Differential expression analysis of broad cell type clusters
Belinda Phipson
10/25/2019
Last updated: 2019-10-28
Checks: 6 0
Knit directory: Porello-heart-snRNAseq/
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| Rmd | d06c0c8 | Belinda Phipson | 2019-10-28 | add differential expression analysis for broad cell types |
Introduction
Load libraries and functions
library(edgeR)
library(RColorBrewer)
library(org.Hs.eg.db)
library(limma)
library(Seurat)
library(monocle)
library(cowplot)
library(DelayedArray)
library(scran)
library(NMF)
library(workflowr)
library(ggplot2)
library(clustree)
library(dplyr)source("/misc/card2-single_cell_nuclei_rnaseq/Porello-heart-snRNAseq/code/normCounts.R")
source("/misc/card2-single_cell_nuclei_rnaseq/Porello-heart-snRNAseq/code/findModes.R")
source("/misc/card2-single_cell_nuclei_rnaseq/Porello-heart-snRNAseq/code/ggplotColors.R")Load the data
targets <- read.delim("/misc/card2-single_cell_nuclei_rnaseq/Porello-heart-snRNAseq/data/targets.txt",header=TRUE, stringsAsFactors = FALSE)
targets$FileName2 <- paste(targets$FileName,"/",sep="")
targets$Group_ID2 <- gsub("LV_","",targets$Group_ID)
group <- c("Fetal_1","Fetal_2","Fetal_3",
"Young_1","Young_2","Young_3",
"Adult_1","Adult_2","Adult_3",
"Diseased_1","Diseased_2",
"Diseased_3","Diseased_4")
m <- match(group, targets$Group_ID2)
targets <- targets[m,]fetal.integrated <- readRDS(file="./output/RDataObjects/fetal-int.Rds")
load(file="./output/RDataObjects/fetalObjs.Rdata")
young.integrated <- readRDS(file="./output/RDataObjects/young-int.Rds")
load(file="./output/RDataObjects/youngObjs.Rdata")
adult.integrated <- readRDS(file="./output/RDataObjects/adult-int.Rds")
load(file="./output/RDataObjects/adultObjs.Rdata")# Load unfiltered counts matrix for every sample (object all)
load("./output/RDataObjects/all-counts.Rdata")Set default clustering resolution
# Default 0.3
Idents(fetal.integrated) <- fetal.integrated$integrated_snn_res.0.3
DimPlot(fetal.integrated, reduction = "tsne",label=TRUE,label.size = 6)+NoLegend()
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
# Default 0.3
DimPlot(young.integrated, reduction = "tsne",label=TRUE,label.size = 6)+NoLegend()
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
# Default 0.6
DimPlot(adult.integrated, reduction = "tsne",label=TRUE,label.size = 6)+NoLegend()
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
Merge all data together
heart <- merge(fetal.integrated, y = c(young.integrated, adult.integrated), project = "heart")
table(heart$orig.ident)
adult fetal young
9416 27760 16964 table(heart$biorep)
a1 a2 a3 f1 f2 f3 y1 y2 y3
4360 3375 1681 8296 10948 8516 4422 5558 6984 table(heart$Broad_celltype,heart$biorep)
a1 a2 a3 f1 f2 f3 y1 y2 y3
Cardiomyocytes 1856 564 383 5475 8580 5140 1073 2221 4456
Endothelial cells 599 466 165 735 715 1298 511 462 550
Epicardial cells 343 493 92 564 425 404 613 280 260
Erythroid 0 0 0 43 49 31 0 0 0
Fibroblast 1034 1230 495 1029 755 1201 1622 1688 805
Immune cells 449 530 519 287 274 196 337 808 731
Neurons 57 43 14 109 130 110 207 71 133
Smooth muscle cells 22 49 13 54 20 136 59 28 49Remove erythroid cells
heart <- subset(heart,subset = Broad_celltype != "Erythroid")
heart$biorep <- factor(heart$biorep,levels=c("f1","f2","f3","y1","y2","y3","a1","a2","a3"))
table(heart$Broad_celltype,heart$biorep)
f1 f2 f3 y1 y2 y3 a1 a2 a3
Cardiomyocytes 5475 8580 5140 1073 2221 4456 1856 564 383
Endothelial cells 735 715 1298 511 462 550 599 466 165
Epicardial cells 564 425 404 613 280 260 343 493 92
Fibroblast 1029 755 1201 1622 1688 805 1034 1230 495
Immune cells 287 274 196 337 808 731 449 530 519
Neurons 109 130 110 207 71 133 57 43 14
Smooth muscle cells 54 20 136 59 28 49 22 49 13Get gene annotation
columns(org.Hs.eg.db) [1] "ACCNUM" "ALIAS" "ENSEMBL" "ENSEMBLPROT"
[5] "ENSEMBLTRANS" "ENTREZID" "ENZYME" "EVIDENCE"
[9] "EVIDENCEALL" "GENENAME" "GO" "GOALL"
[13] "IPI" "MAP" "OMIM" "ONTOLOGY"
[17] "ONTOLOGYALL" "PATH" "PFAM" "PMID"
[21] "PROSITE" "REFSEQ" "SYMBOL" "UCSCKG"
[25] "UNIGENE" "UNIPROT" ann <- AnnotationDbi:::select(org.Hs.eg.db,keys=rownames(all),columns=c("SYMBOL","ENTREZID","ENSEMBL","GENENAME","CHR"),keytype = "SYMBOL")
m <- match(rownames(all),ann$SYMBOL)
ann <- ann[m,]
table(ann$SYMBOL==rownames(all))
TRUE
33939 mito <- grep("mitochondrial",ann$GENENAME)
length(mito)[1] 226ribo <- grep("ribosomal",ann$GENENAME)
length(ribo)[1] 198missingEZID <- which(is.na(ann$ENTREZID))
length(missingEZID)[1] 10530Filter out non-informative genes
m <- match(colnames(heart),colnames(all))
all.counts <- all[,m]chuck <- unique(c(mito,ribo,missingEZID))
length(chuck)[1] 10875all.counts.keep <- all.counts[-chuck,]
ann.keep <- ann[-chuck,]
table(ann.keep$SYMBOL==rownames(all.counts.keep))
TRUE
23064 # remove x y genes
xy <- ann.keep$CHR %in% c("X","Y")
all.counts.keep <- all.counts.keep[!xy,]
ann.keep <- ann.keep[!xy,]numzero.genes <- rowSums(all.counts.keep==0)
#avg.exp <- rowMeans(cpm.DGEList(y.kid,log=TRUE))
#plot(avg.exp,numzero.genes,xlab="Average log-normalised-counts",ylab="Number zeroes per gene")
table(numzero.genes > (ncol(all.counts.keep)-20))
FALSE TRUE
18500 3557 keep.genes <- numzero.genes < (ncol(all.counts.keep)-20)
table(keep.genes)keep.genes
FALSE TRUE
3593 18464 all.keep <- all.counts.keep[keep.genes,]
dim(all.keep)[1] 18464 54017ann.keep <- ann.keep[keep.genes,]
table(colnames(heart)==colnames(all.keep))
TRUE
54017 table(rownames(all.keep)==ann.keep$SYMBOL)
TRUE
18464 Create pseudobulk samples
broadct <- factor(heart$Broad_celltype)
sam <- factor(heart$biorep,levels=c("f1","f2","f3","y1","y2","y3","a1","a2","a3"))
newgrp <- paste(broadct,sam,sep=".")
newgrp <- factor(newgrp,levels=paste(rep(levels(broadct),each=9),levels(sam),sep="."))
table(newgrp)newgrp
Cardiomyocytes.f1 Cardiomyocytes.f2 Cardiomyocytes.f3
5475 8580 5140
Cardiomyocytes.y1 Cardiomyocytes.y2 Cardiomyocytes.y3
1073 2221 4456
Cardiomyocytes.a1 Cardiomyocytes.a2 Cardiomyocytes.a3
1856 564 383
Endothelial cells.f1 Endothelial cells.f2 Endothelial cells.f3
735 715 1298
Endothelial cells.y1 Endothelial cells.y2 Endothelial cells.y3
511 462 550
Endothelial cells.a1 Endothelial cells.a2 Endothelial cells.a3
599 466 165
Epicardial cells.f1 Epicardial cells.f2 Epicardial cells.f3
564 425 404
Epicardial cells.y1 Epicardial cells.y2 Epicardial cells.y3
613 280 260
Epicardial cells.a1 Epicardial cells.a2 Epicardial cells.a3
343 493 92
Fibroblast.f1 Fibroblast.f2 Fibroblast.f3
1029 755 1201
Fibroblast.y1 Fibroblast.y2 Fibroblast.y3
1622 1688 805
Fibroblast.a1 Fibroblast.a2 Fibroblast.a3
1034 1230 495
Immune cells.f1 Immune cells.f2 Immune cells.f3
287 274 196
Immune cells.y1 Immune cells.y2 Immune cells.y3
337 808 731
Immune cells.a1 Immune cells.a2 Immune cells.a3
449 530 519
Neurons.f1 Neurons.f2 Neurons.f3
109 130 110
Neurons.y1 Neurons.y2 Neurons.y3
207 71 133
Neurons.a1 Neurons.a2 Neurons.a3
57 43 14
Smooth muscle cells.f1 Smooth muscle cells.f2 Smooth muscle cells.f3
54 20 136
Smooth muscle cells.y1 Smooth muscle cells.y2 Smooth muscle cells.y3
59 28 49
Smooth muscle cells.a1 Smooth muscle cells.a2 Smooth muscle cells.a3
22 49 13 des <- model.matrix(~0+newgrp)
colnames(des) <- levels(newgrp)
dim(des)[1] 54017 63dim(all.counts.keep)[1] 22057 54017pb <- all.keep %*% desy.pb <- DGEList(pb)
saminfo <- matrix(unlist(strsplit(colnames(y.pb$counts),split="[.]")),ncol=2,byrow=TRUE)
bct <- factor(saminfo[,1])
indiv <- factor(saminfo[,2])
group <- rep(NA,ncol(y.pb))
group[grep("f",indiv)] <- "fetal"
group[grep("y",indiv)] <- "young"
group[grep("a",indiv)] <- "adult"
group <- factor(group,levels=c("fetal","young","adult"))
targets.pb <- data.frame(bct,indiv,group)
targets.pb$Sex <- targets$Sex[1:9]par(mfrow=c(1,1))
sexgroup <- paste(group,targets.pb$Sex,sep=".")
plotMDS.DGEList(y.pb,gene.selection="common",col=ggplotColors(7)[bct],pch=c(0,15,1,16,2,17)[factor(sexgroup)],cex=2)
legend("bottomright",legend=levels(bct),fill=ggplotColors(7),bty="n")
legend("bottomleft",legend=c("Female","Male"),pch=c(1,16),cex=1.5)
legend("topright",legend=c("Fetal","Young","Adult"),pch=c(1,2,0),cex=1.5)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plotMDS.DGEList(y.pb,gene.selection="common",col=ggplotColors(7)[bct],pch=c(0,15,1,16,2,17)[factor(sexgroup)],cex=2,dim=c(3,4))
legend("bottomright",legend=levels(bct),fill=ggplotColors(7),bty="n")
legend("top",legend=c("Female","Male"),pch=c(1,16),cex=1.5)
legend("topright",legend=c("Fetal","Young","Adult"),pch=c(1,2,0),cex=1.5)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plotMDS.DGEList(y.pb,gene.selection="common",col=ggplotColors(7)[bct],pch=c(0,15,1,16,2,17)[factor(sexgroup)],cex=2,dim=c(5,6))
legend("bottomleft",legend=levels(bct),fill=ggplotColors(7),bty="n")
legend("top",legend=c("Female","Male"),pch=c(1,16),cex=1.5)
legend("bottomright",legend=c("Fetal","Young","Adult"),pch=c(1,2,0),cex=1.5)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
Differential expression analysis
table(rownames(y.pb)==ann.keep$SYMBOL)
TRUE
18464 y.pb$genes <- ann.keep
#logcounts <- normCounts(y.pb,log=TRUE,prior.count=0.5)
bct2 <- as.character(bct)
bct2[bct2 == "Cardiomyocytes"] <- "cardio"
bct2[bct2 == "Endothelial cells"] <- "endo"
bct2[bct2 == "Epicardial cells"] <- "epicardial"
bct2[bct2 == "Fibroblast"] <- "fibro"
bct2[bct2 == "Immune cells"] <- "immune"
bct2[bct2 == "Neurons"] <- "neurons"
bct2[bct2 == "Smooth muscle cells"] <- "smc"
newgrp <- paste(bct2,group,targets.pb$Sex,sep=".")
newgrp <- factor(newgrp)
design <- model.matrix(~0+newgrp)
colnames(design) <- levels(newgrp)
v <- voom(y.pb,design,plot=TRUE,normalize.method = "cyclicloess")
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
fit <- lmFit(v,design)
#fit <- lmFit(logcounts,design)Cardiomyocytes
cont.cardio <- makeContrasts(YvF = 0.5*(cardio.young.Male + cardio.young.Female) - 0.5*(cardio.fetal.Male + cardio.fetal.Female),
AvF = 0.5*(cardio.adult.Male + cardio.adult.Female) - 0.5*(cardio.fetal.Male + cardio.fetal.Female),
AvY = 0.5*(cardio.adult.Male + cardio.adult.Female) - 0.5*(cardio.young.Male + cardio.young.Female),
SexFetal = cardio.fetal.Male - cardio.fetal.Female,
SexYoung = cardio.young.Male - cardio.young.Female,
SexAdult = cardio.adult.Male - cardio.adult.Female,
InteractionAF = (cardio.adult.Male - cardio.fetal.Male) - (cardio.adult.Female - cardio.fetal.Female),
InteractionYF = (cardio.young.Male - cardio.fetal.Male) - (cardio.young.Female - cardio.fetal.Female),
InteractionAY = (cardio.adult.Male - cardio.young.Male) - (cardio.adult.Female - cardio.young.Female),
levels=design)
fit.cardio <- contrasts.fit(fit,contrasts = cont.cardio)
fit.cardio <- eBayes(fit.cardio,robust=TRUE)
summary(decideTests(fit.cardio)) YvF AvF AvY SexFetal SexYoung SexAdult InteractionAF
Down 3203 3109 250 243 489 287 251
NotSig 11705 11686 17703 18159 17860 18002 17955
Up 3556 3669 511 62 115 175 258
InteractionYF InteractionAY
Down 87 133
NotSig 18309 17995
Up 68 336treat.cardio <- treat(fit.cardio,lfc=0.5)
dt.cardio<-decideTests(treat.cardio)
summary(dt.cardio) YvF AvF AvY SexFetal SexYoung SexAdult InteractionAF
Down 1387 1496 16 107 93 63 57
NotSig 15645 15481 18397 18349 18367 18384 18351
Up 1432 1487 51 8 4 17 56
InteractionYF InteractionAY
Down 23 22
NotSig 18419 18374
Up 22 68par(mfrow=c(3,3))
for(i in 1:9){
plotMD(treat.cardio,coef=i,status=dt.cardio[,i],hl.col=c("blue","red"))
abline(h=0,col="grey")
}
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
par(mfrow=c(1,1))
par(mar=c(7,4,2,2))
barplot(summary(dt.cardio)[-2,],beside=TRUE,legend=TRUE,col=c("blue","red"),ylab="Number of significant genes",las=2,xlab="")
title("Cardiomyocytes")
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
Young vs Fetal
options(digits=3)
topTreat(treat.cardio,coef=1,n=20,p.value=0.05)[,-c(1:3)] GENENAME
TMEM178B transmembrane protein 178B
MBOAT2 membrane bound O-acyltransferase domain containing 2
GRAMD1B GRAM domain containing 1B
TOGARAM2 TOG array regulator of axonemal microtubules 2
DGKG diacylglycerol kinase gamma
IGF2BP3 insulin like growth factor 2 mRNA binding protein 3
MIR29B2CHG MIR29B2 and MIR29C host gene
PEBP4 phosphatidylethanolamine binding protein 4
NCEH1 neutral cholesterol ester hydrolase 1
NEAT1 nuclear paraspeckle assembly transcript 1
CCSER1 coiled-coil serine rich protein 1
DAPK2 death associated protein kinase 2
LINC01621 long intergenic non-protein coding RNA 1621
ADRA1A adrenoceptor alpha 1A
PRICKLE1 prickle planar cell polarity protein 1
FRMD5 FERM domain containing 5
THRB thyroid hormone receptor beta
HECW2 HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2
USP31 ubiquitin specific peptidase 31
CHPT1 choline phosphotransferase 1
CHR logFC AveExpr t P.Value adj.P.Val
TMEM178B 7 7.65 4.39 21.6 3.89e-18 7.18e-14
MBOAT2 2 -3.22 6.07 -20.5 1.33e-17 1.22e-13
GRAMD1B 11 3.58 5.35 20.1 2.27e-17 1.40e-13
TOGARAM2 2 7.80 2.76 19.2 7.09e-17 3.27e-13
DGKG 3 4.76 6.21 17.9 3.64e-16 1.13e-12
IGF2BP3 7 -5.30 4.68 -17.8 3.67e-16 1.13e-12
MIR29B2CHG 1 3.92 6.61 17.7 4.46e-16 1.18e-12
PEBP4 8 4.52 4.25 17.5 5.66e-16 1.27e-12
NCEH1 3 4.08 5.33 17.5 6.19e-16 1.27e-12
NEAT1 11 3.14 10.87 17.3 7.29e-16 1.35e-12
CCSER1 4 3.32 6.59 16.8 1.42e-15 2.38e-12
DAPK2 15 3.01 5.21 16.7 1.75e-15 2.69e-12
LINC01621 6 -5.84 -1.51 -16.6 1.90e-15 2.71e-12
ADRA1A 8 4.40 3.13 15.8 6.58e-15 8.68e-12
PRICKLE1 12 -2.46 7.05 -15.6 7.93e-15 9.28e-12
FRMD5 15 -4.21 6.15 -15.6 8.04e-15 9.28e-12
THRB 3 5.02 6.58 15.3 1.25e-14 1.36e-11
HECW2 2 -4.32 6.28 -15.0 2.10e-14 2.15e-11
USP31 16 2.77 5.91 14.8 2.62e-14 2.43e-11
CHPT1 12 2.85 6.80 14.8 2.63e-14 2.43e-11Adult vs Fetal
topTreat(treat.cardio,coef=2,n=20,p.value=0.05)[,-c(1:3)] GENENAME
FILIP1L filamin A interacting protein 1 like
TMEM178B transmembrane protein 178B
MBOAT2 membrane bound O-acyltransferase domain containing 2
AAK1 AP2 associated kinase 1
MIR29B2CHG MIR29B2 and MIR29C host gene
DGKG diacylglycerol kinase gamma
CCSER1 coiled-coil serine rich protein 1
TOGARAM2 TOG array regulator of axonemal microtubules 2
IGF2BP3 insulin like growth factor 2 mRNA binding protein 3
NEAT1 nuclear paraspeckle assembly transcript 1
TMEM155 transmembrane protein 155
LINC01621 long intergenic non-protein coding RNA 1621
PPP1R13L protein phosphatase 1 regulatory subunit 13 like
NCEH1 neutral cholesterol ester hydrolase 1
EMILIN2 elastin microfibril interfacer 2
EMC10 ER membrane protein complex subunit 10
HOOK2 hook microtubule tethering protein 2
AGPAT4 1-acylglycerol-3-phosphate O-acyltransferase 4
HECW2 HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2
BARD1 BRCA1 associated RING domain 1
CHR logFC AveExpr t P.Value adj.P.Val
FILIP1L 3 3.92 7.639 21.7 3.62e-18 4.36e-14
TMEM178B 7 7.63 4.393 21.5 4.72e-18 4.36e-14
MBOAT2 2 -3.21 6.065 -19.8 3.01e-17 1.47e-13
AAK1 2 1.90 8.115 19.8 3.19e-17 1.47e-13
MIR29B2CHG 1 4.25 6.614 19.5 4.43e-17 1.64e-13
DGKG 3 5.06 6.211 19.1 7.05e-17 2.17e-13
CCSER1 4 3.67 6.590 19.0 8.43e-17 2.22e-13
TOGARAM2 2 7.65 2.758 18.5 1.68e-16 3.89e-13
IGF2BP3 7 -5.52 4.676 -17.1 9.95e-16 2.04e-12
NEAT1 11 3.09 10.866 17.0 1.16e-15 2.14e-12
TMEM155 4 -8.30 -0.498 -16.8 1.49e-15 2.34e-12
LINC01621 6 -5.83 -1.513 -16.8 1.55e-15 2.34e-12
PPP1R13L 19 3.69 4.399 16.7 1.65e-15 2.34e-12
NCEH1 3 3.95 5.332 16.4 2.51e-15 3.24e-12
EMILIN2 18 -4.04 4.507 -16.4 2.64e-15 3.24e-12
EMC10 19 -3.45 6.132 -16.1 3.84e-15 4.43e-12
HOOK2 19 2.30 5.762 15.8 6.45e-15 7.01e-12
AGPAT4 6 -3.90 5.821 -15.7 7.39e-15 7.58e-12
HECW2 2 -5.38 6.279 -15.4 1.10e-14 1.06e-11
BARD1 2 -2.94 5.740 -15.2 1.63e-14 1.50e-11Adult vs Young
topTreat(treat.cardio,coef=3,n=20,p.value=0.05)[,-c(1:3)] GENENAME CHR logFC
ZFP57 ZFP57 zinc finger protein 6 5.52
FAM153A family with sequence similarity 153 member A 5 3.96
DNAAF3 dynein axonemal assembly factor 3 19 3.14
SVOP SV2 related protein 12 2.88
CACNA1E calcium voltage-gated channel subunit alpha1 E 1 3.08
AGBL4 ATP/GTP binding protein like 4 1 2.94
FILIP1L filamin A interacting protein 1 like 3 1.49
TNNT1 troponin T1, slow skeletal type 19 2.88
GLIS3 GLIS family zinc finger 3 9 -2.96
TBC1D3D TBC1 domain family member 3D 17 3.28
ARG2 arginase 2 14 -2.15
LINC02506 long intergenic non-protein coding RNA 2506 4 3.27
CYP2J2 cytochrome P450 family 2 subfamily J member 2 1 2.05
LINC02232 long intergenic non-protein coding RNA 2232 4 4.90
EXOG exo/endonuclease G 3 1.27
DNAH14 dynein axonemal heavy chain 14 1 2.35
OR4C3 olfactory receptor family 4 subfamily C member 3 11 2.70
POU6F2 POU class 6 homeobox 2 7 1.65
LINC01699 long intergenic non-protein coding RNA 1699 1 3.53
ASB2 ankyrin repeat and SOCS box containing 2 14 2.09
AveExpr t P.Value adj.P.Val
ZFP57 0.270 10.72 3.36e-11 4.42e-07
FAM153A 1.699 10.53 4.79e-11 4.42e-07
