "GSPT1" "RPL10A"
##
## [[1]]$`DOWN genesets.GO:0022627 cytosolic small ribosomal subunit`
## [1] "RPS27A" "RPS7" "RPS3A" "RPS3" "RACK1" "RPS19" "RPS25" "RPS10"
## [9] "RPS15A" "RPS8" "RPS27L" "RPS13" "RPS14" "RPS23" "RPS5" "RPS12"
## [17] "RPS11" "RPS15" "RPS6" "RPS4X" "RPS20" "FAU" "RPS9" "RPS24"
## [25] "RPS17" "RPS2" "RPS16" "RPS18" "RPS27" "RPS28" "RPSA" "RPS29"
## [33] "DHX29" "DDX3X" "EIF2A" "LARP4" "RPS21" "RPS26" "RPS4Y1"
##
## [[1]]$`DOWN genesets.GO:0030134 COPII-coated ER to Golgi transport vesicle`
## [1] "LMAN1" "TMED4" "GOLGA2" "LMAN2" "YIF1A" "ERGIC3" "CNIH4"
## [8] "TMED3" "DDHD2" "YIPF5" "F8" "TEX261" "TMED10" "TMED7"
## [15] "YIPF6" "CTSC" "YIF1B" "TMED2" "SEC23IP" "APP" "IER3IP1"
## [22] "ERGIC2" "CTSZ" "SEC31A" "STX17" "LMAN2L" "TMED1" "ECPAS"
## [29] "TMED5" "SURF4" "ERGIC1" "KLHL12" "TMED9"
##
## [[1]]$`DOWN genesets.GO:0032391 photoreceptor connecting cilium`
## [1] "SPATA7" "LCA5" "NPHP1" "WDR19" "IFT20" "CEP290"
## [7] "ARL3" "CETN3" "TMEM237" "FAM161A" "CETN2" "KIFAP3"
## [13] "TOPORS" "IFT57" "IQCB1" "RPGRIP1L" "SEPTIN2" "IFT52"
## [19] "MYO7A" "POC5" "WHRN" "RPGRIP1" "IFT140" "CFAP410"
## [25] "TBCC" "KIAA1549" "BBS4" "TTC8" "MAK"
##
## [[1]]$`DOWN genesets.GO:0035578 azurophil granule lumen`
## [1] "GGH" "TUBB" "FABP5" "GUSB" "CREG1" "CTSA"
## [7] "FUCA1" "TXNDC5" "HEXB" "ADA2" "GLB1" "HEBP2"
## [13] "GRN" "DPP7" "CAP1" "CCT8" "BPI" "PRDX6"
## [19] "ARSA" "AGA" "SDCBP" "MAN2B1" "FTL" "RNASET2"
## [25] "NHLRC3" "PLAC8" "ACTR10" "VAT1" "NPC2" "FUCA2"
## [31] "GNS" "GM2A" "TUBB4B" "FAF2" "C3" "CTSC"
## [37] "TOLLIP" "CCT2" "STK11IP" "PYCARD" "VCP" "PYGB"
## [43] "GCA" "IMPDH1" "TRAPPC1" "PTGES2" "GLA" "ARSB"
## [49] "MPO" "C6orf120" "MNDA" "CPPED1" "AZU1" "ANXA2"
## [55] "DYNC1H1" "PA2G4" "ARHGAP45" "GALNS" "ACLY" "PSMD1"
## [61] "MAPK1" "GDI2" "NAPRT" "DNAJC3" "CYB5R3" "LYZ"
## [67] "ACTR2" "IST1"
##
## [[1]]$`DOWN genesets.GO:0042605 peptide antigen binding`
## [1] "HLA-DQA2" "HLA-DOA" "FCGRT" "HLA-DMB" "HLA-DMA" "HFE"
## [7] "SLC7A5" "HLA-B" "HLA-DQA1" "HLA-DPB1" "B2M" "HLA-DRA"
## [13] "HLA-F" "HLA-DQB1" "HLA-A" "HLA-DPA1" "TAPBP" "HLA-C"
## [19] "HLA-E" "HLA-DRB5" "HLA-G" "TAP1" "MAML1" "HLA-DRB1"
## [25] "CD209" "DHCR24" "SLC7A8"
##
## [[1]]$`DOWN genesets.GO:0042613 MHC class II protein complex`
## [1] "HLA-DQA2" "HLA-DOA" "HLA-DMB" "HLA-DMA" "HLA-DQA1" "HLA-DPB1"
## [7] "B2M" "HLA-DRA" "HLA-DQB1" "CD74" "HLA-DPA1" "HLA-DRB5"
## [13] "HLA-DRB1"
##
## [[1]]$`DOWN genesets.GO:0043202 lysosomal lumen`
## [1] "IFI30" "GUSB" "TCN2" "CTSL" "CTSA" "HPSE"
## [7] "FUCA1" "TXNDC5" "HEXB" "HSP90AA1" "CTSK" "HEXA"
## [13] "NEU1" "GALC" "ATP13A2" "GLB1" "EPDR1" "ASAH1"
## [19] "PSAP" "LGMN" "LAMP2" "SDC2" "ARSA" "CHID1"
## [25] "MAN2B1" "RNASET2" "NPC2" "NAGLU" "GPC4" "CSPG4"
## [31] "CTSS" "GNS" "GM2A" "HGSNAT" "GPC1" "SCARB2"