DNAAF3 1.626 8.85 1.58e-09 9.72e-06
SVOP 1.498 8.44 3.90e-09 1.80e-05
CACNA1E 2.080 7.63 2.54e-08 9.36e-05
AGBL4 4.816 7.14 8.05e-08 2.48e-04
FILIP1L 7.639 7.02 1.07e-07 2.83e-04
TNNT1 1.732 6.83 1.71e-07 3.85e-04
GLIS3 7.093 -6.80 1.88e-07 3.85e-04
TBC1D3D -1.750 6.65 2.67e-07 4.93e-04
ARG2 3.449 -6.43 4.63e-07 7.77e-04
LINC02506 1.150 6.24 7.48e-07 1.15e-03
CYP2J2 2.796 5.92 1.65e-06 2.20e-03
LINC02232 0.675 5.94 1.67e-06 2.20e-03
EXOG 5.847 5.78 2.41e-06 2.82e-03
DNAH14 4.038 5.77 2.45e-06 2.82e-03
OR4C3 -1.822 5.52 4.66e-06 5.06e-03
POU6F2 3.111 5.44 5.67e-06 5.82e-03
LINC01699 -1.609 5.39 6.61e-06 6.43e-03
ASB2 3.129 5.35 7.19e-06 6.64e-03Male vs Female in fetal samples
topTreat(treat.cardio,coef=4,n=20,p.value=0.05)[,-c(1:3)] GENENAME CHR logFC AveExpr
BMP10 bone morphogenetic protein 10 2 -8.33 -1.542
ZNF385B zinc finger protein 385B 2 -3.90 3.787
EPHA4 EPH receptor A4 2 -3.38 5.247
APOA2 apolipoprotein A2 1 -4.67 -1.812
FAM155A family with sequence similarity 155 member A 13 -4.60 5.622
ZFP57 ZFP57 zinc finger protein 6 6.13 0.270
SHOX2 short stature homeobox 2 3 -6.93 0.702
GSG1L GSG1 like 16 -4.02 2.272
SYNPR synaptoporin 3 -3.64 2.716
FABP2 fatty acid binding protein 2 4 -6.43 -1.390
FLG-AS1 FLG antisense RNA 1 1 3.63 5.496
IRF4 interferon regulatory factor 4 6 -3.67 0.408
VWDE von Willebrand factor D and EGF domains 7 -3.87 0.899
SLC45A2 solute carrier family 45 member 2 5 -2.37 1.009
TDGF1 teratocarcinoma-derived growth factor 1 3 7.25 -0.681
PPFIA2 PTPRF interacting protein alpha 2 12 -2.99 5.432
PLCB1 phospholipase C beta 1 20 -3.10 8.683
SLC5A12 solute carrier family 5 member 12 11 -4.96 0.421
DAB1 DAB adaptor protein 1 1 2.16 7.416
FAM189A1 family with sequence similarity 189 member A1 15 -2.87 3.589
t P.Value adj.P.Val
BMP10 -16.14 4.05e-15 7.48e-11
ZNF385B -14.04 9.27e-14 6.35e-10
EPHA4 -13.97 1.03e-13 6.35e-10
APOA2 -10.19 9.61e-11 4.11e-07
FAM155A -10.10 1.14e-10 4.11e-07
ZFP57 10.04 1.33e-10 4.11e-07
SHOX2 -9.77 2.35e-10 6.19e-07
GSG1L -9.59 3.27e-10 7.55e-07
SYNPR -9.43 4.60e-10 9.43e-07
FABP2 -9.36 5.52e-10 1.02e-06
FLG-AS1 9.00 1.15e-09 1.91e-06
IRF4 -8.96 1.24e-09 1.91e-06
VWDE -8.79 1.81e-09 2.57e-06
SLC45A2 -8.36 4.75e-09 6.26e-06
TDGF1 8.07 9.70e-09 1.19e-05
PPFIA2 -7.81 1.67e-08 1.85e-05
PLCB1 -7.80 1.71e-08 1.85e-05
SLC5A12 -7.51 3.43e-08 3.52e-05
DAB1 7.42 4.13e-08 4.01e-05
FAM189A1 -7.34 4.97e-08 4.56e-05Male vs Female in young samples
topTreat(treat.cardio,coef=5,n=20,p.value=0.05)[,-c(1:3)] GENENAME CHR logFC
SLC38A8 solute carrier family 38 member 8 16 -5.65
C4orf54 chromosome 4 open reading frame 54 4 -4.60
GBE1 1,4-alpha-glucan branching enzyme 1 3 -1.78
TOGARAM2 TOG array regulator of axonemal microtubules 2 2 -2.23
TSPEAR thrombospondin type laminin G domain and EAR repeats 21 -3.45
ABCC3 ATP binding cassette subfamily C member 3 17 -3.54
ELOVL6 ELOVL fatty acid elongase 6 4 -2.40
LINC00964 long intergenic non-protein coding RNA 964 8 -2.79
MCTP2 multiple C2 and transmembrane domain containing 2 15 -3.97
LUCAT1 lung cancer associated transcript 1 5 -4.20
XIRP2 xin actin binding repeat containing 2 2 -2.74
HMGCS2 3-hydroxy-3-methylglutaryl-CoA synthase 2 1 -4.79
LINC01147 long intergenic non-protein coding RNA 1147 14 -4.50
PDE11A phosphodiesterase 11A 2 -3.42
LINC02137 long intergenic non-protein coding RNA 2137 16 -2.48
IL24 interleukin 24 1 -3.58
TAS2R8 taste 2 receptor member 8 12 -2.81
MIR646HG MIR646 host gene 20 -2.64
LINC02506 long intergenic non-protein coding RNA 2506 4 -5.03
RALYL RALY RNA binding protein like 8 -3.02
AveExpr t P.Value adj.P.Val
SLC38A8 0.289 -11.85 4.02e-12 7.42e-08
C4orf54 -1.271 -10.15 1.03e-10 9.52e-07
GBE1 7.950 -7.85 1.49e-08 9.09e-05
TOGARAM2 2.758 -7.73 2.00e-08 9.09e-05
TSPEAR 2.186 -7.64 2.46e-08 9.09e-05
ABCC3 2.658 -7.23 6.51e-08 2.00e-04
ELOVL6 4.667 -7.14 8.08e-08 2.13e-04
LINC00964 1.979 -6.80 1.84e-07 3.65e-04
MCTP2 3.161 -6.80 1.86e-07 3.65e-04
LUCAT1 2.984 -6.78 1.98e-07 3.65e-04
XIRP2 4.265 -6.32 6.10e-07 1.02e-03
HMGCS2 -0.220 -6.23 7.90e-07 1.22e-03
LINC01147 -0.882 -6.14 9.72e-07 1.38e-03
PDE11A -1.168 -6.03 1.29e-06 1.70e-03
LINC02137 2.129 -5.96 1.50e-06 1.85e-03
IL24 -1.612 -5.89 1.80e-06 2.08e-03
TAS2R8 -1.644 -5.80 2.28e-06 2.47e-03
MIR646HG 5.670 -5.71 2.86e-06 2.59e-03
LINC02506 1.150 -5.72 2.91e-06 2.59e-03
RALYL 4.234 -5.70 2.94e-06 2.59e-03Male vs Female in adult samples
topTreat(treat.cardio,coef=6,n=20,p.value=0.05)[,-c(1:3)] GENENAME CHR logFC
XIRP2-AS1 XIRP2 antisense RNA 1 2 7.38
ABHD18 abhydrolase domain containing 18 4 -2.30
TOGARAM2 TOG array regulator of axonemal microtubules 2 2 2.89
CACNA1E calcium voltage-gated channel subunit alpha1 E 1 3.44
HLA-DMA major histocompatibility complex, class II, DM alpha 6 -3.81
EXOG exo/endonuclease G 3 -1.69
RHOBTB1 Rho related BTB domain containing 1 10 -1.82
TBC1D3D TBC1 domain family member 3D 17 -3.83
PIK3R1 phosphoinositide-3-kinase regulatory subunit 1 5 -2.50
LINC02552 long intergenic non-protein coding RNA 2552 11 -7.62
WNT9A Wnt family member 9A 1 -5.40
KRTAP10-4 keratin associated protein 10-4 21 -3.55
LINC02425 long intergenic non-protein coding RNA 2425 12 -5.24
PLEKHA7 pleckstrin homology domain containing A7 11 -2.46
TKT transketolase 3 1.92
PDK4 pyruvate dehydrogenase kinase 4 7 -3.74
CPLX3 complexin 3 15 3.52
LMAN1L lectin, mannose binding 1 like 15 3.00
MTRNR2L1 MT-RNR2 like 1 17 -4.81
NTN1 netrin 1 17 2.19
AveExpr t P.Value adj.P.Val
XIRP2-AS1 -1.220 11.05 1.85e-11 3.41e-07
ABHD18 7.150 -10.65 3.80e-11 3.50e-07
TOGARAM2 2.758 9.13 8.60e-10 5.29e-06
CACNA1E 2.080 7.77 1.84e-08 8.47e-05
HLA-DMA 2.495 -7.12 8.60e-08 2.65e-04
EXOG 5.847 -7.07 9.48e-08 2.65e-04
RHOBTB1 6.032 -7.03 1.06e-07 2.65e-04
TBC1D3D -1.750 -7.00 1.15e-07 2.65e-04
PIK3R1 8.062 -6.83 1.74e-07 3.56e-04
LINC02552 2.302 -6.69 2.67e-07 4.93e-04
WNT9A 2.522 -6.56 3.49e-07 5.85e-04
KRTAP10-4 -0.179 -6.40 4.99e-07 7.68e-04
LINC02425 -1.107 -6.33 6.14e-07 8.72e-04
PLEKHA7 7.099 -6.19 8.45e-07 1.05e-03
TKT 4.745 6.17 8.78e-07 1.05e-03
PDK4 6.558 -6.16 9.11e-07 1.05e-03
CPLX3 -1.152 6.01 1.33e-06 1.44e-03
LMAN1L -0.370 5.95 1.58e-06 1.62e-03
MTRNR2L1 0.596 -5.92 1.75e-06 1.70e-03
NTN1 5.133 5.86 1.93e-06 1.78e-03Interaction of sex differences between adult and fetal
topTreat(treat.cardio,coef=7,n=20,p.value=0.05)[,-c(1:3)] GENENAME CHR
XIRP2-AS1 XIRP2 antisense RNA 1 2
ABHD18 abhydrolase domain containing 18 4
PPM1K-DT PPM1K divergent transcript 4
BMP10 bone morphogenetic protein 10 2
APOA2 apolipoprotein A2 1
ZFP57 ZFP57 zinc finger protein 6
WNT9A Wnt family member 9A 1
EPHA4 EPH receptor A4 2
FABP2 fatty acid binding protein 2 4
C17orf97 chromosome 17 open reading frame 97 17
LINC02552 long intergenic non-protein coding RNA 2552 11
KCNJ3 potassium voltage-gated channel subfamily J member 3 2
FLG-AS1 FLG antisense RNA 1 1
GNAO1 G protein subunit alpha o1 16
FAM201A family with sequence similarity 201 member A 9
EXOG exo/endonuclease G 3
IRF4 interferon regulatory factor 4 6
PRKAG2 protein kinase AMP-activated non-catalytic subunit gamma 2 7
NTN1 netrin 1 17
LINC02425 long intergenic non-protein coding RNA 2425 12
logFC AveExpr t P.Value adj.P.Val
XIRP2-AS1 8.10 -1.220 11.16 1.51e-11 2.79e-07
ABHD18 -2.47 7.150 -9.85 1.89e-10 1.75e-06
PPM1K-DT 6.42 2.479 9.33 5.85e-10 3.60e-06
BMP10 9.43 -1.542 9.09 1.04e-09 4.81e-06
APOA2 5.76 -1.812 7.71 2.15e-08 7.92e-05
ZFP57 -5.47 0.270 -7.38 4.76e-08 1.46e-04
WNT9A -6.37 2.522 -7.10 9.34e-08 2.46e-04
EPHA4 2.89 5.247 6.99 1.16e-07 2.69e-04
FABP2 9.29 -1.390 6.92 1.61e-07 3.30e-04
C17orf97 3.99 2.388 6.64 2.80e-07 5.17e-04
LINC02552 -7.77 2.302 -6.49 4.42e-07 7.43e-04
KCNJ3 8.39 2.072 6.42 5.38e-07 8.24e-04
FLG-AS1 -3.41 5.496 -6.34 5.80e-07 8.24e-04
GNAO1 6.29 3.776 6.31 6.71e-07 8.85e-04
FAM201A -5.78 -0.994 -6.28 7.19e-07 8.85e-04
EXOG -1.93 5.847 -6.15 9.39e-07 1.00e-03
IRF4 6.42 0.408 6.18 9.43e-07 1.00e-03
PRKAG2 2.22 7.307 6.13 9.78e-07 1.00e-03
NTN1 3.06 5.133 6.09 1.09e-06 1.06e-03
LINC02425 -6.04 -1.107 -6.07 1.22e-06 1.13e-03Interaction of sex differences between young and fetal
topTreat(treat.cardio,coef=8,n=20,p.value=0.05)[,-c(1:3)] GENENAME CHR logFC AveExpr
ZFP57 ZFP57 zinc finger protein 6 -9.53 0.270
SLC38A8 solute carrier family 38 member 8 16 -5.55 0.289
APOA2 apolipoprotein A2 1 5.00 -1.812
DAB1 DAB adaptor protein 1 1 -2.89 7.416
SYNPR synaptoporin 3 4.76 2.716
BMP10 bone morphogenetic protein 10 2 6.01 -1.542
FAM155A family with sequence similarity 155 member A 13 5.89 5.622
SHOX2 short stature homeobox 2 3 8.02 0.702
FLG-AS1 FLG antisense RNA 1 1 -3.16 5.496
NAV1 neuron navigator 1 1 -2.00 8.027
C4orf54 chromosome 4 open reading frame 54 4 -5.77 -1.271
LINC02531 long intergenic non-protein coding RNA 2531 6 -5.62 -1.497
PLCB1 phospholipase C beta 1 20 4.69 8.683
IL24 interleukin 24 1 -5.12 -1.612
MT1H metallothionein 1H 16 6.35 -1.630
ZNF98 zinc finger protein 98 19 -2.71 4.130
NR2F2-AS1 NR2F2 antisense RNA 1 15 5.29 8.198
TDGF1 teratocarcinoma-derived growth factor 1 3 -7.02 -0.681
LINC01147 long intergenic non-protein coding RNA 1147 14 -5.33 -0.882
LINC00964 long intergenic non-protein coding RNA 964 8 -2.71 1.979
t P.Value adj.P.Val
ZFP57 -8.80 2.01e-09 0.000037
SLC38A8 -7.48 3.76e-08 0.000347
APOA2 6.55 3.51e-07 0.001751
DAB1 -6.51 3.79e-07 0.001751
SYNPR 6.35 5.83e-07 0.001859
BMP10 6.35 6.04e-07 0.001859
FAM155A 6.24 7.82e-07 0.002063
SHOX2 6.03 1.44e-06 0.003323
FLG-AS1 -5.84 2.06e-06 0.004233
NAV1 -5.78 2.37e-06 0.004372
C4orf54 -5.66 3.46e-06 0.005813
LINC02531 -5.58 4.25e-06 0.006544
PLCB1 5.51 4.92e-06 0.006983
IL24 -5.48 5.42e-06 0.007143
MT1H 5.37 7.64e-06 0.009403
ZNF98 -5.27 8.98e-06 0.009802
NR2F2-AS1 5.29 9.02e-06 0.009802
TDGF1 -5.28 9.75e-06 0.009999
LINC01147 -5.13 1.37e-05 0.012799
LINC00964 -5.10 1.39e-05 0.012799Interaction of sex differences between adult and young
topTreat(treat.cardio,coef=9,n=20,p.value=0.05)[,-c(1:3)] GENENAME CHR logFC AveExpr
TOGARAM2 TOG array regulator of axonemal microtubules 2 2 5.12 2.758
C4orf54 chromosome 4 open reading frame 54 4 5.66 -1.271
TKT transketolase 3 3.63 4.745
LUCAT1 lung cancer associated transcript 1 5 8.13 2.984
XIRP2-AS1 XIRP2 antisense RNA 1 2 7.32 -1.220
NTN1 netrin 1 17 3.70 5.133
GBE1 1,4-alpha-glucan branching enzyme 1 3 2.41 7.950
RHOBTB1 Rho related BTB domain containing 1 10 -2.56 6.032
INPP5J inositol polyphosphate-5-phosphatase J 22 4.12 0.913
LINC00964 long intergenic non-protein coding RNA 964 8 4.01 1.979
GRAMD1B GRAM domain containing 1B 11 2.35 5.349
PDK4 pyruvate dehydrogenase kinase 4 7 -4.67 6.558
STC2 stanniocalcin 2 5 4.89 1.232
SLC38A8 solute carrier family 38 member 8 16 5.05 0.289
ABCC3 ATP binding cassette subfamily C member 3 17 4.57 2.658
PPM1K-DT PPM1K divergent transcript 4 4.18 2.479
MYL12A myosin light chain 12A 18 -3.10 5.979
PIK3R1 phosphoinositide-3-kinase regulatory subunit 1 5 -2.78 8.062
LINC02506 long intergenic non-protein coding RNA 2506 4 5.43 1.150
MET MET proto-oncogene, receptor tyrosine kinase 7 3.22 2.549
t P.Value adj.P.Val
TOGARAM2 13.42 2.60e-13 4.80e-09
C4orf54 9.61 3.22e-10 2.00e-06
TKT 9.59 3.25e-10 2.00e-06
LUCAT1 8.94 1.42e-09 6.54e-06
XIRP2-AS1 8.75 2.10e-09 7.09e-06
NTN1 8.68 2.31e-09 7.09e-06
GBE1 7.86 1.46e-08 3.86e-05
RHOBTB1 -7.61 2.62e-08 6.04e-05
INPP5J 7.53 3.24e-08 6.65e-05
LINC00964 7.26 6.06e-08 1.12e-04
GRAMD1B 6.74 2.15e-07 3.61e-04
PDK4 -6.65 2.75e-07 4.02e-04
STC2 6.64 2.83e-07 4.02e-04
SLC38A8 6.60 3.11e-07 4.10e-04
ABCC3 5.96 1.53e-06 1.89e-03
PPM1K-DT 5.67 3.21e-06 3.53e-03
MYL12A -5.66 3.25e-06 3.53e-03
PIK3R1 -5.58 4.03e-06 4.13e-03
LINC02506 5.56 4.42e-06 4.30e-03
MET 5.50 4.89e-06 4.47e-03par(mar=c(5,5,3,2))
plot(treat.cardio$coefficients[,1],treat.cardio$coefficients[,2],xlab="logFC: Young vs Fetal", ylab="logFC: Adult vs Fetal",main="Cardiomyocytes: Development",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0,col=colours()[c(175)])
sig.genes <- dt.cardio[,1] !=0 | dt.cardio[,2] != 0
text(treat.cardio$coefficients[sig.genes,1],treat.cardio$coefficients[sig.genes,2],labels=rownames(dt.cardio)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.cardio$coefficients[,4],treat.cardio$coefficients[,5],xlab="logFC: Fetal Male vs Female", ylab="logFC: Young Male vs Female",main="Cardiomyocytes: Sex differences - fetal and young",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
sig.genes <- dt.cardio[,4] !=0 | dt.cardio[,5] != 0
text(treat.cardio$coefficients[sig.genes,4],treat.cardio$coefficients[sig.genes,5],labels=rownames(dt.cardio)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.cardio$coefficients[,4],treat.cardio$coefficients[,6],xlab="logFC: Fetal Male vs Female", ylab="logFC: Adult Male vs Female",main="Cardiomyocytes: Sex differences - fetal and adult",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
sig.genes <- dt.cardio[,4] !=0 | dt.cardio[,6] != 0
text(treat.cardio$coefficients[sig.genes,4],treat.cardio$coefficients[sig.genes,6],labels=rownames(dt.cardio)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.cardio$coefficients[,5],treat.cardio$coefficients[,6],xlab="logFC: Young Male vs Female", ylab="logFC: Adult Male vs Female",main="Cardiomyocytes: Sex differences - young and adult",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
sig.genes <- dt.cardio[,5] !=0 | dt.cardio[,6] != 0
text(treat.cardio$coefficients[sig.genes,5],treat.cardio$coefficients[sig.genes,6],labels=rownames(dt.cardio)[sig.genes],col=2,cex=0.6)
abline(h=0,v=0)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.cardio$coefficients[,4],treat.cardio$coefficients[,5],xlab="logFC: Fetal Male vs Female", ylab="logFC: Young Male vs Female",main="Cardiomyocytes: Interaction term: Fetal vs Young",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
sig.genes <- dt.cardio[,8] !=0
text(treat.cardio$coefficients[sig.genes,4],treat.cardio$coefficients[sig.genes,5],labels=rownames(dt.cardio)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.cardio$coefficients[,4],treat.cardio$coefficients[,6],xlab="logFC: Fetal Male vs Female", ylab="logFC: Adult Male vs Female",main="Cardiomyocytes: Interaction term: fetal and adult",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
sig.genes <- dt.cardio[,7] !=0
text(treat.cardio$coefficients[sig.genes,4],treat.cardio$coefficients[sig.genes,6],labels=rownames(dt.cardio)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.cardio$coefficients[,5],treat.cardio$coefficients[,6],xlab="logFC: Young Male vs Female", ylab="logFC: Adult Male vs Female",main="Cardiomyocytes: Interaction term: young and adult",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
sig.genes <- dt.cardio[,9] !=0
text(treat.cardio$coefficients[sig.genes,5],treat.cardio$coefficients[sig.genes,6],labels=rownames(dt.cardio)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
Epicardial cells
cont.epi <- makeContrasts(YvF = 0.5*(epicardial.young.Male + epicardial.young.Female) - 0.5*(epicardial.fetal.Male + epicardial.fetal.Female),
AvF = 0.5*(epicardial.adult.Male + epicardial.adult.Female) - 0.5*(epicardial.fetal.Male + epicardial.fetal.Female),
AvY = 0.5*(epicardial.adult.Male + epicardial.adult.Female) - 0.5*(epicardial.young.Male + epicardial.young.Female),
SexFetal = epicardial.fetal.Male - epicardial.fetal.Female,
SexYoung = epicardial.young.Male - epicardial.young.Female,
SexAdult = epicardial.adult.Male - epicardial.adult.Female,
InteractionAF = (epicardial.adult.Male - epicardial.fetal.Male) - (epicardial.adult.Female - epicardial.fetal.Female),
InteractionYF = (epicardial.young.Male - epicardial.fetal.Male) - (epicardial.young.Female - epicardial.fetal.Female),
InteractionAY = (epicardial.adult.Male - epicardial.young.Male) - (epicardial.adult.Female - epicardial.young.Female),
levels=design)
fit.epicardial <- contrasts.fit(fit,contrasts = cont.epi)
fit.epicardial <- eBayes(fit.epicardial,robust=TRUE)
summary(decideTests(fit.epicardial)) YvF AvF AvY SexFetal SexYoung SexAdult InteractionAF
Down 1583 1553 0 2 0 0 0
NotSig 15745 15623 18464 18461 18464 18463 18464
Up 1136 1288 0 1 0 1 0
InteractionYF InteractionAY
Down 0 0
NotSig 18464 18464
Up 0 0treat.epicardial <- treat(fit.epicardial,lfc=0.5)
dt.epicardial<-decideTests(treat.epicardial)
summary(dt.epicardial) YvF AvF AvY SexFetal SexYoung SexAdult InteractionAF
Down 906 924 0 2 0 0 0
NotSig 17175 17044 18464 18461 18464 18463 18464
Up 383 496 0 1 0 1 0
InteractionYF InteractionAY
Down 0 0
NotSig 18464 18464
Up 0 0par(mfrow=c(3,3))
for(i in 1:9){
plotMD(treat.epicardial,coef=i,status=dt.epicardial[,i],hl.col=c("blue","red"))
abline(h=0,col="grey")
}
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
par(mfrow=c(1,1))
par(mar=c(7,4,2,2))
barplot(summary(dt.epicardial)[-2,],beside=TRUE,legend=TRUE,col=c("blue","red"),ylab="Number of significant genes",las=2)
title("Epicardial cells")
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
Young vs Fetal
options(digits=3)
topTreat(treat.epicardial,coef=1,n=20,p.value=0.05)[,-c(1:3)] GENENAME CHR
PIEZO2 piezo type mechanosensitive ion channel component 2 18
MOCS1 molybdenum cofactor synthesis 1 6
STEAP4 STEAP4 metalloreductase 7
ABCA5 ATP binding cassette subfamily A member 5 17
DENND3 DENN domain containing 3 8
CNTNAP2 contactin associated protein like 2 7
EFHD1 EF-hand domain family member D1 2
COL6A6 collagen type VI alpha 6 chain 3
IGF2BP1 insulin like growth factor 2 mRNA binding protein 1 17
SULT1E1 sulfotransferase family 1E member 1 4
GLRB glycine receptor beta 4
FRMD3 FERM domain containing 3 9
GLP1R glucagon like peptide 1 receptor 6
MARCH11 membrane associated ring-CH-type finger 11 5
EGFLAM EGF like, fibronectin type III and laminin G domains 5
SLC17A4 solute carrier family 17 member 4 6
PRICKLE1 prickle planar cell polarity protein 1 12
IGF2BP3 insulin like growth factor 2 mRNA binding protein 3 7
PACSIN2 protein kinase C and casein kinase substrate in neurons 2 22
PRSS35 serine protease 35 6
logFC AveExpr t P.Value adj.P.Val
PIEZO2 -5.55 4.448 -11.74 4.92e-12 9.08e-08
MOCS1 3.08 3.916 10.65 3.76e-11 3.21e-07
STEAP4 5.88 4.161 10.50 5.21e-11 3.21e-07
ABCA5 3.34 6.005 10.11 1.12e-10 3.69e-07
DENND3 4.98 5.553 10.10 1.15e-10 3.69e-07
CNTNAP2 -5.51 6.678 -10.08 1.20e-10 3.69e-07
EFHD1 4.18 4.405 9.55 3.54e-10 9.34e-07
COL6A6 -5.52 4.996 -9.47 4.27e-10 9.85e-07
IGF2BP1 -6.52 1.905 -9.40 5.05e-10 1.04e-06
SULT1E1 -7.24 0.545 -9.14 9.04e-10 1.67e-06
GLRB -6.53 2.601 -8.73 2.18e-09 3.24e-06
FRMD3 2.73 7.605 8.67 2.35e-09 3.24e-06
GLP1R -6.18 1.486 -8.66 2.50e-09 3.24e-06
MARCH11 -8.30 3.233 -8.68 2.50e-09 3.24e-06
EGFLAM 3.96 5.588 8.62 2.63e-09 3.24e-06
SLC17A4 4.53 -1.342 8.36 4.75e-09 5.48e-06
PRICKLE1 -4.34 7.047 -8.32 5.22e-09 5.67e-06
IGF2BP3 -5.27 4.676 -8.26 6.00e-09 6.16e-06
PACSIN2 2.21 7.829 8.21 6.53e-09 6.35e-06
PRSS35 -4.86 1.689 -8.13 8.00e-09 7.38e-06Adult vs Fetal
topTreat(treat.epicardial,coef=2,n=20,p.value=0.05)[,-c(1:3)] GENENAME CHR logFC
PIEZO2 piezo type mechanosensitive ion channel component 2 18 -7.06
SULT1E1 sulfotransferase family 1E member 1 4 -9.26
SNX31 sorting nexin 31 8 6.00
PRSS35 serine protease 35 6 -6.35
CNTNAP2 contactin associated protein like 2 7 -4.56
LYPD6 LY6/PLAUR domain containing 6 2 -6.90
EFHD1 EF-hand domain family member D1 2 4.36
EGFLAM EGF like, fibronectin type III and laminin G domains 5 4.24
STEAP4 STEAP4 metalloreductase 7 5.45
IGF2BP1 insulin like growth factor 2 mRNA binding protein 1 17 -6.45
COL6A6 collagen type VI alpha 6 chain 3 -4.83
MOCS1 molybdenum cofactor synthesis 1 6 2.76
SNCG synuclein gamma 10 6.31
ABCA5 ATP binding cassette subfamily A member 5 17 3.01
GDF6 growth differentiation factor 6 8 -6.41
IGF2BP3 insulin like growth factor 2 mRNA binding protein 3 7 -5.73
XKR5 XK related 5 8 -4.88
SGO1 shugoshin 1 3 -5.29
LINC02237 long intergenic non-protein coding RNA 2237 8 3.04
KLHL23 kelch like family member 23 2 2.46
AveExpr t P.Value adj.P.Val
PIEZO2 4.448 -12.52 1.24e-12 2.29e-08
SULT1E1 0.545 -11.93 3.73e-12 3.44e-08
SNX31 2.672 11.27 1.19e-11 7.30e-08
PRSS35 1.689 -10.64 4.04e-11 1.87e-07
CNTNAP2 6.678 -10.27 8.15e-11 2.93e-07
LYPD6 2.890 -10.21 9.53e-11 2.93e-07
EFHD1 4.405 10.05 1.28e-10 3.36e-07
EGFLAM 5.588 9.46 4.27e-10 9.04e-07
STEAP4 4.161 9.46 4.41e-10 9.04e-07
IGF2BP1 1.905 -9.33 5.82e-10 1.07e-06
COL6A6 4.996 -9.19 7.71e-10 1.24e-06
MOCS1 3.916 9.16 8.03e-10 1.24e-06
SNCG 1.517 9.00 1.20e-09 1.70e-06
ABCA5 6.005 8.77 1.88e-09 2.45e-06
GDF6 0.832 -8.76 1.99e-09 2.45e-06
IGF2BP3 4.676 -8.71 2.21e-09 2.55e-06
XKR5 0.124 -8.30 5.45e-09 5.92e-06
SGO1 1.725 -8.13 8.17e-09 8.29e-06
LINC02237 3.300 8.10 8.53e-09 8.29e-06
KLHL23 6.288 8.00 1.05e-08 9.56e-06Adult vs Young
topTreat(treat.epicardial,coef=3)[,-c(1:3)] GENENAME CHR logFC AveExpr
SNX31 sorting nexin 31 8 2.20 2.6724
PQLC2L PQ loop repeat containing 2 like 3 3.72 1.6416
CCL8 C-C motif chemokine ligand 8 17 -3.15 -0.5607
TNFSF15 TNF superfamily member 15 9 3.27 -0.2964
SCGN secretagogin, EF-hand calcium binding protein 6 -2.46 1.6456
NOS1AP nitric oxide synthase 1 adaptor protein 1 -2.69 4.4866
SPTSSB serine palmitoyltransferase small subunit B 3 3.85 -0.0464
GALNT8 polypeptide N-acetylgalactosaminyltransferase 8 12 -3.01 2.2605
FOSL1 FOS like 1, AP-1 transcription factor subunit 11 -3.27 1.1629
NXPH3 neurexophilin 3 17 2.28 0.6529
t P.Value adj.P.Val
SNX31 4.30 0.000112 1
PQLC2L 4.06 0.000218 1
CCL8 -3.96 0.000276 1
TNFSF15 3.87 0.000345 1
SCGN -3.75 0.000464 1
NOS1AP -3.52 0.000837 1
SPTSSB 3.44 0.001086 1
GALNT8 -3.38 0.001199 1
FOSL1 -3.25 0.001698 1
NXPH3 3.23 0.001719 1Male vs Female in fetal samples
topTreat(treat.epicardial,coef=4)[,-c(1:3)] GENENAME CHR logFC AveExpr
ZFP57 ZFP57 zinc finger protein 6 6.35 0.270
NMUR2 neuromedin U receptor 2 5 -4.32 -0.989
EPHA4 EPH receptor A4 2 -3.73 5.247
HIST1H2AG histone cluster 1 H2A family member g 6 4.16 -0.464
ZNF385B zinc finger protein 385B 2 -3.40 3.787
GRM7 glutamate metabotropic receptor 7 3 -2.52 3.350
TDGF1 teratocarcinoma-derived growth factor 1 3 4.51 -0.681
PATE2 prostate and testis expressed 2 11 -3.80 -1.342
FAM155A family with sequence similarity 155 member A 13 -2.53 5.622
LMX1A LIM homeobox transcription factor 1 alpha 1 -3.08 -0.189
t P.Value adj.P.Val
ZFP57 6.11 1.10e-06 0.0203
NMUR2 -5.48 5.26e-06 0.0417
EPHA4 -5.38 6.78e-06 0.0417
HIST1H2AG 4.47 7.54e-05 0.3151
ZNF385B -4.41 8.53e-05 0.3151
GRM7 -4.20 1.44e-04 0.4425
TDGF1 4.16 1.69e-04 0.4470
PATE2 -3.96 2.83e-04 0.5943
FAM155A -3.93 2.90e-04 0.5943
LMX1A -3.71 5.29e-04 0.9270Male vs Female in young samples
topTreat(treat.epicardial,coef=5)[,-c(1:3)] GENENAME CHR logFC AveExpr
NXPH3 neurexophilin 3 17 4.51 0.653
ALLC allantoicase 2 -3.41 0.904
ZNF304 zinc finger protein 304 19 4.29 2.425
CCL8 C-C motif chemokine ligand 8 17 -4.38 -0.561
SLC17A4 solute carrier family 17 member 4 6 -3.18 -1.342
TESC-AS1 TESC antisense RNA 1 (head to head) 12 3.48 1.742
THSD7B thrombospondin type 1 domain containing 7B 2 -2.88 3.773
TMEM54 transmembrane protein 54 1 3.85 1.041
CTXND2 cortexin domain containing 2 1 3.05 0.558
KLF5 Kruppel like factor 5 13 3.92 2.466
t P.Value adj.P.Val
NXPH3 4.97 2.00e-05 0.369
ALLC -4.43 8.12e-05 0.489
ZNF304 4.32 1.13e-04 0.489
CCL8 -4.26 1.29e-04 0.489
SLC17A4 -4.18 1.54e-04 0.489
TESC-AS1 4.17 1.59e-04 0.489
THSD7B -4.08 2.00e-04 0.527
TMEM54 4.04 2.29e-04 0.529
CTXND2 3.77 4.44e-04 0.882
KLF5 3.76 4.78e-04 0.882Male vs Female in adult samples
topTreat(treat.epicardial,coef=6)[,-c(1:3)] GENENAME CHR logFC AveExpr
HESX1 HESX homeobox 1 3 5.45 2.750
THNSL2 threonine synthase like 2 2 5.55 3.382
RIMS1 regulating synaptic membrane exocytosis 1 6 7.80 3.166
LINC01768 long intergenic non-protein coding RNA 1768 1 4.30 1.303
LINC01703 long intergenic non-protein coding RNA 1703 1 3.32 1.078
TMEM17 transmembrane protein 17 2 3.86 1.245
CPB2 carboxypeptidase B2 13 3.36 0.912
SCG5 secretogranin V 15 3.62 2.342
LINC02507 long intergenic non-protein coding RNA 2507 4 4.69 0.616
MT1A metallothionein 1A 16 -4.85 0.061
t P.Value adj.P.Val
HESX1 6.36 5.79e-07 0.0107
THNSL2 4.45 8.42e-05 0.7770
RIMS1 4.31 1.31e-04 0.8089
LINC01768 3.96 2.84e-04 0.8834
LINC01703 3.92 3.06e-04 0.8834
TMEM17 3.87 3.54e-04 0.8834
CPB2 3.85 3.72e-04 0.8834
SCG5 3.84 3.83e-04 0.8834
LINC02507 3.76 4.91e-04 0.9475
MT1A -3.73 5.44e-04 0.9475Interaction of sex differences between adult and fetal
topTreat(treat.epicardial,coef=7)[,-c(1:3)] GENENAME CHR logFC
HESX1 HESX homeobox 1 3 5.76
CLDN7 claudin 7 17 -7.59
LINC01768 long intergenic non-protein coding RNA 1768 1 5.85
C1orf141 chromosome 1 open reading frame 141 1 5.29
UFSP1 UFM1 specific peptidase 1 (inactive) 7 -5.36
LINC02604 long intergenic non-protein coding RNA 2604 7 5.16
GLRA3 glycine receptor alpha 3 4 5.08
THNSL2 threonine synthase like 2 2 5.68
OR7D2 olfactory receptor family 7 subfamily D member 2 19 -5.53
MT1A metallothionein 1A 16 -7.84
AveExpr t P.Value adj.P.Val
HESX1 2.7500 5.08 1.58e-05 0.291
CLDN7 -0.3517 -4.35 1.17e-04 0.881
LINC01768 1.3032 4.25 1.43e-04 0.881
C1orf141 1.2605 3.90 3.48e-04 1.000
UFSP1 -0.0981 -3.84 4.08e-04 1.000
LINC02604 0.7727 3.81 4.41e-04 1.000
GLRA3 -0.1054 3.79 4.69e-04 1.000
THNSL2 3.3820 3.76 5.20e-04 1.000
OR7D2 -0.3870 -3.69 6.18e-04 1.000
MT1A 0.0610 -3.71 6.45e-04 1.000Interaction of sex differences between young and fetal
topTreat(treat.epicardial,coef=8)[,-c(1:3)] GENENAME CHR logFC AveExpr
ZFP57 ZFP57 zinc finger protein 6 -6.78 0.2703
DCLK3 doublecortin like kinase 3 3 -4.28 -0.1446
NMUR2 neuromedin U receptor 2 5 4.76 -0.9891
PI4K2B phosphatidylinositol 4-kinase type 2 beta 4 5.10 1.3328
LRP1-AS LRP1 antisense RNA 12 -4.26 -1.5297
LINC02242 long intergenic non-protein coding RNA 2242 5 4.31 -0.4070
CCL8 C-C motif chemokine ligand 8 17 -5.24 -0.5607
ANGPT4 angiopoietin 4 20 -5.76 -0.1577
LINC00589 long intergenic non-protein coding RNA 589 8 4.94 0.0723
OASL 2'-5'-oligoadenylate synthetase like 12 -4.40 0.5243
t P.Value adj.P.Val
ZFP57 -4.41 9.85e-05 1
DCLK3 -4.10 1.99e-04 1
NMUR2 3.97 2.85e-04 1
PI4K2B 3.57 8.21e-04 1
LRP1-AS -3.55 8.33e-04 1
LINC02242 3.50 9.45e-04 1
CCL8 -3.47 1.08e-03 1
ANGPT4 -3.43 1.22e-03 1
LINC00589 3.41 1.24e-03 1
OASL -3.29 1.63e-03 1Interaction of sex differences between adult and young
topTreat(treat.epicardial,coef=9)[,-c(1:3)] GENENAME CHR logFC
HESX1 HESX homeobox 1 3 5.98
LINC00587 long intergenic non-protein coding RNA 587 9 4.87
GALNT3 polypeptide N-acetylgalactosaminyltransferase 3 2 7.91
PLA2G4C-AS1 PLA2G4C antisense RNA 1 19 -5.21
NR1D2 nuclear receptor subfamily 1 group D member 2 3 -2.88
TOX2 TOX high mobility group box family member 2 20 6.32
C4orf51 chromosome 4 open reading frame 51 4 -4.60
FBXL13 F-box and leucine rich repeat protein 13 7 -2.96
NXPH3 neurexophilin 3 17 -4.41
E2F1 E2F transcription factor 1 20 6.84
AveExpr t P.Value adj.P.Val
HESX1 2.750 4.82 3.13e-05 0.578
LINC00587 -0.337 4.10 2.04e-04 1.000
GALNT3 1.793 4.14 2.08e-04 1.000
PLA2G4C-AS1 -0.240 -3.78 4.85e-04 1.000
NR1D2 6.278 -3.73 4.90e-04 1.000
TOX2 3.868 3.74 5.70e-04 1.000
C4orf51 1.512 -3.69 5.84e-04 1.000
FBXL13 5.165 -3.57 7.44e-04 1.000
NXPH3 0.653 -3.55 8.50e-04 1.000
E2F1 1.392 3.58 8.74e-04 1.000par(mar=c(5,5,3,2))
plot(treat.epicardial$coefficients[,1],treat.epicardial$coefficients[,2],xlab="logFC: Young vs Fetal", ylab="logFC: Adult vs Fetal",main="Epicardial: Development",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0,col=colours()[c(175)])
sig.genes <- dt.epicardial[,1] !=0 | dt.epicardial[,2] != 0
text(treat.epicardial$coefficients[sig.genes,1],treat.epicardial$coefficients[sig.genes,2],labels=rownames(dt.epicardial)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.epicardial$coefficients[,4],treat.epicardial$coefficients[,5],xlab="logFC: Fetal Male vs Female", ylab="logFC: Young Male vs Female",main="epicardial: Sex differences - fetal and young",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
sig.genes <- dt.epicardial[,4] !=0 | dt.epicardial[,5] != 0
text(treat.epicardial$coefficients[sig.genes,4],treat.epicardial$coefficients[sig.genes,5],labels=rownames(dt.epicardial)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.epicardial$coefficients[,4],treat.epicardial$coefficients[,6],xlab="logFC: Fetal Male vs Female", ylab="logFC: Adult Male vs Female",main="epicardial: Sex differences - fetal and adult",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
sig.genes <- dt.epicardial[,4] !=0 | dt.epicardial[,6] != 0
text(treat.epicardial$coefficients[sig.genes,4],treat.epicardial$coefficients[sig.genes,6],labels=rownames(dt.epicardial)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.epicardial$coefficients[,5],treat.epicardial$coefficients[,6],xlab="logFC: Young Male vs Female", ylab="logFC: Adult Male vs Female",main="epicardial: Sex differences - young and adult",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
sig.genes <- dt.epicardial[,5] !=0 | dt.epicardial[,6] != 0
text(treat.epicardial$coefficients[sig.genes,5],treat.epicardial$coefficients[sig.genes,6],labels=rownames(dt.epicardial)[sig.genes],col=2,cex=0.6)
abline(h=0,v=0)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.epicardial$coefficients[,4],treat.epicardial$coefficients[,5],xlab="logFC: Fetal Male vs Female", ylab="logFC: Young Male vs Female",main="epicardial: Interaction term: Fetal vs Young",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
sig.genes <- dt.epicardial[,8] !=0
if(sum(sig.genes)!=0){
text(treat.epicardial$coefficients[sig.genes,4],treat.epicardial$coefficients[sig.genes,5],
labels=rownames(dt.epicardial)[sig.genes],col=2,cex=0.6)
}plot(treat.epicardial$coefficients[,4],treat.epicardial$coefficients[,6],xlab="logFC: Fetal Male vs Female", ylab="logFC: Adult Male vs Female",main="epicardial: Interaction term: fetal and adult",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
sig.genes <- dt.epicardial[,7] !=0
if(sum(sig.genes)!=0){
text(treat.epicardial$coefficients[sig.genes,4],treat.epicardial$coefficients[sig.genes,6],
labels=rownames(dt.epicardial)[sig.genes],col=2,cex=0.6)
}plot(treat.epicardial$coefficients[,5],treat.epicardial$coefficients[,6],xlab="logFC: Young Male vs Female", ylab="logFC: Adult Male vs Female",main="epicardial: Interaction term: young and adult",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
sig.genes <- dt.epicardial[,9] !=0
if(sum(sig.genes)!=0){
text(treat.epicardial$coefficients[sig.genes,5],treat.epicardial$coefficients[sig.genes,6],
labels=rownames(dt.epicardial)[sig.genes],col=2,cex=0.6)
}Fibroblasts
cont.fibro <- makeContrasts(YvF = 0.5*(fibro.young.Male + fibro.young.Female) - 0.5*(fibro.fetal.Male + fibro.fetal.Female),
AvF = 0.5*(fibro.adult.Male + fibro.adult.Female) - 0.5*(fibro.fetal.Male + fibro.fetal.Female),
AvY = 0.5*(fibro.adult.Male + fibro.adult.Female) - 0.5*(fibro.young.Male + fibro.young.Female),
SexFetal = fibro.fetal.Male - fibro.fetal.Female,
SexYoung = fibro.young.Male - fibro.young.Female,
SexAdult = fibro.adult.Male - fibro.adult.Female,
InteractionAF = (fibro.adult.Male - fibro.fetal.Male) - (fibro.adult.Female - fibro.fetal.Female),
InteractionYF = (fibro.young.Male - fibro.fetal.Male) - (fibro.young.Female - fibro.fetal.Female),
InteractionAY = (fibro.adult.Male - fibro.young.Male) - (fibro.adult.Female - fibro.young.Female),
levels=design)
fit.fibro <- contrasts.fit(fit,contrasts = cont.fibro)
fit.fibro <- eBayes(fit.fibro,robust=TRUE)
summary(decideTests(fit.fibro)) YvF AvF AvY SexFetal SexYoung SexAdult InteractionAF
Down 1983 1546 63 10 25 15 4
NotSig 14894 15710 18356 18452 18433 18445 18459
Up 1587 1208 45 2 6 4 1
InteractionYF InteractionAY
Down 0 12
NotSig 18464 18444
Up 0 8treat.fibro <- treat(fit.fibro,lfc=0.5)
dt.fibro<-decideTests(treat.fibro)
summary(dt.fibro) YvF AvF AvY SexFetal SexYoung SexAdult InteractionAF
Down 830 668 5 4 4 5 2
NotSig 17012 17299 18451 18460 18459 18459 18461
Up 622 497 8 0 1 0 1
InteractionYF InteractionAY
Down 0 7
NotSig 18464 18453
Up 0 4par(mfrow=c(3,3))
for(i in 1:9){
plotMD(treat.fibro,coef=i,status=dt.fibro[,i],hl.col=c("blue","red"))
abline(h=0,col="grey")
}
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
par(mfrow=c(1,1))
par(mar=c(7,4,2,2))
barplot(summary(dt.fibro)[-2,],beside=TRUE,legend=TRUE,col=c("blue","red"),ylab="Number of significant genes",las=2)
title("fibroblast cells")
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
Young vs Fetal
options(digits=3)
topTreat(treat.fibro,coef=1,n=20,p.value=0.05)[,-c(1:3)] GENENAME
CNTNAP2 contactin associated protein like 2
PIEZO2 piezo type mechanosensitive ion channel component 2
LAMA2 laminin subunit alpha 2
COL6A6 collagen type VI alpha 6 chain
MTUS1 microtubule associated scaffold protein 1
MEST mesoderm specific transcript
IGF2BP3 insulin like growth factor 2 mRNA binding protein 3
MANCR mitotically associated long non coding RNA
SULT1E1 sulfotransferase family 1E member 1
ABCA5 ATP binding cassette subfamily A member 5
JADE1 jade family PHD finger 1
CACNB4 calcium voltage-gated channel auxiliary subunit beta 4
ELFN2 extracellular leucine rich repeat and fibronectin type III domain containing 2
KHDRBS2 KH RNA binding domain containing, signal transduction associated 2
HHIP hedgehog interacting protein
DPP10 dipeptidyl peptidase like 10
GRID2 glutamate ionotropic receptor delta type subunit 2
HUNK hormonally up-regulated Neu-associated kinase
HTATIP2 HIV-1 Tat interactive protein 2
PTCH2 patched 2
CHR logFC AveExpr t P.Value adj.P.Val
CNTNAP2 7 -3.49 6.678 -18.0 2.87e-16 5.29e-12