## [37] "LIPA" "GYG1" "CD74" "GPC3" "PPT2" "SDC1"
## [43] "CTSF" "GLA" "NAAA" "ARSB" "SGSH" "CTSD"
## [49] "VCAN" "CUBN" "GAA" "CTSV" "GALNS" "ACP2"
## [55] "MANBA" "SMPD1" "SDC3" "PLD3" "IDUA" "PLBD2"
## [61] "SDC4" "HSPA8" "TPP1" "MAN2B2"
##
## [[1]]$`DOWN genesets.GO:0050714 positive regulation of protein secretion`
## [1] "SYTL4" "APBB1" "ADAM8" "BMP6" "PPIA" "ATP13A2" "CD2AP"
## [8] "ANG" "IGF1" "APBB3" "MYH10" "PPID" "TREM2" "TGFB1"
## [15] "TMED10" "KCNN4" "GOLPH3L" "ARF6" "IL1A" "FRMD4A" "GOLPH3"
## [22] "P2RX7" "IER3IP1" "DNM1L" "CD33" "PARD6A" "MYOM1" "ADAM9"
## [29] "UNC13B" "PCSK1" "SEC24A" "MYO18A" "ABCG1" "TTN"
##
## [[1]]$`DOWN genesets.GO:0071007 U2-type catalytic step 2 spliceosome`
## [1] "SNRPD3" "SNRPD2" "CDC5L" "SNRPB2" "BCAS2" "SYF2" "SNRPG"
## [8] "PPIE" "SNRPE" "SNW1" "AQR" "CDC40" "CRNKL1" "PRPF8"
## [15] "SNRPA1" "SNRPD1" "SRRM2" "CWC15" "SNRPF" "PLRG1" "DHX8"
## [22] "BUD31" "CWC22" "RBM22" "XAB2" "PRPF19" "PPIL1" "EFTUD2"
## [29] "SNRPB" "SNRNP40"
##
## [[1]]$`DOWN genesets.GO:0071011 precatalytic spliceosome`
## [1] "SNRPD3" "SNRPD2" "SF3B4" "RBMX2" "SF3B2" "SNRPG" "SNRPE"
## [8] "PRPF31" "LSM8" "WBP4" "SMU1" "SNRPD1" "SF3B5" "LSM2"
## [15] "LSM3" "PHF5A" "SNU13" "PRPF38A" "PRPF38B"
##
## [[1]]$`DOWN genesets.GO:0071944 cell periphery`
## [1] "SLC24A3" "SMPD2" "CD36" "PRKCE" "CIB2" "STK26"
## [7] "KRT18" "NME2" "TUBB3" "FBLIM1" "TOMM20" "SLC8A1"
## [13] "ARHGEF5" "RHOA" "EZR" "CTNNB1" "ITGB1BP1" "THSD1"
## [19] "RAC3" "CLU" "SLC12A2" "RDX" "MAGI1" "MBP"
## [25] "SLC12A5" "SLC2A13" "AXIN1" "ITGA3" "CIB1" "BAX"
## [31] "PHB2" "MYO1B" "CORO1B" "SNORC" "FERMT1" "TRAP1"
## [37] "FUT4" "AGAP3" "MSN"
##
## [[1]]$`DOWN genesets.GO:0097435 supramolecular fiber organization`
## [1] "SNCA" "MFAP4" "BID" "FKBP1A" "MFAP5" "BASP1"
## [7] "HSP90AB1" "B4GALT7" "CST3" "BAX"
##
## [[1]]$`DOWN genesets.GO:0097542 ciliary tip`
## [1] "KIF3A" "IFT22" "ARMC9" "DYNLRB1" "WDR19" "IFT20"
## [7] "KIF3C" "WDR35" "IFT43" "DYNLL1" "DYNLRB2" "KIFAP3"
## [13] "DYNC2LI1" "IFT57" "DYNC2H1" "CLUAP1" "TRAF3IP1" "TTC21B"
## [19] "IFT52" "IFT88" "CYLD" "IFT81" "IFT140" "DYNLL2"
## [25] "IFT172" "IFT27" "CDKL5" "SUFU" "IFT80" "IFT74"
## [31] "IFT46" "ULK3" "KIF3B"
##
## [[1]]$`DOWN genesets.GO:0101003 ficolin-1-rich granule membrane`
## [1] "CD300A" "ADAM8" "ADGRE3" "TRPM2" "SERPINB6" "LILRB2"
## [7] "FPR2" "DYNC1LI1" "ENPP4" "CD55" "SLC2A3" "ARL8A"
## [13] "LAMP2" "COPB1" "PRCP" "PTPRN2" "FCER1G" "FPR1"
## [19] "RHOA" "RAC1" "DYNLL1" "LAMP1" "ITGAX" "ATP6V0A1"
## [25] "CD58" "VPS35L" "ATAD3B" "FCAR" "SIRPA" "STBD1"
## [31] "UBR4" "NCKAP1L" "DSP" "SIGLEC5" "ITGB2" "GAA"
## [37] "TCIRG1" "ATP6V0C" "CR1" "LAMTOR1" "TMEM179B" "ATP6AP2"
## [43] "SIGLEC14" "SLC11A1" "NBEAL2" "LGALS3"Session information
For reproducibility.