PIEZO2 18 -4.71 4.448 -14.7 3.14e-14 2.90e-10
LAMA2 6 3.91 10.484 14.4 4.89e-14 3.01e-10
COL6A6 3 -2.83 4.996 -13.7 1.70e-13 7.87e-10
MTUS1 8 3.38 7.791 13.2 3.75e-13 1.38e-09
MEST 7 -5.99 3.378 -13.1 4.79e-13 1.48e-09
IGF2BP3 7 -5.84 4.676 -12.8 8.06e-13 2.12e-09
MANCR 10 8.96 0.425 12.4 1.49e-12 3.43e-09
SULT1E1 4 -9.64 0.545 -12.1 2.82e-12 5.79e-09
ABCA5 17 3.39 6.005 11.9 3.59e-12 6.63e-09
JADE1 4 3.50 6.188 11.7 5.67e-12 9.41e-09
CACNB4 2 -3.79 4.275 -11.6 6.20e-12 9.41e-09
ELFN2 22 -6.29 0.103 -11.6 6.62e-12 9.41e-09
KHDRBS2 6 -4.56 3.746 -11.5 8.02e-12 1.06e-08
HHIP 4 -4.75 3.428 -11.1 1.56e-11 1.91e-08
DPP10 2 -4.41 4.348 -10.9 2.28e-11 2.63e-08
GRID2 4 -5.35 5.329 -10.8 2.95e-11 3.21e-08
HUNK 21 -4.14 3.464 -10.6 4.04e-11 3.97e-08
HTATIP2 11 5.56 2.925 10.6 4.09e-11 3.97e-08
PTCH2 1 -3.97 3.542 -10.5 5.15e-11 4.68e-08Adult vs Fetal
topTreat(treat.fibro,coef=2,n=20,p.value=0.05)[,-c(1:3)] GENENAME
CNTNAP2 contactin associated protein like 2
LAMA2 laminin subunit alpha 2
PIEZO2 piezo type mechanosensitive ion channel component 2
MTUS1 microtubule associated scaffold protein 1
COL6A6 collagen type VI alpha 6 chain
C11orf87 chromosome 11 open reading frame 87
LINC02511 long intergenic non-protein coding RNA 2511
IGF2BP3 insulin like growth factor 2 mRNA binding protein 3
MEST mesoderm specific transcript
COL28A1 collagen type XXVIII alpha 1 chain
PRSS35 serine protease 35
PEG10 paternally expressed 10
TMEM26 transmembrane protein 26
HHIP hedgehog interacting protein
MANCR mitotically associated long non coding RNA
STRA6 stimulated by retinoic acid 6
VIT vitrin
KHDRBS2 KH RNA binding domain containing, signal transduction associated 2
SAMD5 sterile alpha motif domain containing 5
GRID2 glutamate ionotropic receptor delta type subunit 2
CHR logFC AveExpr t P.Value adj.P.Val
CNTNAP2 7 -3.13 6.678 -15.5 1.00e-14 1.85e-10
LAMA2 6 3.88 10.484 14.0 9.34e-14 8.62e-10
PIEZO2 18 -5.84 4.448 -13.8 1.43e-13 8.79e-10
MTUS1 8 3.41 7.791 13.0 5.07e-13 2.34e-09
COL6A6 3 -2.61 4.996 -11.8 4.19e-12 1.41e-08
C11orf87 11 -6.61 -0.653 -11.8 4.80e-12 1.41e-08
LINC02511 4 4.81 2.366 11.6 6.50e-12 1.41e-08
IGF2BP3 7 -5.78 4.676 -11.6 6.58e-12 1.41e-08
MEST 7 -6.12 3.378 -11.6 6.86e-12 1.41e-08
COL28A1 7 4.52 3.797 11.3 1.03e-11 1.72e-08
PRSS35 6 -6.82 1.689 -11.3 1.10e-11 1.72e-08
PEG10 7 -6.71 1.558 -11.3 1.12e-11 1.72e-08
TMEM26 10 -8.65 1.029 -11.2 1.49e-11 2.11e-08
HHIP 4 -5.80 3.428 -11.1 1.67e-11 2.21e-08
MANCR 10 8.25 0.425 11.0 2.03e-11 2.50e-08
STRA6 15 -6.17 -0.210 -10.8 3.09e-11 3.56e-08
VIT 2 5.66 2.889 10.5 5.17e-11 5.61e-08
KHDRBS2 6 -5.24 3.746 -10.4 6.52e-11 6.69e-08
SAMD5 6 -4.70 5.148 -10.3 7.13e-11 6.84e-08
GRID2 4 -5.14 5.329 -10.3 7.41e-11 6.84e-08Adult vs Young
topTreat(treat.fibro,coef=3,n=20,p.value=0.05)[,-c(1:3)] GENENAME CHR
LINC02511 long intergenic non-protein coding RNA 2511 4
TLL2 tolloid like 2 10
CCL11 C-C motif chemokine ligand 11 17
LGR5 leucine rich repeat containing G protein-coupled receptor 5 12
KCNN3 potassium calcium-activated channel subfamily N member 3 1
HIST1H1D histone cluster 1 H1 family member d 6
LINC01807 long intergenic non-protein coding RNA 1807 2
OR2A5 olfactory receptor family 2 subfamily A member 5 7
TBC1D3D TBC1 domain family member 3D 17
LMX1A LIM homeobox transcription factor 1 alpha 1
CLSTN2 calsyntenin 2 3
JADRR JADE1 adjacent regulatory RNA 4
LMO3 LIM domain only 3 12
logFC AveExpr t P.Value adj.P.Val
LINC02511 3.27 2.366 9.69 2.62e-10 4.84e-06
TLL2 3.38 3.375 7.55 3.06e-08 2.83e-04
CCL11 3.63 0.421 6.91 1.42e-07 8.74e-04
LGR5 -3.73 1.544 -6.48 4.11e-07 1.90e-03
KCNN3 3.96 3.689 6.30 6.45e-07 2.22e-03
HIST1H1D -5.45 1.959 -6.24 7.80e-07 2.22e-03
LINC01807 -3.00 1.589 -6.19 8.42e-07 2.22e-03
OR2A5 3.48 -1.639 5.84 2.05e-06 4.74e-03
TBC1D3D 2.99 -1.750 5.71 2.89e-06 5.93e-03
LMX1A 2.74 -0.189 5.30 8.18e-06 1.51e-02
CLSTN2 -2.10 5.208 -5.20 1.08e-05 1.70e-02
JADRR -4.09 -1.077 -5.20 1.10e-05 1.70e-02
LMO3 2.94 1.571 4.89 2.40e-05 3.41e-02Male vs Female in fetal samples
topTreat(treat.fibro,coef=4)[,-c(1:3)] GENENAME CHR logFC
NMUR2 neuromedin U receptor 2 5 -4.81
PDZRN4 PDZ domain containing ring finger 4 12 -3.78
COMP cartilage oligomeric matrix protein 19 -4.94
APOA2 apolipoprotein A2 1 -3.15
CILP2 cartilage intermediate layer protein 2 19 -3.12
PIEZO2 piezo type mechanosensitive ion channel component 2 18 -1.59
GREM1 gremlin 1, DAN family BMP antagonist 15 -4.85
LINC02117 long intergenic non-protein coding RNA 2117 5 3.12
GRM7 glutamate metabotropic receptor 7 3 -2.01
BTBD17 BTB domain containing 17 17 -4.05
AveExpr t P.Value adj.P.Val
NMUR2 -0.989 -7.05 1.03e-07 0.00191
PDZRN4 3.678 -6.62 2.91e-07 0.00269
COMP -0.265 -5.70 3.08e-06 0.01707
APOA2 -1.812 -5.61 3.70e-06 0.01707
CILP2 -0.780 -4.77 3.33e-05 0.09358
PIEZO2 4.448 -4.75 3.42e-05 0.09358
GREM1 0.200 -4.74 3.74e-05 0.09358
LINC02117 -1.503 4.69 4.05e-05 0.09358
GRM7 3.350 -4.45 7.65e-05 0.14471
BTBD17 -0.983 -4.42 8.41e-05 0.14471Male vs Female in young samples
topTreat(treat.fibro,coef=5)[,-c(1:3)] GENENAME CHR logFC
NR1D2 nuclear receptor subfamily 1 group D member 2 3 2.42
NTRK1 neurotrophic receptor tyrosine kinase 1 1 -2.52
LIPG lipase G, endothelial type 18 -4.25
VEPH1 ventricular zone expressed PH domain containing 1 3 -2.58
STC2 stanniocalcin 2 5 -4.15
PVT1 Pvt1 oncogene 8 -2.31
LINC01442 long intergenic non-protein coding RNA 1442 13 -3.94
CNBD1 cyclic nucleotide binding domain containing 1 8 2.48
UHRF1 ubiquitin like with PHD and ring finger domains 1 19 -2.97
NR1D1 nuclear receptor subfamily 1 group D member 1 17 4.27
AveExpr t P.Value adj.P.Val
NR1D2 6.278 5.78 2.39e-06 0.0351
NTRK1 1.790 -5.60 3.80e-06 0.0351
LIPG 0.838 -5.39 6.74e-06 0.0384
VEPH1 2.539 -5.30 8.33e-06 0.0384
STC2 1.232 -5.18 1.15e-05 0.0426
PVT1 5.407 -4.93 2.14e-05 0.0659
LINC01442 -1.202 -4.68 4.28e-05 0.1130
CNBD1 3.440 4.26 1.24e-04 0.2860
UHRF1 2.694 -4.21 1.42e-04 0.2874
NR1D1 2.081 4.19 1.56e-04 0.2874Male vs Female in adult samples
topTreat(treat.fibro,coef=6)[,-c(1:3)] GENENAME CHR logFC
CCL19 C-C motif chemokine ligand 19 9 -7.44
OR2A5 olfactory receptor family 2 subfamily A member 5 7 -4.58
LINC02511 long intergenic non-protein coding RNA 2511 4 -2.46
DPP10-AS1 DPP10 antisense RNA 1 2 -4.33
TBC1D3D TBC1 domain family member 3D 17 -3.75
DLD dihydrolipoamide dehydrogenase 7 -1.82
FAM90A26 family with sequence similarity 90 member A26 4 -3.73
LINC02026 long intergenic non-protein coding RNA 2026 3 4.64
BBOX1 gamma-butyrobetaine hydroxylase 1 11 -2.70
MME-AS1 MME antisense RNA 1 3 -3.11
AveExpr t P.Value adj.P.Val
CCL19 -0.977 -9.99 1.51e-10 2.79e-06
OR2A5 -1.639 -6.73 2.24e-07 1.51e-03
LINC02511 2.366 -6.69 2.45e-07 1.51e-03
DPP10-AS1 -1.138 -5.92 1.71e-06 7.83e-03
TBC1D3D -1.750 -5.83 2.12e-06 7.83e-03
DLD 5.526 -4.90 2.35e-05 5.28e-02
FAM90A26 -1.365 -4.90 2.40e-05 5.28e-02
LINC02026 0.804 4.90 2.43e-05 5.28e-02
BBOX1 0.750 -4.82 2.86e-05 5.28e-02
MME-AS1 -1.139 -4.83 2.86e-05 5.28e-02Interaction of sex differences between adult and fetal
topTreat(treat.fibro,coef=7)[,-c(1:3)] GENENAME
ADAMTS1 ADAM metallopeptidase with thrombospondin type 1 motif 1
PDZRN4 PDZ domain containing ring finger 4
DPP10-AS1 DPP10 antisense RNA 1
LINC01686 long intergenic non-protein coding RNA 1686
COMP cartilage oligomeric matrix protein
KCNG4 potassium voltage-gated channel modifier subfamily G member 4
OR2A5 olfactory receptor family 2 subfamily A member 5
LINC02026 long intergenic non-protein coding RNA 2026
TBC1D3D TBC1 domain family member 3D
NMUR2 neuromedin U receptor 2
CHR logFC AveExpr t P.Value adj.P.Val
ADAMTS1 21 -4.91 5.302 -6.00 1.43e-06 0.0187
PDZRN4 12 6.38 3.678 5.88 2.02e-06 0.0187
DPP10-AS1 2 -4.67 -1.138 -5.39 6.75e-06 0.0415
LINC01686 1 -7.01 -1.180 -5.03 1.88e-05 0.0866
COMP 19 6.83 -0.265 4.83 3.19e-05 0.1179
KCNG4 16 -5.16 -1.553 -4.68 4.51e-05 0.1387
OR2A5 7 -5.14 -1.639 -4.60 5.54e-05 0.1436
LINC02026 3 5.47 0.804 4.46 8.09e-05 0.1436
TBC1D3D 17 -4.30 -1.750 -4.37 9.65e-05 0.1436
NMUR2 5 5.02 -0.989 4.36 1.02e-04 0.1436Interaction of sex differences between young and fetal
topTreat(treat.fibro,coef=8)[,-c(1:3)] GENENAME CHR
CNBD1 cyclic nucleotide binding domain containing 1 8
NR1D2 nuclear receptor subfamily 1 group D member 2 3
BTBD17 BTB domain containing 17 17
PVT1 Pvt1 oncogene 8
LINC01799 long intergenic non-protein coding RNA 1799 2
ADAMTS1 ADAM metallopeptidase with thrombospondin type 1 motif 1 21
LINC01781 long intergenic non-protein coding RNA 1781 1
LINC02583 long intergenic non-protein coding RNA 2583 2
LINC01139 long intergenic non-protein coding RNA 1139 1
LRRTM4 leucine rich repeat transmembrane neuronal 4 2
logFC AveExpr t P.Value adj.P.Val
CNBD1 3.47 3.440 4.81 2.99e-05 0.415
NR1D2 2.56 6.278 4.45 7.61e-05 0.415
BTBD17 6.11 -0.983 4.45 8.58e-05 0.415
PVT1 -2.87 5.407 -4.39 9.00e-05 0.415
LINC01799 5.83 -0.899 4.24 1.45e-04 0.451
ADAMTS1 -3.06 5.302 -4.15 1.69e-04 0.451
LINC01781 5.39 -0.987 4.18 1.71e-04 0.451
LINC02583 -4.82 -1.576 -4.07 2.20e-04 0.465
LINC01139 5.21 -0.939 4.03 2.52e-04 0.465
LRRTM4 3.13 5.063 3.94 2.87e-04 0.465Interaction of sex differences between adult and young
topTreat(treat.fibro,coef=9)[,-c(1:3)] GENENAME CHR logFC
NTRK1 neurotrophic receptor tyrosine kinase 1 1 4.73
CCL19 C-C motif chemokine ligand 19 9 -6.99
NR1D2 nuclear receptor subfamily 1 group D member 2 3 -3.18
CYP4Z1 cytochrome P450 family 4 subfamily Z member 1 1 4.80
PER3 period circadian regulator 3 1 -4.06
SH3RF3-AS1 SH3RF3 antisense RNA 1 2 -6.15
LINC02511 long intergenic non-protein coding RNA 2511 4 -3.53
AKR1C1 aldo-keto reductase family 1 member C1 10 3.10
ARNTL aryl hydrocarbon receptor nuclear translocator like 11 4.32
BBOX1 gamma-butyrobetaine hydroxylase 1 11 -4.13
AveExpr t P.Value adj.P.Val
NTRK1 1.790 6.86 1.64e-07 0.00274
CCL19 -0.977 -6.64 2.97e-07 0.00274
NR1D2 6.278 -6.12 1.01e-06 0.00620
CYP4Z1 2.090 5.99 1.45e-06 0.00672
PER3 6.458 -5.39 6.63e-06 0.02133
SH3RF3-AS1 -1.236 -5.40 6.93e-06 0.02133
LINC02511 2.366 -5.30 8.35e-06 0.02201
AKR1C1 3.666 5.19 1.10e-05 0.02544
ARNTL 5.082 5.05 1.65e-05 0.03383
BBOX1 0.750 -4.93 2.24e-05 0.04134par(mar=c(5,5,3,2))
plot(treat.fibro$coefficients[,1],treat.fibro$coefficients[,2],xlab="logFC: Young vs Fetal", ylab="logFC: Adult vs Fetal",main="Fibroblasts: Development",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0,col=colours()[c(175)])
sig.genes <- dt.fibro[,1] !=0 | dt.fibro[,2] != 0
text(treat.fibro$coefficients[sig.genes,1],treat.fibro$coefficients[sig.genes,2],labels=rownames(dt.fibro)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.fibro$coefficients[,4],treat.fibro$coefficients[,5],xlab="logFC: Fetal Male vs Female", ylab="logFC: Young Male vs Female",main="Fibroblasts: Sex differences - fetal and young",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
sig.genes <- dt.fibro[,4] !=0 | dt.fibro[,5] != 0
text(treat.fibro$coefficients[sig.genes,4],treat.fibro$coefficients[sig.genes,5],labels=rownames(dt.fibro)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.fibro$coefficients[,4],treat.fibro$coefficients[,6],xlab="logFC: Fetal Male vs Female", ylab="logFC: Adult Male vs Female",main="Fibroblasts: Sex differences - fetal and adult",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
sig.genes <- dt.fibro[,4] !=0 | dt.fibro[,6] != 0
text(treat.fibro$coefficients[sig.genes,4],treat.fibro$coefficients[sig.genes,6],labels=rownames(dt.fibro)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.fibro$coefficients[,5],treat.fibro$coefficients[,6],xlab="logFC: Young Male vs Female", ylab="logFC: Adult Male vs Female",main="Fibroblasts: Sex differences - young and adult",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
sig.genes <- dt.fibro[,5] !=0 | dt.fibro[,6] != 0
text(treat.fibro$coefficients[sig.genes,5],treat.fibro$coefficients[sig.genes,6],labels=rownames(dt.fibro)[sig.genes],col=2,cex=0.6)
abline(h=0,v=0)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.fibro$coefficients[,4],treat.fibro$coefficients[,5],xlab="logFC: Fetal Male vs Female", ylab="logFC: Young Male vs Female",main="Fibroblasts: Interaction term: Fetal vs Young",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
sig.genes <- dt.fibro[,8] !=0
if(sum(sig.genes)!=0){
text(treat.fibro$coefficients[sig.genes,4],treat.fibro$coefficients[sig.genes,5],
labels=rownames(dt.fibro)[sig.genes],col=2,cex=0.6)
}plot(treat.fibro$coefficients[,4],treat.fibro$coefficients[,6],xlab="logFC: Fetal Male vs Female", ylab="logFC: Adult Male vs Female",main="Fibroblast: Interaction term: fetal and adult",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
sig.genes <- dt.fibro[,7] !=0
text(treat.fibro$coefficients[sig.genes,4],treat.fibro$coefficients[sig.genes,6],labels=rownames(dt.fibro)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.fibro$coefficients[,5],treat.fibro$coefficients[,6],xlab="logFC: Young Male vs Female", ylab="logFC: Adult Male vs Female",main="Fibroblasts: Interaction term: young and adult",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
sig.genes <- dt.fibro[,9] !=0
text(treat.fibro$coefficients[sig.genes,5],treat.fibro$coefficients[sig.genes,6],labels=rownames(dt.fibro)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
Smooth muscle cells
cont.smc <- makeContrasts(YvF = 0.5*(smc.young.Male + smc.young.Female) - 0.5*(smc.fetal.Male + smc.fetal.Female),
AvF = 0.5*(smc.adult.Male + smc.adult.Female) - 0.5*(smc.fetal.Male + smc.fetal.Female),
AvY = 0.5*(smc.adult.Male + smc.adult.Female) - 0.5*(smc.young.Male + smc.young.Female),
SexFetal = smc.fetal.Male - smc.fetal.Female,
SexYoung = smc.young.Male - smc.young.Female,
SexAdult = smc.adult.Male - smc.adult.Female,
InteractionAF = (smc.adult.Male - smc.fetal.Male) - (smc.adult.Female - smc.fetal.Female),
InteractionYF = (smc.young.Male - smc.fetal.Male) - (smc.young.Female - smc.fetal.Female),
InteractionAY = (smc.adult.Male - smc.young.Male) - (smc.adult.Female - smc.young.Female),
levels=design)
fit.smc <- contrasts.fit(fit,contrasts = cont.smc)
fit.smc <- eBayes(fit.smc,robust=TRUE)
summary(decideTests(fit.smc)) YvF AvF AvY SexFetal SexYoung SexAdult InteractionAF
Down 110 158 3 54 0 0 1
NotSig 18295 18250 18460 18381 18455 18433 18446
Up 59 56 1 29 9 31 17
InteractionYF InteractionAY
Down 3 0
NotSig 18456 18464
Up 5 0treat.smc <- treat(fit.smc,lfc=0.5)
dt.smc<-decideTests(treat.smc)
summary(dt.smc) YvF AvF AvY SexFetal SexYoung SexAdult InteractionAF
Down 32 53 0 30 0 0 0
NotSig 18418 18398 18464 18424 18461 18457 18460
Up 14 13 0 10 3 7 4
InteractionYF InteractionAY
Down 1 0
NotSig 18461 18464
Up 2 0par(mfrow=c(3,3))
for(i in 1:9){
plotMD(treat.smc,coef=i,status=dt.smc[,i],hl.col=c("blue","red"))
abline(h=0,col="grey")
}
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
par(mfrow=c(1,1))
par(mar=c(7,4,2,2))
barplot(summary(dt.smc)[-2,],beside=TRUE,legend=TRUE,col=c("blue","red"),ylab="Number of significant genes",las=2)
title("smooth muscle cells")
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
Young vs Fetal
options(digits=3)
topTreat(treat.smc,coef=1,n=20,p.value=0.05)[,-c(1:3)] GENENAME CHR logFC
SCN3A sodium voltage-gated channel alpha subunit 3 2 8.12
PIEZO2 piezo type mechanosensitive ion channel component 2 18 -4.77
PRSS35 serine protease 35 6 -4.81
GREM2 gremlin 2, DAN family BMP antagonist 1 -4.66
SULT1E1 sulfotransferase family 1E member 1 4 -6.12
EFNA5 ephrin A5 5 -7.63
ABCA5 ATP binding cassette subfamily A member 5 17 3.54
MEG3 maternally expressed 3 14 -6.54
CBFA2T3 CBFA2/RUNX1 translocation partner 3 16 5.53
SEMA6A semaphorin 6A 5 -3.69
IGF2BP3 insulin like growth factor 2 mRNA binding protein 3 7 -4.18
PRDM6 PR/SET domain 6 5 -4.83
SMO smoothened, frizzled class receptor 7 -3.44
TMEM140 transmembrane protein 140 7 4.75
LINC02507 long intergenic non-protein coding RNA 2507 4 -4.45
DIPK2A divergent protein kinase domain 2A 3 -2.56
CACNA1A calcium voltage-gated channel subunit alpha1 A 19 2.53
BCL7C BAF chromatin remodeling complex subunit BCL7C 16 -2.78
GPR137C G protein-coupled receptor 137C 14 -3.91
RAB7B RAB7B, member RAS oncogene family 1 -4.45
AveExpr t P.Value adj.P.Val
SCN3A 2.955 8.71 2.33e-09 0.000043
PIEZO2 4.448 -7.37 4.70e-08 0.000326
PRSS35 1.689 -7.33 5.29e-08 0.000326
GREM2 1.334 -7.18 7.42e-08 0.000343
SULT1E1 0.545 -6.72 2.41e-07 0.000889
EFNA5 6.711 -6.62 3.18e-07 0.000979
ABCA5 6.005 5.98 1.44e-06 0.003737
MEG3 4.906 -5.97 1.62e-06 0.003737
CBFA2T3 3.714 5.91 1.83e-06 0.003753
SEMA6A 5.381 -5.68 3.12e-06 0.005757
IGF2BP3 4.676 -5.62 3.65e-06 0.006123
PRDM6 3.380 -5.46 5.67e-06 0.008163
SMO 4.381 -5.43 5.89e-06 0.008163
TMEM140 4.006 5.43 6.19e-06 0.008163
LINC02507 0.616 -5.29 8.86e-06 0.010904
DIPK2A 5.372 -5.20 1.07e-05 0.012352
CACNA1A 4.507 5.11 1.34e-05 0.013870
BCL7C 6.149 -5.11 1.35e-05 0.013870
GPR137C 4.948 -5.04 1.64e-05 0.015402
RAB7B 2.594 -5.04 1.67e-05 0.015402Adult vs Fetal
topTreat(treat.smc,coef=2,n=20,p.value=0.05)[,-c(1:3)] GENENAME CHR
PIEZO2 piezo type mechanosensitive ion channel component 2 18
SCN3A sodium voltage-gated channel alpha subunit 3 2
GREM2 gremlin 2, DAN family BMP antagonist 1
MBOAT2 membrane bound O-acyltransferase domain containing 2 2
PRSS35 serine protease 35 6
ST6GALNAC5 ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 5 1
SULT1E1 sulfotransferase family 1E member 1 4
PRDM6 PR/SET domain 6 5
PRCD photoreceptor disc component 17
FSTL4 follistatin like 4 5
CNTN6 contactin 6 3
DIPK2A divergent protein kinase domain 2A 3
GRID2 glutamate ionotropic receptor delta type subunit 2 4
STRBP spermatid perinuclear RNA binding protein 9
ABCA5 ATP binding cassette subfamily A member 5 17
CBFA2T3 CBFA2/RUNX1 translocation partner 3 16
DIAPH3 diaphanous related formin 3 13
PRTFDC1 phosphoribosyl transferase domain containing 1 10
SEMA6A semaphorin 6A 5
MEGF6 multiple EGF like domains 6 1
logFC AveExpr t P.Value adj.P.Val
PIEZO2 -5.64 4.448 -9.25 6.91e-10 1.28e-05
SCN3A 8.27 2.955 8.61 2.97e-09 2.74e-05
GREM2 -4.87 1.334 -7.56 3.01e-08 1.86e-04
MBOAT2 -3.55 6.065 -7.24 6.37e-08 2.94e-04
PRSS35 -4.59 1.689 -6.94 1.35e-07 4.98e-04
ST6GALNAC5 -6.48 3.879 -6.79 2.01e-07 6.18e-04
SULT1E1 -6.00 0.545 -6.58 3.40e-07 8.94e-04
PRDM6 -5.54 3.380 -6.52 3.87e-07 8.94e-04
PRCD 4.58 2.370 6.44 4.56e-07 9.23e-04
FSTL4 4.71 1.475 6.41 5.00e-07 9.23e-04
CNTN6 -4.45 3.613 -6.15 9.52e-07 1.60e-03
DIPK2A -2.87 5.372 -5.83 2.10e-06 2.87e-03
GRID2 -5.63 5.329 -5.85 2.12e-06 2.87e-03
STRBP -3.28 5.934 -5.82 2.18e-06 2.87e-03
ABCA5 3.45 6.005 5.60 3.88e-06 4.61e-03
CBFA2T3 5.46 3.714 5.60 4.00e-06 4.61e-03
DIAPH3 -5.85 4.974 -5.56 4.48e-06 4.76e-03
PRTFDC1 -3.77 4.176 -5.52 4.79e-06 4.76e-03
SEMA6A -3.61 5.381 -5.48 5.26e-06 4.76e-03
MEGF6 -4.54 3.712 -5.47 5.51e-06 4.76e-03Adult vs Young
topTreat(treat.smc,coef=3)[,-c(1:3)] GENENAME CHR logFC AveExpr t
GBA glucosylceramidase beta 1 2.96 3.42 5.51
TUBGCP6 tubulin gamma complex associated protein 6 22 -2.86 3.60 -4.88
LIN52 lin-52 DREAM MuvB core complex component 14 -2.60 6.61 -4.68
ATXN7 ataxin 7 3 -2.92 4.72 -4.68
FSTL4 follistatin like 4 5 3.40 1.47 4.52
ALDH1A2 aldehyde dehydrogenase 1 family member A2 15 -4.16 5.63 -4.04
POLR2H RNA polymerase II subunit H 3 2.42 4.12 4.01
ZNF12 zinc finger protein 12 7 -2.43 4.69 -3.90
SUPV3L1 Suv3 like RNA helicase 10 -2.29 4.82 -3.73
PHF2 PHD finger protein 2 9 2.13 5.45 3.70
P.Value adj.P.Val
GBA 4.78e-06 0.0883
TUBGCP6 2.45e-05 0.1927
LIN52 4.13e-05 0.1927
ATXN7 4.17e-05 0.1927
FSTL4 6.36e-05 0.2349
ALDH1A2 2.28e-04 0.6205
POLR2H 2.35e-04 0.6205
ZNF12 3.18e-04 0.7336
SUPV3L1 4.92e-04 0.8469
PHF2 5.30e-04 0.8469Male vs Female in fetal samples
topTreat(treat.smc,coef=4,n=20,p.value=0.05)[,-c(1:3)] GENENAME CHR
GREM2 gremlin 2, DAN family BMP antagonist 1
OSR1 odd-skipped related transcription factor 1 2
GPHA2 glycoprotein hormone alpha 2 11
ADORA2B adenosine A2b receptor 17
SFRP2 secreted frizzled related protein 2 4
MOV10L1 Mov10 like RISC complex RNA helicase 1 22
LINC01886 long intergenic non-protein coding RNA 1886 2
RSPO2 R-spondin 2 8
CHRD chordin 3
IQCA1 IQ motif containing with AAA domain 1 2
ENPP1 ectonucleotide pyrophosphatase/phosphodiesterase 1 6
MIR3681HG MIR3681 host gene 2
RAB3C RAB3C, member RAS oncogene family 5
SLITRK5 SLIT and NTRK like family member 5 13
ADAM22 ADAM metallopeptidase domain 22 7
ADAMTS17 ADAM metallopeptidase with thrombospondin type 1 motif 17 15
LRRC3B leucine rich repeat containing 3B 3
SLC22A3 solute carrier family 22 member 3 6
THSD7B thrombospondin type 1 domain containing 7B 2
LRRTM4 leucine rich repeat transmembrane neuronal 4 2
logFC AveExpr t P.Value adj.P.Val
GREM2 -8.55 1.334 -13.07 4.95e-13 9.14e-09
OSR1 -7.05 0.756 -7.96 1.25e-08 1.15e-04
GPHA2 -4.84 -1.777 -6.77 2.03e-07 1.25e-03
ADORA2B 6.41 2.743 6.62 3.11e-07 1.44e-03
SFRP2 -8.53 -0.817 -6.52 4.24e-07 1.50e-03
MOV10L1 -6.23 1.635 -6.43 4.87e-07 1.50e-03
LINC01886 -5.54 0.260 -6.19 8.92e-07 2.35e-03
RSPO2 -5.43 2.084 -5.98 1.49e-06 3.15e-03
CHRD 6.17 2.010 5.98 1.54e-06 3.15e-03
IQCA1 -5.65 2.517 -5.87 2.04e-06 3.51e-03
ENPP1 -5.02 4.216 -5.85 2.09e-06 3.51e-03
MIR3681HG -4.82 3.305 -5.72 2.90e-06 4.47e-03
RAB3C -6.03 2.110 -5.51 5.13e-06 6.92e-03
SLITRK5 -5.82 0.513 -5.50 5.25e-06 6.92e-03
ADAM22 -4.87 4.266 -5.45 5.88e-06 7.24e-03
ADAMTS17 -5.12 4.708 -5.34 7.87e-06 8.78e-03
LRRC3B -5.74 1.042 -5.34 8.09e-06 8.78e-03
SLC22A3 -4.86 3.158 -5.26 9.64e-06 9.89e-03
THSD7B -5.21 3.773 -5.12 1.38e-05 1.28e-02
LRRTM4 -5.66 5.063 -5.12 1.42e-05 1.28e-02Male vs Female in young samples
topTreat(treat.smc,coef=5)[,-c(1:3)] GENENAME CHR
PHF2 PHD finger protein 2 9
ACTR6 actin related protein 6 12
MPHOSPH10 M-phase phosphoprotein 10 2
MALT1 MALT1 paracaspase 18
MAGOH mago homolog, exon junction complex subunit 1
ZNF121 zinc finger protein 121 19
EIF2B5 eukaryotic translation initiation factor 2B subunit epsilon 3
MED21 mediator complex subunit 21 12
GABPA GA binding protein transcription factor subunit alpha 21
BCL9 BCL9 transcription coactivator 1
logFC AveExpr t P.Value adj.P.Val
PHF2 4.04 5.45 5.89 1.84e-06 0.0340
ACTR6 3.50 4.49 5.58 4.04e-06 0.0373
MPHOSPH10 3.89 5.08 5.38 6.90e-06 0.0425
MALT1 4.06 5.91 4.97 2.02e-05 0.0855
MAGOH 3.08 4.42 4.91 2.32e-05 0.0855
ZNF121 3.12 4.68 4.79 3.15e-05 0.0894
EIF2B5 2.92 3.72 4.76 3.39e-05 0.0894
MED21 3.48 4.49 4.71 3.92e-05 0.0905
GABPA 3.09 5.15 4.43 8.06e-05 0.1653
BCL9 4.06 5.50 4.32 1.11e-04 0.1859Male vs Female in adult samples
topTreat(treat.smc,coef=6)[,-c(1:3)] GENENAME CHR logFC
LIN52 lin-52 DREAM MuvB core complex component 14 4.82
TOX4 TOX high mobility group box family member 4 14 4.16
PPM1G protein phosphatase, Mg2+/Mn2+ dependent 1G 2 3.94
EPM2AIP1 EPM2A interacting protein 1 3 3.62
DNAJC16 DnaJ heat shock protein family (Hsp40) member C16 1 4.03
ZDHHC5 zinc finger DHHC-type containing 5 11 3.40
TESK2 testis associated actin remodelling kinase 2 1 4.65
NDST1 N-deacetylase and N-sulfotransferase 1 5 4.01
CCDC174 coiled-coil domain containing 174 3 3.27
FAHD2A fumarylacetoacetate hydrolase domain containing 2A 2 3.68
AveExpr t P.Value adj.P.Val
LIN52 6.61 6.53 3.68e-07 0.00461
TOX4 5.53 6.41 4.99e-07 0.00461
PPM1G 5.40 5.92 1.69e-06 0.01037
EPM2AIP1 5.75 5.42 6.15e-06 0.02840
DNAJC16 5.38 5.28 8.81e-06 0.03253
ZDHHC5 5.22 5.17 1.16e-05 0.03583
TESK2 5.30 5.03 1.74e-05 0.04595
NDST1 5.68 4.90 2.39e-05 0.05300
CCDC174 4.70 4.83 2.84e-05 0.05300
FAHD2A 4.25 4.80 3.12e-05 0.05300Interaction of sex differences between adult and fetal
topTreat(treat.smc,coef=7)[,-c(1:3)] GENENAME CHR logFC AveExpr
GREM2 gremlin 2, DAN family BMP antagonist 1 8.35 1.334
LRRC42 leucine rich repeat containing 42 1 6.34 3.562
LIN52 lin-52 DREAM MuvB core complex component 14 4.92 6.606
GTF3C3 general transcription factor IIIC subunit 3 2 4.47 5.039
PPM1G protein phosphatase, Mg2+/Mn2+ dependent 1G 2 4.05 5.401
OSR1 odd-skipped related transcription factor 1 2 7.67 0.756
TRAM2 translocation associated membrane protein 2 6 4.66 5.691
EPM2AIP1 EPM2A interacting protein 1 3 3.90 5.753
BTBD11 BTB domain containing 11 12 7.37 3.016
GPHA2 glycoprotein hormone alpha 2 11 4.89 -1.777
t P.Value adj.P.Val
GREM2 6.80 2.09e-07 0.00386
LRRC42 6.05 1.31e-06 0.01208
LIN52 5.56 4.34e-06 0.02673
GTF3C3 5.42 6.17e-06 0.02850
PPM1G 4.88 2.56e-05 0.05703
OSR1 4.91 2.68e-05 0.05703
TRAM2 4.85 2.82e-05 0.05703
EPM2AIP1 4.83 2.85e-05 0.05703
BTBD11 4.83 3.26e-05 0.05703
GPHA2 4.76 3.52e-05 0.05703Interaction of sex differences between young and fetal
topTreat(treat.smc,coef=8)[,-c(1:3)] GENENAME CHR
GREM2 gremlin 2, DAN family BMP antagonist 1
PHF2 PHD finger protein 2 9
CACNA1A calcium voltage-gated channel subunit alpha1 A 19
ACTR6 actin related protein 6 12
SNN stannin 16
GPHA2 glycoprotein hormone alpha 2 11
EIF2B5 eukaryotic translation initiation factor 2B subunit epsilon 3
HARBI1 harbinger transposase derived 1 11
ADORA2B adenosine A2b receptor 17
OSR1 odd-skipped related transcription factor 1 2
logFC AveExpr t P.Value adj.P.Val
GREM2 8.66 1.334 7.05 1.14e-07 0.00211
PHF2 5.39 5.453 6.38 5.45e-07 0.00503
CACNA1A -4.93 4.507 -5.57 4.28e-06 0.02635
ACTR6 4.22 4.492 5.16 1.21e-05 0.05578
SNN -5.35 2.078 -4.99 1.98e-05 0.07111
GPHA2 5.04 -1.777 4.93 2.31e-05 0.07111
EIF2B5 3.86 3.719 4.84 2.80e-05 0.07391
HARBI1 -7.04 2.035 -4.83 3.21e-05 0.07412
ADORA2B -6.68 2.743 -4.72 4.24e-05 0.08306
OSR1 7.33 0.756 4.69 4.77e-05 0.08306Interaction of sex differences between adult and young
topTreat(treat.smc,coef=9)[,-c(1:3)] GENENAME CHR logFC
TOX4 TOX high mobility group box family member 4 14 4.68
NRBF2 nuclear receptor binding factor 2 10 -6.27
MPHOSPH10 M-phase phosphoprotein 10 2 -4.80
PPM1G protein phosphatase, Mg2+/Mn2+ dependent 1G 2 4.26
DNAJC16 DnaJ heat shock protein family (Hsp40) member C16 1 4.99
ASB3 ankyrin repeat and SOCS box containing 3 2 4.89
LINC01572 long intergenic non-protein coding RNA 1572 16 5.00
CCDC174 coiled-coil domain containing 174 3 4.18
ACTR6 actin related protein 6 12 -3.90
LIN52 lin-52 DREAM MuvB core complex component 14 4.32
AveExpr t P.Value adj.P.Val
TOX4 5.53 5.11 1.42e-05 0.219
NRBF2 3.88 -4.67 4.76e-05 0.219
MPHOSPH10 5.08 -4.57 5.88e-05 0.219
PPM1G 5.40 4.56 5.92e-05 0.219
DNAJC16 5.38 4.54 6.43e-05 0.219
ASB3 3.28 4.50 7.13e-05 0.219
LINC01572 5.65 4.44 8.32e-05 0.220
CCDC174 4.70 4.36 1.01e-04 0.222
ACTR6 4.49 -4.26 1.28e-04 0.222
LIN52 6.61 4.26 1.30e-04 0.222par(mar=c(5,5,3,2))
plot(treat.smc$coefficients[,1],treat.smc$coefficients[,2],xlab="logFC: Young vs Fetal", ylab="logFC: Adult vs Fetal",main="smooth muscle cells: Development",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0,col=colours()[c(175)])
sig.genes <- dt.smc[,1] !=0 | dt.smc[,2] != 0
text(treat.smc$coefficients[sig.genes,1],treat.smc$coefficients[sig.genes,2],labels=rownames(dt.smc)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.smc$coefficients[,4],treat.smc$coefficients[,5],xlab="logFC: Fetal Male vs Female", ylab="logFC: Young Male vs Female",main="smooth muscle cells: Sex differences - fetal and young",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
sig.genes <- dt.smc[,4] !=0 | dt.smc[,5] != 0
text(treat.smc$coefficients[sig.genes,4],treat.smc$coefficients[sig.genes,5],labels=rownames(dt.smc)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.smc$coefficients[,4],treat.smc$coefficients[,6],xlab="logFC: Fetal Male vs Female", ylab="logFC: Adult Male vs Female",main="smooth muscle cells: Sex differences - fetal and adult",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
sig.genes <- dt.smc[,4] !=0 | dt.smc[,6] != 0
text(treat.smc$coefficients[sig.genes,4],treat.smc$coefficients[sig.genes,6],labels=rownames(dt.smc)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.smc$coefficients[,5],treat.smc$coefficients[,6],xlab="logFC: Young Male vs Female", ylab="logFC: Adult Male vs Female",main="smooth muscle cells: Sex differences - young and adult",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
sig.genes <- dt.smc[,5] !=0 | dt.smc[,6] != 0
text(treat.smc$coefficients[sig.genes,5],treat.smc$coefficients[sig.genes,6],labels=rownames(dt.smc)[sig.genes],col=2,cex=0.6)
abline(h=0,v=0)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.smc$coefficients[,4],treat.smc$coefficients[,5],xlab="logFC: Fetal Male vs Female", ylab="logFC: Young Male vs Female",main="smooth muscle cells: Interaction term: Fetal vs Young",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
sig.genes <- dt.smc[,8] !=0
text(treat.smc$coefficients[sig.genes,4],treat.smc$coefficients[sig.genes,5],labels=rownames(dt.smc)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.smc$coefficients[,4],treat.smc$coefficients[,6],xlab="logFC: Fetal Male vs Female", ylab="logFC: Adult Male vs Female",main="smooth muscle cells: Interaction term: fetal and adult",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
sig.genes <- dt.smc[,7] !=0
text(treat.smc$coefficients[sig.genes,4],treat.smc$coefficients[sig.genes,6],labels=rownames(dt.smc)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.smc$coefficients[,5],treat.smc$coefficients[,6],xlab="logFC: Young Male vs Female", ylab="logFC: Adult Male vs Female",main="smooth muscle cells: Interaction term: young and adult",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
sig.genes <- dt.smc[,9] !=0
if(sum(sig.genes)!=0){
text(treat.smc$coefficients[sig.genes,5],treat.smc$coefficients[sig.genes,6],
labels=rownames(dt.smc)[sig.genes],col=2,cex=0.6)
}Endothelial cells
cont.endo <- makeContrasts(YvF = 0.5*(endo.young.Male + endo.young.Female) - 0.5*(endo.fetal.Male + endo.fetal.Female),
AvF = 0.5*(endo.adult.Male + endo.adult.Female) - 0.5*(endo.fetal.Male + endo.fetal.Female),
AvY = 0.5*(endo.adult.Male + endo.adult.Female) - 0.5*(endo.young.Male + endo.young.Female),
SexFetal = endo.fetal.Male - endo.fetal.Female,
SexYoung = endo.young.Male - endo.young.Female,
SexAdult = endo.adult.Male - endo.adult.Female,
InteractionAF = (endo.adult.Male - endo.fetal.Male) - (endo.adult.Female - endo.fetal.Female),
InteractionYF = (endo.young.Male - endo.fetal.Male) - (endo.young.Female - endo.fetal.Female),
InteractionAY = (endo.adult.Male - endo.young.Male) - (endo.adult.Female - endo.young.Female),
levels=design)
fit.endo <- contrasts.fit(fit,contrasts = cont.endo)
fit.endo <- eBayes(fit.endo,robust=TRUE)
summary(decideTests(fit.endo)) YvF AvF AvY SexFetal SexYoung SexAdult InteractionAF
Down 772 892 0 6 0 1 2
NotSig 16982 16753 18464 18457 18463 18463 18461
Up 710 819 0 1 1 0 1
InteractionYF InteractionAY
Down 0 2
NotSig 18462 18462
Up 2 0treat.endo <- treat(fit.endo,lfc=0.5)
dt.endo<-decideTests(treat.endo)
summary(dt.endo) YvF AvF AvY SexFetal SexYoung SexAdult InteractionAF
Down 316 422 0 4 0 0 1
NotSig 17922 17781 18464 18460 18463 18464 18463
Up 226 261 0 0 1 0 0
InteractionYF InteractionAY
Down 0 2
NotSig 18462 18462
Up 2 0par(mfrow=c(3,3))
for(i in 1:9){
plotMD(treat.endo,coef=i,status=dt.endo[,i],hl.col=c("blue","red"))
abline(h=0,col="grey")
}
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
par(mfrow=c(1,1))
par(mar=c(7,4,2,2))
barplot(summary(dt.endo)[-2,],beside=TRUE,legend=TRUE,col=c("blue","red"),ylab="Number of significant genes",las=2)
title("Endothelial cells")
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
Young vs Fetal
options(digits=3)
topTreat(treat.endo,coef=1,n=20,p.value=0.05)[,-c(1:3)] GENENAME CHR
PRND prion like protein doppel 20
NTS neurotensin 12
TMTC1 transmembrane and tetratricopeptide repeat containing 1 12
PEG10 paternally expressed 10 7
HOXD9 homeobox D9 2
PIEZO2 piezo type mechanosensitive ion channel component 2 18
OR51E1 olfactory receptor family 51 subfamily E member 1 11
TIMP4 TIMP metallopeptidase inhibitor 4 3
RASGRF2 Ras protein specific guanine nucleotide releasing factor 2 5
IGF2BP3 insulin like growth factor 2 mRNA binding protein 3 7
PRSS35 serine protease 35 6
GPR182 G protein-coupled receptor 182 12
HOXD-AS2 HOXD cluster antisense RNA 2 2
HBA1 hemoglobin subunit alpha 1 16
CCL21 C-C motif chemokine ligand 21 9
SOX11 SRY-box 11 2
JADE2 jade family PHD finger 2 5
CLVS1 clavesin 1 8
L1TD1 LINE1 type transposase domain containing 1 1
IGF2BP1 insulin like growth factor 2 mRNA binding protein 1 17
logFC AveExpr t P.Value adj.P.Val
PRND -7.67 -1.201 -23.13 7.67e-19 1.42e-14
NTS -6.82 -0.384 -13.46 2.49e-13 2.30e-09
TMTC1 3.75 7.751 10.87 2.47e-11 1.52e-07
PEG10 -6.23 1.558 -10.49 5.41e-11 2.50e-07
HOXD9 -4.76 -1.728 -10.27 8.15e-11 3.01e-07
PIEZO2 -5.61 4.448 -10.07 1.23e-10 3.77e-07
OR51E1 6.40 0.658 9.45 4.58e-10 1.10e-06
TIMP4 7.57 1.237 9.44 4.78e-10 1.10e-06
RASGRF2 3.63 4.285 9.31 5.84e-10 1.20e-06
IGF2BP3 -5.69 4.676 -8.85 1.65e-09 2.78e-06
PRSS35 -5.55 1.689 -8.84 1.66e-09 2.78e-06
GPR182 -4.28 -1.607 -8.56 3.02e-09 4.65e-06
HOXD-AS2 -4.93 -1.028 -8.09 8.81e-09 1.25e-05
HBA1 -8.20 1.612 -7.98 1.24e-08 1.63e-05
CCL21 -4.71 1.302 -7.82 1.64e-08 2.02e-05
SOX11 -6.30 1.386 -7.80 1.80e-08 2.07e-05
JADE2 2.85 4.433 7.68 2.23e-08 2.42e-05
CLVS1 -4.04 3.973 -7.64 2.50e-08 2.42e-05
L1TD1 -4.95 0.565 -7.63 2.57e-08 2.42e-05
IGF2BP1 -5.70 1.905 -7.60 2.84e-08 2.42e-05Adult vs Fetal
topTreat(treat.endo,coef=2,n=20,p.value=0.05)[,-c(1:3)] GENENAME CHR
PRND prion like protein doppel 20
NTS neurotensin 12
PEG10 paternally expressed 10 7
HOXD9 homeobox D9 2
RASGRF2 Ras protein specific guanine nucleotide releasing factor 2 5
CLRN1-AS1 CLRN1 antisense RNA 1 3
TMTC1 transmembrane and tetratricopeptide repeat containing 1 12