sessionInfo()## R version 4.4.3 (2025-02-28)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.5 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Australia/Melbourne
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] reshape2_1.4.4 dplyr_1.1.4 mitch_1.19.3 eulerr_7.0.2
## [5] network_1.19.0 ggplot2_3.5.1 kableExtra_1.4.0 gplots_3.2.0
##
## loaded via a namespace (and not attached):
## [1] RColorBrewer_1.1-3 rstudioapi_0.17.1 jsonlite_1.9.1
## [4] magrittr_2.0.3 spatstat.utils_3.1-3 farver_2.1.2
## [7] rmarkdown_2.29 vctrs_0.6.5 ROCR_1.0-11
## [10] spatstat.explore_3.4-2 htmltools_0.5.8.1 sass_0.4.9
## [13] sctransform_0.4.1 parallelly_1.43.0 KernSmooth_2.23-26
## [16] bslib_0.9.0 htmlwidgets_1.6.4 ica_1.0-3
## [19] plyr_1.8.9 echarts4r_0.4.5 plotly_4.10.4
## [22] zoo_1.8-13 cachem_1.1.0 igraph_2.1.4
## [25] mime_0.13 lifecycle_1.0.4 pkgconfig_2.0.3
## [28] Matrix_1.7-3 R6_2.6.1 fastmap_1.2.0
## [31] fitdistrplus_1.2-2 future_1.34.0 shiny_1.10.0
## [34] digest_0.6.37 colorspace_2.1-1 GGally_2.2.1
## [37] patchwork_1.3.0 Seurat_5.2.1 tensor_1.5
## [40] RSpectra_0.16-2 irlba_2.3.5.1 progressr_0.15.1
## [43] spatstat.sparse_3.1-0 httr_1.4.7 polyclip_1.10-7
## [46] abind_1.4-8 compiler_4.4.3 withr_3.0.2
## [49] ggstats_0.9.0 fastDummies_1.7.5 MASS_7.3-65
## [52] gtools_3.9.5 caTools_1.18.3 tools_4.4.3
## [55] lmtest_0.9-40 beeswarm_0.4.0 httpuv_1.6.15
## [58] future.apply_1.11.3 goftest_1.2-3 glue_1.8.0
## [61] nlme_3.1-167 promises_1.3.2 grid_4.4.3
## [64] Rtsne_0.17 cluster_2.1.8.1 generics_0.1.3
## [67] gtable_0.3.6 spatstat.data_3.1-6 tidyr_1.3.1
## [70] data.table_1.17.0 sp_2.2-0 xml2_1.3.8
## [73] spatstat.geom_3.3-6 RcppAnnoy_0.0.22 ggrepel_0.9.6
## [76] RANN_2.6.2 pillar_1.10.1 stringr_1.5.1
## [79] spam_2.11-1 RcppHNSW_0.6.0 later_1.4.1
## [82] splines_4.4.3 lattice_0.22-6 survival_3.8-3
## [85] deldir_2.0-4 tidyselect_1.2.1 miniUI_0.1.1.1
## [88] pbapply_1.7-2 knitr_1.50 gridExtra_2.3
## [91] svglite_2.1.3 scattermore_1.2 xfun_0.51
## [94] matrixStats_1.5.0 stringi_1.8.4 statnet.common_4.11.0
## [97] lazyeval_0.2.2 yaml_2.3.10 evaluate_1.0.3
## [100] codetools_0.2-20 tibble_3.2.1 cli_3.6.4
## [103] uwot_0.2.3 xtable_1.8-4 reticulate_1.42.0
## [106] systemfonts_1.2.1 munsell_0.5.1 jquerylib_0.1.4
## [109] Rcpp_1.0.14 globals_0.16.3 spatstat.random_3.3-3
## [112] coda_0.19-4.1 png_0.1-8 spatstat.univar_3.1-2
## [115] parallel_4.4.3 dotCall64_1.2 bitops_1.0-9
## [118] listenv_0.9.1 viridisLite_0.4.2 scales_1.3.0
## [121] ggridges_0.5.6 SeuratObject_5.0.2 purrr_1.0.4
## [124] rlang_1.1.5 cowplot_1.1.3