LINC02100 long intergenic non-protein coding RNA 2100 5
IGF2BP3 insulin like growth factor 2 mRNA binding protein 3 7
PIEZO2 piezo type mechanosensitive ion channel component 2 18
CABP1 calcium binding protein 1 12
SYNE1 spectrin repeat containing nuclear envelope protein 1 6
TIMP4 TIMP metallopeptidase inhibitor 4 3
HBA2 hemoglobin subunit alpha 2 16
PRSS35 serine protease 35 6
SOX11 SRY-box 11 2
JADE2 jade family PHD finger 2 5
RGS20 regulator of G protein signaling 20 8
CALCOCO2 calcium binding and coiled-coil domain 2 17
HAGLR HOXD antisense growth-associated long non-coding RNA 2
logFC AveExpr t P.Value adj.P.Val
PRND -7.64 -1.201 -22.99 8.88e-19 1.64e-14
NTS -7.13 -0.384 -14.27 6.65e-14 6.14e-10
PEG10 -6.46 1.558 -10.96 2.14e-11 1.32e-07
HOXD9 -4.75 -1.728 -10.24 8.69e-11 4.01e-07
RASGRF2 3.87 4.285 10.12 1.09e-10 4.03e-07
CLRN1-AS1 -5.76 0.978 -9.99 1.45e-10 4.47e-07
TMTC1 3.45 7.751 9.77 2.22e-10 5.87e-07
LINC02100 4.08 1.383 9.57 3.39e-10 7.82e-07
IGF2BP3 -5.64 4.676 -9.10 9.47e-10 1.83e-06
PIEZO2 -4.02 4.448 -9.03 1.07e-09 1.83e-06
CABP1 6.43 1.974 9.04 1.09e-09 1.83e-06
SYNE1 2.25 8.640 8.43 4.02e-09 6.18e-06
TIMP4 7.07 1.237 8.34 5.19e-09 7.38e-06
HBA2 -7.73 2.179 -8.14 8.29e-09 1.03e-05
PRSS35 -5.16 1.689 -8.12 8.33e-09 1.03e-05
SOX11 -6.35 1.386 -7.97 1.19e-08 1.35e-05
JADE2 2.93 4.433 7.94 1.24e-08 1.35e-05
RGS20 -3.99 2.554 -7.69 2.21e-08 2.26e-05
CALCOCO2 2.45 6.451 7.57 2.91e-08 2.83e-05
HAGLR -5.44 -1.172 -7.52 3.36e-08 3.10e-05Adult vs Young
topTreat(treat.endo,coef=3)[,-c(1:3)] GENENAME CHR logFC AveExpr
SCN4B sodium voltage-gated channel beta subunit 4 11 4.01 1.534
ITGBL1 integrin subunit beta like 1 13 6.22 2.168
PTCHD4 patched domain containing 4 6 3.87 2.284
G6PC2 glucose-6-phosphatase catalytic subunit 2 2 3.98 -1.190
NOTCH3 notch receptor 3 19 4.47 4.992
ADGRF2 adhesion G protein-coupled receptor F2 6 3.07 -1.173
TUBB8 tubulin beta 8 class VIII 10 -3.25 1.019
LSAMP limbic system associated membrane protein 3 -3.03 7.186
MTRNR2L1 MT-RNR2 like 1 17 3.34 0.596
UNC5B-AS1 UNC5B antisense RNA 1 10 2.72 -0.226
t P.Value adj.P.Val
SCN4B 5.00 1.87e-05 0.294
ITGBL1 4.82 3.18e-05 0.294
PTCHD4 4.61 5.10e-05 0.314
G6PC2 4.50 6.80e-05 0.314
NOTCH3 4.18 1.63e-04 0.602
ADGRF2 3.77 4.49e-04 1.000
TUBB8 -3.73 5.03e-04 1.000
LSAMP -3.49 9.11e-04 1.000
MTRNR2L1 3.45 1.03e-03 1.000
UNC5B-AS1 3.44 1.03e-03 1.000Male vs Female in fetal samples
topTreat(treat.endo,coef=4)[,-c(1:3)] GENENAME CHR logFC AveExpr
APOA2 apolipoprotein A2 1 -3.74 -1.812
BMP10 bone morphogenetic protein 10 2 -4.40 -1.542
COMP cartilage oligomeric matrix protein 19 -5.22 -0.265
GPHA2 glycoprotein hormone alpha 2 11 -3.74 -1.777
ADGRA1 adhesion G protein-coupled receptor A1 10 -4.16 -1.388
ADGRF2 adhesion G protein-coupled receptor F2 6 -4.58 -1.173
PRG4 proteoglycan 4 1 -3.37 0.409
C2CD4B C2 calcium dependent domain containing 4B 15 2.85 -0.113
SMAD1-AS1 SMAD1 antisense RNA 1 4 4.12 -0.852
SLC6A11 solute carrier family 6 member 11 3 -4.07 -0.521
t P.Value adj.P.Val
APOA2 -6.95 1.30e-07 0.00239
BMP10 -5.61 3.78e-06 0.03486
COMP -5.35 7.64e-06 0.04208
GPHA2 -5.27 9.12e-06 0.04208
ADGRA1 -4.73 3.77e-05 0.13923
ADGRF2 -4.60 5.39e-05 0.16597
PRG4 -4.47 7.26e-05 0.18954
C2CD4B 4.42 8.21e-05 0.18954
SMAD1-AS1 4.25 1.32e-04 0.27115
SLC6A11 -4.19 1.55e-04 0.28606Male vs Female in young samples
topTreat(treat.endo,coef=5)[,-c(1:3)] GENENAME CHR logFC AveExpr
UMODL1 uromodulin like 1 21 6.55 -0.404
ITLN1 intelectin 1 1 -3.86 -0.125
CHRNA2 cholinergic receptor nicotinic alpha 2 subunit 8 -3.33 -1.583
MAFA MAF bZIP transcription factor A 8 -4.41 -1.370
SLC9C1 solute carrier family 9 member C1 3 2.69 4.306
OPN5 opsin 5 6 5.29 -0.194
ZNF750 zinc finger protein 750 17 4.67 0.683
GSDMC gasdermin C 8 -4.24 -0.886
CLDN6 claudin 6 16 -4.00 -0.509
GBX1 gastrulation brain homeobox 1 7 -4.65 1.261
t P.Value adj.P.Val
UMODL1 7.12 8.94e-08 0.00165
ITLN1 -4.81 3.03e-05 0.28010
CHRNA2 -4.41 8.57e-05 0.45091
MAFA -4.37 9.77e-05 0.45091
SLC9C1 4.11 1.84e-04 0.53329
OPN5 4.11 2.04e-04 0.53329
ZNF750 4.08 2.11e-04 0.53329
GSDMC -4.03 2.41e-04 0.53329
CLDN6 -3.99 2.60e-04 0.53329
GBX1 -3.96 2.93e-04 0.54022Male vs Female in adult samples
topTreat(treat.endo,coef=6)[,-c(1:3)] GENENAME CHR logFC
SLCO4A1-AS1 SLCO4A1 antisense RNA 1 20 -4.06
CYP8B1 cytochrome P450 family 8 subfamily B member 1 3 -4.46
UNC5B-AS1 UNC5B antisense RNA 1 10 -4.45
LINC01060 long intergenic non-protein coding RNA 1060 4 -5.28
L1TD1 LINE1 type transposase domain containing 1 1 -4.27
OR2A5 olfactory receptor family 2 subfamily A member 5 7 -3.74
GPR12 G protein-coupled receptor 12 13 -3.51
SUCNR1 succinate receptor 1 3 -4.72
GHRHR growth hormone releasing hormone receptor 7 -4.83
SH3RF3-AS1 SH3RF3 antisense RNA 1 2 -3.59
AveExpr t P.Value adj.P.Val
SLCO4A1-AS1 -1.6254 -5.47 5.39e-06 0.0996
CYP8B1 -0.0337 -4.99 1.90e-05 0.1469
UNC5B-AS1 -0.2265 -4.67 4.51e-05 0.1469
LINC01060 3.3689 -4.56 6.14e-05 0.1469
L1TD1 0.5651 -4.50 6.91e-05 0.1469
OR2A5 -1.6389 -4.49 7.03e-05 0.1469
GPR12 -1.5994 -4.47 7.33e-05 0.1469
SUCNR1 -0.7171 -4.48 7.44e-05 0.1469
GHRHR -0.5781 -4.48 7.46e-05 0.1469
SH3RF3-AS1 -1.2361 -4.44 7.95e-05 0.1469Interaction of sex differences between adult and fetal
topTreat(treat.endo,coef=7)[,-c(1:3)] GENENAME CHR logFC
SH3RF3-AS1 SH3RF3 antisense RNA 1 2 -6.52
L1TD1 LINE1 type transposase domain containing 1 1 -5.93
GHRHR growth hormone releasing hormone receptor 7 -8.39
APOA2 apolipoprotein A2 1 4.03
FOXN3-AS2 FOXN3 antisense RNA 2 14 -7.58
SLCO4A1-AS1 SLCO4A1 antisense RNA 1 20 -5.20
SMAD1-AS1 SMAD1 antisense RNA 1 4 -5.81
ONECUT3 one cut homeobox 3 19 -5.13
BMP10 bone morphogenetic protein 10 2 4.79
CYP8B1 cytochrome P450 family 8 subfamily B member 1 3 -4.82
AveExpr t P.Value adj.P.Val
SH3RF3-AS1 -1.2361 -5.81 2.40e-06 0.0443
L1TD1 0.5651 -5.12 1.41e-05 0.0734
GHRHR -0.5781 -5.14 1.48e-05 0.0734
APOA2 -1.8119 5.06 1.59e-05 0.0734
FOXN3-AS2 -0.5031 -4.57 6.62e-05 0.2446
SLCO4A1-AS1 -1.6254 -4.46 7.99e-05 0.2459
SMAD1-AS1 -0.8519 -4.35 1.08e-04 0.2852
ONECUT3 -0.8844 -4.04 2.45e-04 0.5416
BMP10 -1.5421 4.00 2.64e-04 0.5416
CYP8B1 -0.0337 -3.87 3.74e-04 0.6330Interaction of sex differences between young and fetal
topTreat(treat.endo,coef=8)[,-c(1:3)] GENENAME CHR logFC AveExpr t
UMODL1 uromodulin like 1 21 9.33 -0.4040 6.82
PRG4 proteoglycan 4 1 6.57 0.4090 6.04
ADGRF2 adhesion G protein-coupled receptor F2 6 7.08 -1.1731 4.72
APOA2 apolipoprotein A2 1 3.58 -1.8119 4.42
OPN5 opsin 5 6 5.43 -0.1936 3.95
SLC9C1 solute carrier family 9 member C1 3 2.88 4.3058 3.85
NCBP2-AS1 NCBP2 antisense RNA 1 3 -6.15 0.4250 -3.84
INMT indolethylamine N-methyltransferase 7 5.14 0.7208 3.77
OOEP-AS1 OOEP antisense RNA 1 6 -5.94 0.0219 -3.78
SMAD1-AS1 SMAD1 antisense RNA 1 4 -5.21 -0.8519 -3.77
P.Value adj.P.Val
UMODL1 2.04e-07 0.00377
PRG4 1.34e-06 0.01238
ADGRF2 4.35e-05 0.26754
APOA2 8.27e-05 0.38187
OPN5 3.10e-04 0.92168
SLC9C1 3.61e-04 0.92168
NCBP2-AS1 4.30e-04 0.92168
INMT 4.94e-04 0.92168
OOEP-AS1 4.94e-04 0.92168
SMAD1-AS1 4.99e-04 0.92168Interaction of sex differences between adult and young
topTreat(treat.endo,coef=9)[,-c(1:3)] GENENAME CHR logFC
SH3RF3-AS1 SH3RF3 antisense RNA 1 2 -6.68
UMODL1 uromodulin like 1 21 -7.83
C16orf78 chromosome 16 open reading frame 78 16 -6.84
TNFRSF10A-AS1 TNFRSF10A antisense RNA 1 8 -5.63
TNFRSF8 TNF receptor superfamily member 8 1 3.80
SLCO4A1-AS1 SLCO4A1 antisense RNA 1 20 -5.12
OR2A5 olfactory receptor family 2 subfamily A member 5 7 -5.16
ABCC3 ATP binding cassette subfamily C member 3 17 5.98
HEMGN hemogen 9 -5.11
ZNF750 zinc finger protein 750 17 -6.05
AveExpr t P.Value adj.P.Val
SH3RF3-AS1 -1.236 -6.04 1.35e-06 0.0249
UMODL1 -0.404 -5.56 4.80e-06 0.0443
C16orf78 -0.263 -5.12 1.48e-05 0.0909
TNFRSF10A-AS1 -1.506 -4.63 5.24e-05 0.2419
TNFRSF8 1.650 4.36 9.91e-05 0.2995
SLCO4A1-AS1 -1.625 -4.34 1.09e-04 0.2995
OR2A5 -1.639 -4.33 1.14e-04 0.2995
ABCC3 2.658 4.29 1.30e-04 0.3011
HEMGN -0.134 -4.10 2.08e-04 0.3244
ZNF750 0.683 -4.09 2.19e-04 0.3244par(mar=c(5,5,3,2))
plot(treat.endo$coefficients[,1],treat.endo$coefficients[,2],xlab="logFC: Young vs Fetal", ylab="logFC: Adult vs Fetal",main="endothelial cells: Development",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0,col=colours()[c(175)])
sig.genes <- dt.endo[,1] !=0 | dt.endo[,2] != 0
text(treat.endo$coefficients[sig.genes,1],treat.endo$coefficients[sig.genes,2],labels=rownames(dt.endo)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.endo$coefficients[,4],treat.endo$coefficients[,5],xlab="logFC: Fetal Male vs Female", ylab="logFC: Young Male vs Female",main="endothelial cells: Sex differences - fetal and young",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
sig.genes <- dt.endo[,4] !=0 | dt.endo[,5] != 0
text(treat.endo$coefficients[sig.genes,4],treat.endo$coefficients[sig.genes,5],labels=rownames(dt.endo)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.endo$coefficients[,4],treat.endo$coefficients[,6],xlab="logFC: Fetal Male vs Female", ylab="logFC: Adult Male vs Female",main="endothelial cells: Sex differences - fetal and adult",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
sig.genes <- dt.endo[,4] !=0 | dt.endo[,6] != 0
text(treat.endo$coefficients[sig.genes,4],treat.endo$coefficients[sig.genes,6],labels=rownames(dt.endo)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.endo$coefficients[,5],treat.endo$coefficients[,6],xlab="logFC: Young Male vs Female", ylab="logFC: Adult Male vs Female",main="endothelial cells: Sex differences - young and adult",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
sig.genes <- dt.endo[,5] !=0 | dt.endo[,6] != 0
text(treat.endo$coefficients[sig.genes,5],treat.endo$coefficients[sig.genes,6],labels=rownames(dt.endo)[sig.genes],col=2,cex=0.6)
abline(h=0,v=0)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.endo$coefficients[,4],treat.endo$coefficients[,5],xlab="logFC: Fetal Male vs Female", ylab="logFC: Young Male vs Female",main="endothelial cells: Interaction term: Fetal vs Young",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
sig.genes <- dt.endo[,8] !=0
text(treat.endo$coefficients[sig.genes,4],treat.endo$coefficients[sig.genes,5],labels=rownames(dt.endo)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.endo$coefficients[,4],treat.endo$coefficients[,6],xlab="logFC: Fetal Male vs Female", ylab="logFC: Adult Male vs Female",main="endothelial cells: Interaction term: fetal and adult",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
sig.genes <- dt.endo[,7] !=0
text(treat.endo$coefficients[sig.genes,4],treat.endo$coefficients[sig.genes,6],labels=rownames(dt.endo)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.endo$coefficients[,5],treat.endo$coefficients[,6],xlab="logFC: Young Male vs Female", ylab="logFC: Adult Male vs Female",main="endothelial cells: Interaction term: young and adult",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
sig.genes <- dt.endo[,9] !=0
text(treat.endo$coefficients[sig.genes,5],treat.endo$coefficients[sig.genes,6],labels=rownames(dt.endo)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
Immune cells
cont.immune <- makeContrasts(YvF = 0.5*(immune.young.Male + immune.young.Female) - 0.5*(immune.fetal.Male + immune.fetal.Female),
AvF = 0.5*(immune.adult.Male + immune.adult.Female) - 0.5*(immune.fetal.Male + immune.fetal.Female),
AvY = 0.5*(immune.adult.Male + immune.adult.Female) - 0.5*(immune.young.Male + immune.young.Female),
SexFetal = immune.fetal.Male - immune.fetal.Female,
SexYoung = immune.young.Male - immune.young.Female,
SexAdult = immune.adult.Male - immune.adult.Female,
InteractionAF = (immune.adult.Male - immune.fetal.Male) - (immune.adult.Female - immune.fetal.Female),
InteractionYF = (immune.young.Male - immune.fetal.Male) - (immune.young.Female - immune.fetal.Female),
InteractionAY = (immune.adult.Male - immune.young.Male) - (immune.adult.Female - immune.young.Female),
levels=design)
fit.immune <- contrasts.fit(fit,contrasts = cont.immune)
fit.immune <- eBayes(fit.immune,robust=TRUE)
summary(decideTests(fit.immune)) YvF AvF AvY SexFetal SexYoung SexAdult InteractionAF
Down 305 403 5 0 12 7 1
NotSig 17852 17738 18457 18464 18451 18449 18463
Up 307 323 2 0 1 8 0
InteractionYF InteractionAY
Down 0 12
NotSig 18464 18381
Up 0 71treat.immune <- treat(fit.immune,lfc=0.5)
dt.immune<-decideTests(treat.immune)
summary(dt.immune) YvF AvF AvY SexFetal SexYoung SexAdult InteractionAF
Down 115 198 0 0 7 5 1
NotSig 18251 18167 18463 18464 18457 18457 18463
Up 98 99 1 0 0 2 0
InteractionYF InteractionAY
Down 0 5
NotSig 18464 18426
Up 0 33par(mfrow=c(3,3))
for(i in 1:9){
plotMD(treat.immune,coef=i,status=dt.immune[,i],hl.col=c("blue","red"))
abline(h=0,col="grey")
}
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
par(mfrow=c(1,1))
par(mar=c(7,4,2,2))
barplot(summary(dt.immune)[-2,],beside=TRUE,legend=TRUE,col=c("blue","red"),ylab="Number of significant genes",las=2)
title("Immune cells")
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
Young vs Fetal
options(digits=3)
topTreat(treat.immune,coef=1,n=20,p.value=0.05)[,-c(1:3)] GENENAME CHR logFC
IGF2BP3 insulin like growth factor 2 mRNA binding protein 3 7 -4.85
MSLN mesothelin 16 -4.99
IGHM immunoglobulin heavy constant mu 14 -4.86
IGF2BP1 insulin like growth factor 2 mRNA binding protein 1 17 -6.05
HBA1 hemoglobin subunit alpha 1 16 -8.00
ME1 malic enzyme 1 6 3.73
LINC01127 long intergenic non-protein coding RNA 1127 2 3.56
LINC02513 long intergenic non-protein coding RNA 2513 4 -5.40
SMIM34B small integral membrane protein 34B 21 4.23
SGMS2 sphingomyelin synthase 2 4 4.19
PRICKLE1 prickle planar cell polarity protein 1 12 -3.40
HBA2 hemoglobin subunit alpha 2 16 -7.11
CX3CR1 C-X3-C motif chemokine receptor 1 3 -4.11
SAP30 Sin3A associated protein 30 4 3.38
AGFG1 ArfGAP with FG repeats 1 2 1.99
LINC02621 long intergenic non-protein coding RNA 2621 10 3.85
VPREB3 V-set pre-B cell surrogate light chain 3 22 -4.26
WWP1 WW domain containing E3 ubiquitin protein ligase 1 8 -1.54
IGF2R insulin like growth factor 2 receptor 6 1.93
LINC00996 long intergenic non-protein coding RNA 996 7 -4.59
AveExpr t P.Value adj.P.Val
IGF2BP3 4.676 -9.44 4.49e-10 8.29e-06
MSLN -1.367 -8.72 2.13e-09 1.97e-05
IGHM -0.960 -8.06 9.55e-09 5.88e-05
IGF2BP1 1.905 -7.67 2.43e-08 1.12e-04
HBA1 1.612 -7.35 5.44e-08 1.62e-04
ME1 5.175 7.30 5.58e-08 1.62e-04
LINC01127 -1.398 7.26 6.15e-08 1.62e-04
LINC02513 -1.429 -7.08 9.61e-08 2.17e-04
SMIM34B -0.168 7.03 1.06e-07 2.17e-04
SGMS2 4.569 6.65 2.70e-07 4.75e-04
PRICKLE1 7.047 -6.63 2.83e-07 4.75e-04
HBA2 2.179 -6.47 4.57e-07 7.03e-04
CX3CR1 0.380 -6.40 5.09e-07 7.23e-04
SAP30 3.772 6.36 5.55e-07 7.32e-04
AGFG1 7.242 6.16 9.14e-07 1.06e-03
LINC02621 -0.992 6.15 9.40e-07 1.06e-03
VPREB3 -1.284 -6.14 9.78e-07 1.06e-03
WWP1 7.724 -6.03 1.26e-06 1.29e-03
IGF2R 6.997 5.94 1.60e-06 1.49e-03
LINC00996 -0.702 -5.94 1.62e-06 1.49e-03Adult vs Fetal
topTreat(treat.immune,coef=2,n=20,p.value=0.05)[,-c(1:3)] GENENAME
ME1 malic enzyme 1
IGF2BP3 insulin like growth factor 2 mRNA binding protein 3
MSLN mesothelin
LINC02513 long intergenic non-protein coding RNA 2513
GSDMA gasdermin A
TLR10 toll like receptor 10
CCL3L1 C-C motif chemokine ligand 3 like 1
AGR2 anterior gradient 2, protein disulphide isomerase family member
TIFAB TIFA inhibitor
IGF2BP1 insulin like growth factor 2 mRNA binding protein 1
IGHM immunoglobulin heavy constant mu
HBA2 hemoglobin subunit alpha 2
LINC01684 long intergenic non-protein coding RNA 1684
MARCH11 membrane associated ring-CH-type finger 11
PRICKLE1 prickle planar cell polarity protein 1
LINC01839 long intergenic non-protein coding RNA 1839
IGHG3 immunoglobulin heavy constant gamma 3 (G3m marker)
DAAM2 dishevelled associated activator of morphogenesis 2
MS4A1 membrane spanning 4-domains A1
FBXL7 F-box and leucine rich repeat protein 7
CHR logFC AveExpr t P.Value adj.P.Val
ME1 6 4.59 5.175 9.25 6.74e-10 1.17e-05
IGF2BP3 7 -4.54 4.676 -8.82 1.72e-09 1.17e-05
MSLN 16 -4.98 -1.367 -8.77 1.91e-09 1.17e-05
LINC02513 4 -6.18 -1.429 -8.53 3.36e-09 1.55e-05
GSDMA 17 4.54 0.783 8.31 5.34e-09 1.97e-05
TLR10 4 -5.40 -0.798 -7.37 4.79e-08 1.47e-04
CCL3L1 17 -5.84 -1.374 -7.21 7.18e-08 1.89e-04
AGR2 7 -5.36 -0.339 -6.97 1.27e-07 2.74e-04
TIFAB 5 -4.34 -1.206 -6.91 1.44e-07 2.74e-04
IGF2BP1 17 -5.55 1.905 -6.91 1.48e-07 2.74e-04
IGHM 14 -4.10 -0.960 -6.81 1.83e-07 3.07e-04
HBA2 16 -7.05 2.179 -6.75 2.26e-07 3.48e-04
LINC01684 21 5.52 1.529 6.65 2.78e-07 3.94e-04
MARCH11 5 -7.04 3.233 -6.57 3.58e-07 4.45e-04
PRICKLE1 12 -3.84 7.047 -6.53 3.61e-07 4.45e-04
LINC01839 3 3.86 -1.579 6.38 5.33e-07 6.13e-04
IGHG3 14 5.02 -1.009 6.36 5.74e-07 6.13e-04
DAAM2 6 6.80 6.334 6.36 5.97e-07 6.13e-04
MS4A1 11 -3.73 -0.994 -6.25 7.40e-07 7.20e-04
FBXL7 5 -3.39 9.909 -6.15 9.41e-07 8.32e-04Adult vs Young
topTreat(treat.immune,coef=3)[,-c(1:3)] GENENAME CHR logFC
LINC01839 long intergenic non-protein coding RNA 1839 3 3.13
LINC01127 long intergenic non-protein coding RNA 1127 2 -2.70
CCL3L1 C-C motif chemokine ligand 3 like 1 17 -4.18
CLNK cytokine dependent hematopoietic cell linker 4 -2.55
HIST1H4E histone cluster 1 H4 family member e 6 -3.41
DNM1 dynamin 1 9 1.78
ZFP57 ZFP57 zinc finger protein 6 3.88
SIGLEC10 sialic acid binding Ig like lectin 10 19 -2.75
HS3ST2 heparan sulfate-glucosamine 3-sulfotransferase 2 16 3.88
SLC39A8 solute carrier family 39 member 8 4 -1.75
AveExpr t P.Value adj.P.Val
LINC01839 -1.5788 6.11 1.04e-06 0.0192
LINC01127 -1.3980 -4.99 1.84e-05 0.1335
CCL3L1 -1.3741 -4.94 2.17e-05 0.1335
CLNK 2.7053 -4.72 3.72e-05 0.1716
HIST1H4E 0.3600 -4.53 6.28e-05 0.1786
DNM1 4.9970 4.49 6.76e-05 0.1786
ZFP57 0.2703 4.50 6.77e-05 0.1786
SIGLEC10 -0.0423 -4.13 1.74e-04 0.4025
HS3ST2 2.7275 4.02 2.40e-04 0.4918
SLC39A8 3.0931 -3.90 3.12e-04 0.5762Male vs Female in fetal samples
topTreat(treat.immune,coef=4)[,-c(1:3)] GENENAME CHR logFC AveExpr t
MT1H metallothionein 1H 16 -4.14 -1.630 -4.49
ACTG2 actin gamma 2, smooth muscle 2 -5.51 0.555 -4.42
MOCOS molybdenum cofactor sulfurase 18 -4.04 2.316 -3.93
FBXW9 F-box and WD repeat domain containing 9 19 3.60 1.500 3.80
HOXA9 homeobox A9 7 3.27 -1.673 3.78
PRDM6 PR/SET domain 6 5 -4.69 3.380 -3.77
PI15 peptidase inhibitor 15 8 -5.84 1.285 -3.74
CLNK cytokine dependent hematopoietic cell linker 4 -2.16 2.705 -3.60
TLR3 toll like receptor 3 4 -4.53 1.145 -3.61
PLET1 placenta expressed transcript 1 11 4.19 2.155 3.60
P.Value adj.P.Val
MT1H 7.03e-05 0.833
ACTG2 9.02e-05 0.833
MOCOS 3.07e-04 1.000
FBXW9 4.28e-04 1.000
HOXA9 4.38e-04 1.000
PRDM6 4.78e-04 1.000
PI15 5.49e-04 1.000
CLNK 6.72e-04 1.000
TLR3 7.28e-04 1.000
PLET1 7.29e-04 1.000Male vs Female in young samples
topTreat(treat.immune,coef=5)[,-c(1:3)] GENENAME CHR logFC
IGHG3 immunoglobulin heavy constant gamma 3 (G3m marker) 14 -7.55
LINC01839 long intergenic non-protein coding RNA 1839 3 -5.65
IGHG4 immunoglobulin heavy constant gamma 4 (G4m marker) 14 -4.70
SLC39A8 solute carrier family 39 member 8 4 -2.46
IGHG1 immunoglobulin heavy constant gamma 1 (G1m marker) 14 -5.49
SPATA8-AS1 SPATA8 antisense RNA 1 (head to head) 15 -3.38
SPINK1 serine peptidase inhibitor, Kazal type 1 5 -4.70
FCRL5 Fc receptor like 5 1 -5.11
FAM30A family with sequence similarity 30 member A 14 -4.37
LINC01416 long intergenic non-protein coding RNA 1416 18 5.29
AveExpr t P.Value adj.P.Val
IGHG3 -1.009 -8.87 1.62e-09 2.98e-05
LINC01839 -1.579 -7.88 1.45e-08 1.34e-04
IGHG4 -1.571 -6.45 4.52e-07 2.78e-03
SLC39A8 3.093 -5.39 6.50e-06 2.41e-02
IGHG1 -1.240 -5.41 6.53e-06 2.41e-02
SPATA8-AS1 -1.650 -5.25 9.46e-06 2.91e-02
SPINK1 -1.116 -5.14 1.32e-05 3.48e-02
FCRL5 -0.469 -4.89 2.57e-05 5.42e-02
FAM30A -1.688 -4.87 2.64e-05 5.42e-02
LINC01416 1.626 4.63 5.14e-05 9.50e-02Male vs Female in adult samples
topTreat(treat.immune,coef=6)[,-c(1:3)] GENENAME CHR logFC
IGKC immunoglobulin kappa constant 2 -12.19
IGHA1 immunoglobulin heavy constant alpha 1 14 -7.61
JCHAIN joining chain of multimeric IgA and IgM 4 -5.80
IGHG3 immunoglobulin heavy constant gamma 3 (G3m marker) 14 -5.31
LINC02236 long intergenic non-protein coding RNA 2236 5 4.99
IGHG4 immunoglobulin heavy constant gamma 4 (G4m marker) 14 -4.77
FBXO43 F-box protein 43 8 5.48
HJURP Holliday junction recognition protein 2 6.40
CDKN3 cyclin dependent kinase inhibitor 3 14 4.16
TUBB8 tubulin beta 8 class VIII 10 5.14
AveExpr t P.Value adj.P.Val
IGKC 0.1232 -10.33 8.49e-11 1.57e-06
IGHA1 -1.0981 -6.39 5.65e-07 5.21e-03
JCHAIN -0.0733 -6.18 9.05e-07 5.57e-03
IGHG3 -1.0092 -5.69 3.18e-06 1.13e-02
LINC02236 -0.1323 5.67 3.27e-06 1.13e-02
IGHG4 -1.5710 -5.63 3.67e-06 1.13e-02
FBXO43 0.9102 5.02 1.83e-05 4.83e-02
HJURP 0.8771 4.84 3.08e-05 7.12e-02
CDKN3 1.8178 4.58 5.54e-05 1.14e-01
TUBB8 1.0194 4.53 6.60e-05 1.22e-01Interaction of sex differences between adult and fetal
topTreat(treat.immune,coef=7)[,-c(1:3)] GENENAME CHR
IGKC immunoglobulin kappa constant 2
ARHGEF33 Rho guanine nucleotide exchange factor 33 2
FBXO43 F-box protein 43 8
GRM4 glutamate metabotropic receptor 4 6
POMC proopiomelanocortin 2
ZG16B zymogen granule protein 16B 16
IGHG4 immunoglobulin heavy constant gamma 4 (G4m marker) 14
TREML2 triggering receptor expressed on myeloid cells like 2 6
APOBEC3B-AS1 APOBEC3B antisense RNA 1 22
SHISA4 shisa family member 4 1
logFC AveExpr t P.Value adj.P.Val
IGKC -12.75 0.123 -6.85 2.08e-07 0.00384
ARHGEF33 5.18 1.996 4.32 1.15e-04 0.85539
FBXO43 6.90 0.910 4.28 1.39e-04 0.85539
GRM4 4.99 -0.479 3.93 3.18e-04 0.97632
POMC -6.72 0.517 -3.94 3.36e-04 0.97632
ZG16B -5.59 -1.423 -3.87 3.82e-04 0.97632
IGHG4 -4.72 -1.571 -3.77 4.80e-04 0.97632
TREML2 -4.67 -1.534 -3.75 5.03e-04 0.97632
APOBEC3B-AS1 5.19 -0.512 3.67 6.36e-04 0.97632
SHISA4 4.76 1.884 3.65 6.56e-04 0.97632Interaction of sex differences between young and fetal
topTreat(treat.immune,coef=8)[,-c(1:3)] GENENAME CHR logFC
IGHG3 immunoglobulin heavy constant gamma 3 (G3m marker) 14 -7.45
LINC01416 long intergenic non-protein coding RNA 1416 18 7.92
CSTA cystatin A 3 -5.78
C17orf53 chromosome 17 open reading frame 53 17 -5.25
SIGLEC11 sialic acid binding Ig like lectin 11 19 -5.36
SIX5 SIX homeobox 5 19 5.76
FAM30A family with sequence similarity 30 member A 14 -5.49
IGHG4 immunoglobulin heavy constant gamma 4 (G4m marker) 14 -4.65
LILRA4 leukocyte immunoglobulin like receptor A4 19 -4.30
SLC35G5 solute carrier family 35 member G5 8 -5.17
AveExpr t P.Value adj.P.Val
IGHG3 -1.009 -4.99 2.15e-05 0.262
LINC01416 1.626 4.83 3.35e-05 0.262
CSTA 0.499 -4.71 4.26e-05 0.262
C17orf53 1.717 -4.34 1.11e-04 0.512
SIGLEC11 -1.716 -4.21 1.57e-04 0.532
SIX5 2.519 4.18 1.73e-04 0.532
FAM30A -1.688 -4.03 2.54e-04 0.670
IGHG4 -1.571 -3.96 2.95e-04 0.681
LILRA4 -1.580 -3.88 3.56e-04 0.723
SLC35G5 -0.105 -3.86 3.92e-04 0.723Interaction of sex differences between adult and young
topTreat(treat.immune,coef=9)[,-c(1:3)] GENENAME CHR logFC AveExpr
FBXO43 F-box protein 43 8 8.09 0.910
LINC01839 long intergenic non-protein coding RNA 1839 3 5.49 -1.579
ME1 malic enzyme 1 6 3.20 5.175
LINC00676 long intergenic non-protein coding RNA 676 13 -6.81 -1.783
CDKN3 cyclin dependent kinase inhibitor 3 14 6.16 1.818
ESPL1 extra spindle pole bodies like 1, separase 12 7.62 2.213
HJURP Holliday junction recognition protein 2 9.01 0.877
SPC24 SPC24 component of NDC80 kinetochore complex 19 5.34 2.509
DEPDC1B DEP domain containing 1B 5 7.76 2.330
LINC02236 long intergenic non-protein coding RNA 2236 5 6.40 -0.132
t P.Value adj.P.Val
FBXO43 5.96 1.73e-06 0.0122
LINC01839 5.80 2.43e-06 0.0122
ME1 5.76 2.54e-06 0.0122
LINC00676 -5.70 3.23e-06 0.0122
CDKN3 5.68 3.31e-06 0.0122
ESPL1 5.59 4.42e-06 0.0136
HJURP 5.51 5.74e-06 0.0151
SPC24 5.30 8.70e-06 0.0169
DEPDC1B 5.32 9.14e-06 0.0169
LINC02236 5.30 9.14e-06 0.0169par(mar=c(5,5,3,2))
plot(treat.immune$coefficients[,1],treat.immune$coefficients[,2],xlab="logFC: Young vs Fetal", ylab="logFC: Adult vs Fetal",main="immune cells: Development",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0,col=colours()[c(175)])
sig.genes <- dt.immune[,1] !=0 | dt.immune[,2] != 0
text(treat.immune$coefficients[sig.genes,1],treat.immune$coefficients[sig.genes,2],labels=rownames(dt.immune)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.immune$coefficients[,4],treat.immune$coefficients[,5],xlab="logFC: Fetal Male vs Female", ylab="logFC: Young Male vs Female",main="immune cells: Sex differences - fetal and young",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
sig.genes <- dt.immune[,4] !=0 | dt.immune[,5] != 0
text(treat.immune$coefficients[sig.genes,4],treat.immune$coefficients[sig.genes,5],labels=rownames(dt.immune)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.immune$coefficients[,4],treat.immune$coefficients[,6],xlab="logFC: Fetal Male vs Female", ylab="logFC: Adult Male vs Female",main="immune cells: Sex differences - fetal and adult",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
sig.genes <- dt.immune[,4] !=0 | dt.immune[,6] != 0
text(treat.immune$coefficients[sig.genes,4],treat.immune$coefficients[sig.genes,6],labels=rownames(dt.immune)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.immune$coefficients[,5],treat.immune$coefficients[,6],xlab="logFC: Young Male vs Female", ylab="logFC: Adult Male vs Female",main="immune cells: Sex differences - young and adult",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
sig.genes <- dt.immune[,5] !=0 | dt.immune[,6] != 0
text(treat.immune$coefficients[sig.genes,5],treat.immune$coefficients[sig.genes,6],labels=rownames(dt.immune)[sig.genes],col=2,cex=0.6)
abline(h=0,v=0)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.immune$coefficients[,4],treat.immune$coefficients[,5],xlab="logFC: Fetal Male vs Female", ylab="logFC: Young Male vs Female",main="immune cells: Interaction term: Fetal vs Young",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
sig.genes <- dt.immune[,8] !=0
if(sum(sig.genes)!=0){
text(treat.immune$coefficients[sig.genes,4],treat.immune$coefficients[sig.genes,5],
labels=rownames(dt.immune)[sig.genes],col=2,cex=0.6)
}plot(treat.immune$coefficients[,4],treat.immune$coefficients[,6],xlab="logFC: Fetal Male vs Female", ylab="logFC: Adult Male vs Female",main="immune cells: Interaction term: fetal and adult",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
sig.genes <- dt.immune[,7] !=0
text(treat.immune$coefficients[sig.genes,4],treat.immune$coefficients[sig.genes,6],labels=rownames(dt.immune)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.immune$coefficients[,5],treat.immune$coefficients[,6],xlab="logFC: Young Male vs Female", ylab="logFC: Adult Male vs Female",main="immune cells: Interaction term: young and adult",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
sig.genes <- dt.immune[,9] !=0
text(treat.immune$coefficients[sig.genes,5],treat.immune$coefficients[sig.genes,6],labels=rownames(dt.immune)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
Neurons
cont.neurons <- makeContrasts(YvF = 0.5*(neurons.young.Male + neurons.young.Female) - 0.5*(neurons.fetal.Male + neurons.fetal.Female),
AvF = 0.5*(neurons.adult.Male + neurons.adult.Female) - 0.5*(neurons.fetal.Male + neurons.fetal.Female),
AvY = 0.5*(neurons.adult.Male + neurons.adult.Female) - 0.5*(neurons.young.Male + neurons.young.Female),
SexFetal = neurons.fetal.Male - neurons.fetal.Female,
SexYoung = neurons.young.Male - neurons.young.Female,
SexAdult = neurons.adult.Male - neurons.adult.Female,
InteractionAF = (neurons.adult.Male - neurons.fetal.Male) - (neurons.adult.Female - neurons.fetal.Female),
InteractionYF = (neurons.young.Male - neurons.fetal.Male) - (neurons.young.Female - neurons.fetal.Female),
InteractionAY = (neurons.adult.Male - neurons.young.Male) - (neurons.adult.Female - neurons.young.Female),
levels=design)
fit.neurons <- contrasts.fit(fit,contrasts = cont.neurons)
fit.neurons <- eBayes(fit.neurons,robust=TRUE)
summary(decideTests(fit.neurons)) YvF AvF AvY SexFetal SexYoung SexAdult InteractionAF
Down 396 382 5 0 0 0 0
NotSig 17742 17869 18456 18464 18460 18462 18464
Up 326 213 3 0 4 2 0
InteractionYF InteractionAY
Down 0 2
NotSig 18464 18461
Up 0 1treat.neurons <- treat(fit.neurons,lfc=0.5)
dt.neurons<-decideTests(treat.neurons)
summary(dt.neurons) YvF AvF AvY SexFetal SexYoung SexAdult InteractionAF
Down 190 167 0 0 0 0 0
NotSig 18142 18216 18464 18464 18462 18464 18464
Up 132 81 0 0 2 0 0
InteractionYF InteractionAY
Down 0 2
NotSig 18464 18461
Up 0 1par(mfrow=c(3,3))
for(i in 1:9){
plotMD(treat.neurons,coef=i,status=dt.neurons[,i],hl.col=c("blue","red"))
abline(h=0,col="grey")
}
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
par(mfrow=c(1,1))
par(mar=c(7,4,2,2))
barplot(summary(dt.neurons)[-2,],beside=TRUE,legend=TRUE,col=c("blue","red"),ylab="Number of significant genes",las=2)
title("Neurons")
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
Young vs Fetal
options(digits=3)
topTreat(treat.neurons,coef=1,n=20,p.value=0.05)[,-c(1:3)] GENENAME CHR logFC
SLC5A8 solute carrier family 5 member 8 12 -5.72
LINC00598 long intergenic non-protein coding RNA 598 13 4.12
PHOX2B paired like homeobox 2B 4 -6.13
GBP2 guanylate binding protein 2 1 8.46
CADM2 cell adhesion molecule 2 3 3.20
MMD2 monocyte to macrophage differentiation associated 2 7 -5.56
LINC02026 long intergenic non-protein coding RNA 2026 3 5.17
NRN1 neuritin 1 6 7.12
KCNH5 potassium voltage-gated channel subfamily H member 5 14 -5.02
COL2A1 collagen type II alpha 1 chain 12 -6.49
FAM135B family with sequence similarity 135 member B 8 4.60
SHISA9 shisa family member 9 16 3.02
COL20A1 collagen type XX alpha 1 chain 20 -4.73
ADRA1B adrenoceptor alpha 1B 5 7.30
GIMAP8 GTPase, IMAP family member 8 7 6.72
BIRC3 baculoviral IAP repeat containing 3 11 5.47
GRAMD2A GRAM domain containing 2A 15 -3.97
LINC00682 long intergenic non-protein coding RNA 682 4 -4.39
C2orf72 chromosome 2 open reading frame 72 2 -4.85
KIAA1217 KIAA1217 10 3.81
AveExpr t P.Value adj.P.Val
SLC5A8 -0.3421 -9.86 1.92e-10 2.60e-06
LINC00598 4.6402 9.66 2.82e-10 2.60e-06
PHOX2B -1.4883 -9.39 5.17e-10 3.18e-06
GBP2 3.6829 8.83 1.80e-09 8.30e-06
CADM2 5.5407 8.67 2.34e-09 8.66e-06
MMD2 1.1011 -8.53 3.29e-09 1.01e-05
LINC02026 0.8045 7.94 1.26e-08 2.93e-05
NRN1 1.2287 7.93 1.35e-08 2.93e-05
KCNH5 1.8926 -7.88 1.43e-08 2.93e-05
COL2A1 -0.8189 -7.75 1.99e-08 3.67e-05
FAM135B 2.7144 7.69 2.22e-08 3.73e-05
SHISA9 3.0904 7.46 3.77e-08 5.80e-05
COL20A1 -0.8501 -7.38 4.60e-08 6.24e-05
ADRA1B 2.8972 7.40 4.73e-08 6.24e-05
GIMAP8 3.2806 7.22 7.05e-08 8.67e-05
BIRC3 2.6840 7.12 8.73e-08 1.01e-04
GRAMD2A 1.2349 -6.98 1.22e-07 1.32e-04
LINC00682 -1.6322 -6.89 1.50e-07 1.54e-04
C2orf72 -0.0717 -6.74 2.23e-07 2.16e-04
KIAA1217 8.3628 6.67 2.58e-07 2.38e-04Adult vs Fetal
topTreat(treat.neurons,coef=2,n=20,p.value=0.05)[,-c(1:3)] GENENAME CHR
MDGA2 MAM domain containing glycosylphosphatidylinositol anchor 2 14
SLC5A8 solute carrier family 5 member 8 12
COL20A1 collagen type XX alpha 1 chain 20
CADM2 cell adhesion molecule 2 3
PHOX2B paired like homeobox 2B 4
MMD2 monocyte to macrophage differentiation associated 2 7
NRN1 neuritin 1 6
GPR137C G protein-coupled receptor 137C 14
GRAMD2A GRAM domain containing 2A 15
COL2A1 collagen type II alpha 1 chain 12
TFAP2B transcription factor AP-2 beta 6
IGF2BP3 insulin like growth factor 2 mRNA binding protein 3 7
GBP2 guanylate binding protein 2 1
IFIH1 interferon induced with helicase C domain 1 2
NTRK3 neurotrophic receptor tyrosine kinase 3 15
CCN5 cellular communication network factor 5 20
PRTFDC1 phosphoribosyl transferase domain containing 1 10
LGI1 leucine rich glioma inactivated 1 10
LINC01608 long intergenic non-protein coding RNA 1608 8
SOX11 SRY-box 11 2
logFC AveExpr t P.Value adj.P.Val
MDGA2 -7.43 3.442 -11.53 7.42e-12 1.37e-07
SLC5A8 -5.92 -0.342 -10.26 8.48e-11 7.83e-07
COL20A1 -5.91 -0.850 -9.57 3.52e-10 1.69e-06
CADM2 3.51 5.541 9.51 3.82e-10 1.69e-06
PHOX2B -6.13 -1.488 -9.39 5.15e-10 1.69e-06
MMD2 -5.92 1.101 -9.36 5.49e-10 1.69e-06
NRN1 7.36 1.229 8.37 4.89e-09 1.29e-05
GPR137C -5.53 4.948 -7.83 1.64e-08 3.79e-05
GRAMD2A -4.31 1.235 -7.75 1.95e-08 3.99e-05
COL2A1 -6.38 -0.819 -7.61 2.78e-08 5.13e-05
TFAP2B -5.74 -1.242 -7.52 3.43e-08 5.76e-05
IGF2BP3 -5.20 4.676 -7.16 7.96e-08 1.22e-04
GBP2 7.47 3.683 6.87 1.71e-07 2.43e-04
IFIH1 4.91 3.564 6.72 2.34e-07 3.08e-04
NTRK3 -6.08 4.438 -6.55 3.65e-07 4.36e-04
CCN5 6.71 2.044 6.54 3.78e-07 4.36e-04
PRTFDC1 -4.35 4.176 -6.42 4.86e-07 5.27e-04
LGI1 -6.52 2.120 -6.41 5.25e-07 5.38e-04
LINC01608 -4.91 0.607 -6.36 5.62e-07 5.47e-04
SOX11 -5.36 1.386 -6.32 6.37e-07 5.79e-04Adult vs Young
topTreat(treat.neurons,coef=3)[,-c(1:3)] GENENAME
RSPH3 radial spoke head 3
SLC29A2 solute carrier family 29 member 2
ZRANB3 zinc finger RANBP2-type containing 3
GPR137C G protein-coupled receptor 137C
TFAP2B transcription factor AP-2 beta
LSM4 LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated
TRIM11 tripartite motif containing 11
KARS lysyl-tRNA synthetase
IL20RB interleukin 20 receptor subunit beta
EXOSC2 exosome component 2
CHR logFC AveExpr t P.Value adj.P.Val
RSPH3 6 -3.57 4.44 -5.39 6.57e-06 0.105
SLC29A2 11 -3.36 2.65 -5.12 1.32e-05 0.105
ZRANB3 2 2.54 6.79 4.95 2.08e-05 0.105
GPR137C 14 -4.23 4.95 -4.92 2.28e-05 0.105
TFAP2B 6 -4.16 -1.24 -4.61 5.16e-05 0.191
LSM4 19 2.64 3.89 4.31 1.08e-04 0.299
TRIM11 1 -2.36 3.28 -4.30 1.13e-04 0.299
KARS 16 2.26 4.52 4.23 1.35e-04 0.312
IL20RB 3 -2.97 2.90 -4.00 2.49e-04 0.494
EXOSC2 9 -2.93 3.35 -3.97 2.68e-04 0.494Male vs Female in fetal samples
topTreat(treat.neurons,coef=4)[,-c(1:3)] GENENAME
FRS3 fibroblast growth factor receptor substrate 3
NCMAP non-compact myelin associated protein
C1orf194 chromosome 1 open reading frame 194
PRR22 proline rich 22
SLC48A1 solute carrier family 48 member 1
STAC3 SH3 and cysteine rich domain 3
LINC02347 long intergenic non-protein coding RNA 2347
CCDC106 coiled-coil domain containing 106
KCNE4 potassium voltage-gated channel subfamily E regulatory subunit 4
IQCD IQ motif containing D
CHR logFC AveExpr t P.Value adj.P.Val
FRS3 6 3.65 2.693 4.29 0.000117 1
NCMAP 1 -3.77 1.244 -3.97 0.000277 1
C1orf194 1 3.40 -0.466 3.94 0.000292 1
PRR22 19 -3.52 0.785 -3.84 0.000381 1
SLC48A1 12 3.67 3.644 3.75 0.000487 1
STAC3 12 4.10 2.422 3.74 0.000505 1
LINC02347 12 -4.41 -1.066 -3.66 0.000626 1
CCDC106 19 3.19 1.897 3.62 0.000671 1
KCNE4 2 -3.60 3.617 -3.44 0.001066 1
IQCD 12 3.46 2.083 3.41 0.001151 1Male vs Female in young samples
topTreat(treat.neurons,coef=5)[,-c(1:3)] GENENAME CHR
DNTTIP1 deoxynucleotidyltransferase terminal interacting protein 1 20
CREBL2 cAMP responsive element binding protein like 2 12
DEDD death effector domain containing 1
KARS lysyl-tRNA synthetase 16
LPIN2 lipin 2 18
MITD1 microtubule interacting and trafficking domain containing 1 2
ZRANB3 zinc finger RANBP2-type containing 3 2
CCDC18 coiled-coil domain containing 18 1
FTSJ3 FtsJ RNA 2'-O-methyltransferase 3 17
CDIP1 cell death inducing p53 target 1 16
logFC AveExpr t P.Value adj.P.Val
DNTTIP1 3.73 4.32 6.21 8.10e-07 0.00921
CREBL2 4.51 5.01 6.13 9.97e-07 0.00921
DEDD 3.73 4.49 5.21 1.06e-05 0.06502
KARS 3.18 4.52 4.67 4.31e-05 0.19281
LPIN2 4.16 5.70 4.61 5.22e-05 0.19281
MITD1 3.91 4.90 4.53 6.32e-05 0.19453
ZRANB3 3.46 6.79 4.46 7.44e-05 0.19618
CCDC18 4.61 5.58 4.35 1.05e-04 0.21844
FTSJ3 -3.62 3.24 -4.33 1.06e-04 0.21844
CDIP1 2.79 4.22 3.92 3.06e-04 0.56453Male vs Female in adult samples
topTreat(treat.neurons,coef=6)[,-c(1:3)] GENENAME CHR logFC AveExpr
C6orf136 chromosome 6 open reading frame 136 6 4.40 3.59
PFAS phosphoribosylformylglycinamidine synthase 17 4.16 3.03
IKZF4 IKAROS family zinc finger 4 12 3.71 4.08
PALB2 partner and localizer of BRCA2 16 4.80 4.09
SRRD SRR1 domain containing 22 4.04 2.63
CCDC150 coiled-coil domain containing 150 2 4.82 3.75
UXS1 UDP-glucuronate decarboxylase 1 2 4.01 4.85
ATP10B ATPase phospholipid transporting 10B (putative) 5 -5.83 2.44
C3orf62 chromosome 3 open reading frame 62 3 4.33 4.11
RANBP17 RAN binding protein 17 5 -4.54 6.94
t P.Value adj.P.Val
C6orf136 5.40 6.62e-06 0.122
PFAS 5.08 1.52e-05 0.140
IKZF4 4.78 3.26e-05 0.154
PALB2 4.73 3.88e-05 0.154
SRRD 4.69 4.18e-05 0.154
CCDC150 4.62 5.13e-05 0.156
UXS1 4.56 5.90e-05 0.156
ATP10B -4.50 7.40e-05 0.171
C3orf62 4.32 1.13e-04 0.215
RANBP17 -4.31 1.16e-04 0.215Interaction of sex differences between adult and fetal
topTreat(treat.neurons,coef=7)[,-c(1:3)] GENENAME CHR logFC AveExpr
FRS3 fibroblast growth factor receptor substrate 3 6 -5.14 2.69
MED8 mediator complex subunit 8 1 -4.85 3.24
PALB2 partner and localizer of BRCA2 16 5.70 4.09
C6orf136 chromosome 6 open reading frame 136 6 4.78 3.59
RANBP17 RAN binding protein 17 5 -5.19 6.94
ABCA2 ATP binding cassette subfamily A member 2 9 4.40 3.11
CCDC150 coiled-coil domain containing 150 2 5.28 3.75
UXS1 UDP-glucuronate decarboxylase 1 2 4.23 4.85
RPP25L ribonuclease P/MRP subunit p25 like 9 -4.93 1.99
PFAS phosphoribosylformylglycinamidine synthase 17 4.29 3.03
t P.Value adj.P.Val
FRS3 -4.40 9.39e-05 0.490
MED8 -4.33 1.10e-04 0.490
PALB2 4.30 1.23e-04 0.490
C6orf136 4.29 1.24e-04 0.490
RANBP17 -4.27 1.33e-04 0.490
ABCA2 4.06 2.24e-04 0.623
CCDC150 4.03 2.51e-04 0.623
UXS1 3.94 3.02e-04 0.623
RPP25L -3.95 3.03e-04 0.623
PFAS 3.80 4.35e-04 0.803Interaction of sex differences between young and fetal
topTreat(treat.neurons,coef=8)[,-c(1:3)] GENENAME CHR logFC AveExpr
CREBL2 cAMP responsive element binding protein like 2 12 4.65 5.01
DPP3 dipeptidyl peptidase 3 11 -5.08 1.94
KARS lysyl-tRNA synthetase 16 3.63 4.52
LPIN2 lipin 2 18 4.48 5.70
DEDD death effector domain containing 1 3.75 4.49
FAM209A family with sequence similarity 209 member A 20 -4.31 1.33
PMEL premelanosome protein 12 -5.36 1.72
CDIP1 cell death inducing p53 target 1 16 3.47 4.22
NCMAP non-compact myelin associated protein 1 5.04 1.24
ZRANB3 zinc finger RANBP2-type containing 3 2 3.35 6.79
t P.Value adj.P.Val
CREBL2 4.79 3.25e-05 0.599
DPP3 -4.33 1.13e-04 0.868
KARS 4.05 2.20e-04 0.868
LPIN2 4.03 2.41e-04 0.868
DEDD 3.95 2.91e-04 0.868
FAM209A -3.95 2.92e-04 0.868
PMEL -3.90 3.56e-04 0.868
CDIP1 3.83 3.88e-04 0.868
NCMAP 3.82 4.26e-04 0.868
ZRANB3 3.76 4.70e-04 0.868Interaction of sex differences between adult and young
topTreat(treat.neurons,coef=9)[,-c(1:3)] GENENAME CHR
DNTTIP1 deoxynucleotidyltransferase terminal interacting protein 1 20
TRIM11 tripartite motif containing 11 1
RANBP17 RAN binding protein 17 5
SRRD SRR1 domain containing 22
LINC01436 long intergenic non-protein coding RNA 1436 21
SLC2A8 solute carrier family 2 member 8 9
C3orf62 chromosome 3 open reading frame 62 3
ZRANB3 zinc finger RANBP2-type containing 3 2
C6orf136 chromosome 6 open reading frame 136 6
HOXD-AS2 HOXD cluster antisense RNA 2 2
logFC AveExpr t P.Value adj.P.Val
DNTTIP1 -6.14 4.32 -7.27 6.26e-08 0.00116
TRIM11 5.62 3.28 5.91 1.83e-06 0.01175
RANBP17 -9.13 6.94 -5.93 1.91e-06 0.01175
SRRD 5.75 2.63 4.77 3.56e-05 0.16426
LINC01436 -6.29 -1.71 -4.54 6.75e-05 0.19159
SLC2A8 6.71 3.29 4.50 7.64e-05 0.19159
C3orf62 6.23 4.11 4.45 8.54e-05 0.19159
ZRANB3 -4.13 6.79 -4.40 9.06e-05 0.19159
C6orf136 5.09 3.59 4.36 1.03e-04 0.19159
HOXD-AS2 -6.00 -1.03 -4.29 1.29e-04 0.19159par(mar=c(5,5,3,2))
plot(treat.neurons$coefficients[,1],treat.neurons$coefficients[,2],xlab="logFC: Young vs Fetal", ylab="logFC: Adult vs Fetal",main="neurons: Development",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0,col=colours()[c(175)])
sig.genes <- dt.neurons[,1] !=0 | dt.neurons[,2] != 0
text(treat.neurons$coefficients[sig.genes,1],treat.neurons$coefficients[sig.genes,2],labels=rownames(dt.neurons)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.neurons$coefficients[,4],treat.neurons$coefficients[,5],xlab="logFC: Fetal Male vs Female", ylab="logFC: Young Male vs Female",main="neurons: Sex differences - fetal and young",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
sig.genes <- dt.neurons[,4] !=0 | dt.neurons[,5] != 0
text(treat.neurons$coefficients[sig.genes,4],treat.neurons$coefficients[sig.genes,5],labels=rownames(dt.neurons)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.neurons$coefficients[,4],treat.neurons$coefficients[,6],xlab="logFC: Fetal Male vs Female", ylab="logFC: Adult Male vs Female",main="neurons: Sex differences - fetal and adult",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
sig.genes <- dt.neurons[,4] !=0 | dt.neurons[,6] != 0
if(sum(sig.genes)!=0){
text(treat.neurons$coefficients[sig.genes,4],treat.neurons$coefficients[sig.genes,6],
labels=rownames(dt.neurons)[sig.genes],col=2,cex=0.6)
}plot(treat.neurons$coefficients[,5],treat.neurons$coefficients[,6],xlab="logFC: Young Male vs Female", ylab="logFC: Adult Male vs Female",main="neurons: Sex differences - young and adult",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
sig.genes <- dt.neurons[,5] !=0 | dt.neurons[,6] != 0
text(treat.neurons$coefficients[sig.genes,5],treat.neurons$coefficients[sig.genes,6],labels=rownames(dt.neurons)[sig.genes],col=2,cex=0.6)
abline(h=0,v=0)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
plot(treat.neurons$coefficients[,4],treat.neurons$coefficients[,5],xlab="logFC: Fetal Male vs Female", ylab="logFC: Young Male vs Female",main="neurons: Interaction term: Fetal vs Young",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
sig.genes <- dt.neurons[,8] !=0
if(sum(sig.genes)!=0){
text(treat.neurons$coefficients[sig.genes,4],treat.neurons$coefficients[sig.genes,5],
labels=rownames(dt.neurons)[sig.genes],col=2,cex=0.6)
}plot(treat.neurons$coefficients[,4],treat.neurons$coefficients[,6],xlab="logFC: Fetal Male vs Female", ylab="logFC: Adult Male vs Female",main="neurons: Interaction term: fetal and adult",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
sig.genes <- dt.neurons[,7] !=0
if(sum(sig.genes)!=0){
text(treat.neurons$coefficients[sig.genes,4],treat.neurons$coefficients[sig.genes,6],
labels=rownames(dt.neurons)[sig.genes],col=2,cex=0.6)
}plot(treat.neurons$coefficients[,5],treat.neurons$coefficients[,6],xlab="logFC: Young Male vs Female", ylab="logFC: Adult Male vs Female",main="neurons: Interaction term: young and adult",col=rgb(0,0,1,alpha=0.25),pch=16,cex=0.8)
abline(h=0,v=0)
sig.genes <- dt.neurons[,9] !=0
text(treat.neurons$coefficients[sig.genes,5],treat.neurons$coefficients[sig.genes,6],labels=rownames(dt.neurons)[sig.genes],col=2,cex=0.6)
| Version | Author | Date |
|---|---|---|
| f474878 | Belinda Phipson | 2019-10-28 |
Write out results
fdr.cardio <- apply(treat.cardio$p.value, 2, function(x) p.adjust(x, method="BH"))
output.cardio <- data.frame(treat.cardio$genes,LogFC=treat.cardio$coefficients,AveExp=treat.cardio$Amean,tstat=treat.cardio$t, pvalue=treat.cardio$p.value, fdr=fdr.cardio)
write.csv(output.cardio,file="./output/DEAnalysis/BroadCellTypes/de-cardio-all.csv")
fdr.endo <- apply(treat.endo$p.value, 2, function(x) p.adjust(x, method="BH"))
output.endo <- data.frame(treat.endo$genes,LogFC=treat.endo$coefficients,AveExp=treat.endo$Amean,tstat=treat.endo$t, pvalue=treat.endo$p.value, fdr=fdr.endo)
write.csv(output.endo,file="./output/DEAnalysis/BroadCellTypes/de-endo-all.csv")
fdr.epicardial <- apply(treat.epicardial$p.value, 2, function(x) p.adjust(x, method="BH"))
output.epicardial <- data.frame(treat.epicardial$genes,LogFC=treat.epicardial$coefficients,AveExp=treat.epicardial$Amean,tstat=treat.epicardial$t, pvalue=treat.epicardial$p.value, fdr=fdr.epicardial)
write.csv(output.epicardial,file="./output/DEAnalysis/BroadCellTypes/de-epicardial-all.csv")
fdr.fibro <- apply(treat.fibro$p.value, 2, function(x) p.adjust(x, method="BH"))
output.fibro <- data.frame(treat.fibro$genes,LogFC=treat.fibro$coefficients,AveExp=treat.fibro$Amean,tstat=treat.fibro$t, pvalue=treat.fibro$p.value, fdr=fdr.fibro)
write.csv(output.fibro,file="./output/DEAnalysis/BroadCellTypes/de-fibro-all.csv")
fdr.immune <- apply(treat.immune$p.value, 2, function(x) p.adjust(x, method="BH"))
output.immune <- data.frame(treat.immune$genes,LogFC=treat.immune$coefficients,AveExp=treat.immune$Amean,tstat=treat.immune$t, pvalue=treat.immune$p.value, fdr=fdr.immune)
write.csv(output.immune,file="./output/DEAnalysis/BroadCellTypes/de-immune-all.csv")
fdr.neurons <- apply(treat.neurons$p.value, 2, function(x) p.adjust(x, method="BH"))
output.neurons <- data.frame(treat.neurons$genes,LogFC=treat.neurons$coefficients,AveExp=treat.neurons$Amean,tstat=treat.neurons$t, pvalue=treat.neurons$p.value, fdr=fdr.neurons)
write.csv(output.neurons,file="./output/DEAnalysis/BroadCellTypes/de-neurons-all.csv")
fdr.smc <- apply(treat.smc$p.value, 2, function(x) p.adjust(x, method="BH"))
output.smc <- data.frame(treat.smc$genes,LogFC=treat.smc$coefficients,AveExp=treat.smc$Amean,tstat=treat.smc$t, pvalue=treat.smc$p.value, fdr=fdr.smc)
write.csv(output.smc,file="./output/DEAnalysis/BroadCellTypes/de-smc-all.csv")# Standard limma analysis with no fold change cut-off
# Cardiomyocytes
for(i in 1:ncol(fit.cardio)){
write.csv(topTable(fit.cardio,coef=i,n="Inf"),
file=paste("./output/DEAnalysis/BroadCellTypes/STD-ind/de-cardio-",colnames(fit.cardio)[i],".csv",sep=""),
row.names = FALSE)
}
# Endothelium
for(i in 1:ncol(fit.endo)){
write.csv(topTable(fit.endo,coef=i,n="Inf"),
file=paste("./output/DEAnalysis/BroadCellTypes/STD-ind/de-endo-",colnames(fit.endo)[i],".csv",sep=""),
row.names = FALSE)
}
# Epicardial
for(i in 1:ncol(fit.epicardial)){
write.csv(topTable(fit.epicardial,coef=i,n="Inf"),
file=paste("./output/DEAnalysis/BroadCellTypes/STD-ind/de-epicardial-",colnames(fit.epicardial)[i],".csv",sep=""),
row.names = FALSE)
}
# Fibroblasts
for(i in 1:ncol(fit.fibro)){
write.csv(topTable(fit.fibro,coef=i,n="Inf"),
file=paste("./output/DEAnalysis/BroadCellTypes/STD-ind/de-fibro-",colnames(fit.fibro)[i],".csv",sep=""),
row.names = FALSE)
}
# Immune
for(i in 1:ncol(fit.immune)){
write.csv(topTable(fit.immune,coef=i,n="Inf"),
file=paste("./output/DEAnalysis/BroadCellTypes/STD-ind/de-immune-",colnames(fit.immune)[i],".csv",sep=""),
row.names = FALSE)
}
# Neurons
for(i in 1:ncol(fit.neurons)){
write.csv(topTable(fit.neurons,coef=i,n="Inf"),
file=paste("./output/DEAnalysis/BroadCellTypes/STD-ind/de-neurons-",colnames(fit.neurons)[i],".csv",sep=""),
row.names = FALSE)
}
# smooth muscle cells
for(i in 1:ncol(fit.smc)){
write.csv(topTable(fit.smc,coef=i,n="Inf"),
file=paste("./output/DEAnalysis/BroadCellTypes/STD-ind/de-smc-",colnames(fit.smc)[i],".csv",sep=""),
row.names = FALSE)
}
# TREAT analysis with log-fold change cut-off of 0.5
# Cardiomyocytes
for(i in 1:ncol(treat.cardio)){
write.csv(topTreat(treat.cardio,coef=i,n="Inf"),
file=paste("./output/DEAnalysis/BroadCellTypes/TREAT-indiv/de-cardio-",colnames(treat.cardio)[i],".csv",sep=""),
row.names = FALSE)
}
# Endothelium
for(i in 1:ncol(treat.endo)){
write.csv(topTreat(treat.endo,coef=i,n="Inf"),
file=paste("./output/DEAnalysis/BroadCellTypes/TREAT-indiv/de-endo-",colnames(treat.endo)[i],".csv",sep=""),
row.names = FALSE)
}
# Epicardial
for(i in 1:ncol(treat.epicardial)){
write.csv(topTreat(treat.epicardial,coef=i,n="Inf"),
file=paste("./output/DEAnalysis/BroadCellTypes/TREAT-indiv/de-epicardial-",colnames(treat.epicardial)[i],".csv",sep=""),
row.names = FALSE)
}
# Fibroblasts
for(i in 1:ncol(treat.fibro)){
write.csv(topTreat(treat.fibro,coef=i,n="Inf"),
file=paste("./output/DEAnalysis/BroadCellTypes/TREAT-indiv/de-fibro-",colnames(treat.fibro)[i],".csv",sep=""),
row.names = FALSE)
}
# Immune
for(i in 1:ncol(treat.immune)){
write.csv(topTreat(treat.immune,coef=i,n="Inf"),
file=paste("./output/DEAnalysis/BroadCellTypes/TREAT-indiv/de-immune-",colnames(treat.immune)[i],".csv",sep=""),
row.names = FALSE)
}
# Neurons
for(i in 1:ncol(treat.neurons)){
write.csv(topTreat(treat.neurons,coef=i,n="Inf"),
file=paste("./output/DEAnalysis/BroadCellTypes/TREAT-indiv/de-neurons-",colnames(treat.neurons)[i],".csv",sep=""),
row.names = FALSE)
}
# smooth muscle cells
for(i in 1:ncol(treat.smc)){
write.csv(topTreat(treat.smc,coef=i,n="Inf"),
file=paste("./output/DEAnalysis/BroadCellTypes/TREAT-indiv/de-smc-",colnames(treat.smc)[i],".csv",sep=""),
row.names = FALSE)
}
sessionInfo()R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.7 (Final)
Matrix products: default
BLAS: /usr/local/installed/R/3.6.0/lib64/R/lib/libRblas.so
LAPACK: /usr/local/installed/R/3.6.0/lib64/R/lib/libRlapack.so
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
attached base packages:
[1] splines parallel stats4 stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] dplyr_0.8.3 clustree_0.4.0
[3] ggraph_1.0.2 workflowr_1.3.0
[5] NMF_0.21.0 bigmemory_4.5.33
[7] cluster_2.1.0 rngtools_1.4
[9] pkgmaker_0.27 registry_0.5-1
[11] scran_1.12.0 SingleCellExperiment_1.6.0
[13] SummarizedExperiment_1.14.1 GenomicRanges_1.36.0
[15] GenomeInfoDb_1.20.0 DelayedArray_0.10.0
[17] BiocParallel_1.18.1 matrixStats_0.55.0
[19] cowplot_1.0.0 monocle_2.12.0
[21] DDRTree_0.1.5 irlba_2.3.3
[23] VGAM_1.1-1 ggplot2_3.2.1
[25] Matrix_1.2-17 Seurat_3.0.3.9019
[27] org.Hs.eg.db_3.8.2 AnnotationDbi_1.46.1
[29] IRanges_2.18.1 S4Vectors_0.22.0
[31] Biobase_2.44.0 BiocGenerics_0.30.0
[33] RColorBrewer_1.1-2 edgeR_3.26.3
[35] limma_3.40.2
loaded via a namespace (and not attached):
[1] reticulate_1.13 R.utils_2.9.0
[3] tidyselect_0.2.5 RSQLite_2.1.2
[5] htmlwidgets_1.5 grid_3.6.0
[7] combinat_0.0-8 docopt_0.6.1
[9] Rtsne_0.15 munsell_0.5.0
[11] codetools_0.2-16 ica_1.0-2
[13] statmod_1.4.30 future_1.14.0
[15] withr_2.1.2 colorspace_1.4-1
[17] fastICA_1.2-2 knitr_1.25
[19] ROCR_1.0-7 gbRd_0.4-11
[21] listenv_0.7.0 labeling_0.3
[23] Rdpack_0.11-0 git2r_0.26.1
[25] slam_0.1-45 GenomeInfoDbData_1.2.1
[27] polyclip_1.10-0 farver_1.1.0
[29] bit64_0.9-7 pheatmap_1.0.12
[31] rprojroot_1.3-2 vctrs_0.2.0
[33] xfun_0.10 R6_2.4.0
[35] doParallel_1.0.15 ggbeeswarm_0.6.0
[37] rsvd_1.0.2 locfit_1.5-9.1
[39] bitops_1.0-6 assertthat_0.2.1
[41] SDMTools_1.1-221.1 scales_1.0.0
[43] beeswarm_0.2.3 gtable_0.3.0
[45] npsurv_0.4-0 globals_0.12.4
[47] rlang_0.4.0 zeallot_0.1.0
[49] lazyeval_0.2.2 yaml_2.2.0
[51] reshape2_1.4.3 backports_1.1.5
[53] tools_3.6.0 gridBase_0.4-7
[55] gplots_3.0.1.1 dynamicTreeCut_1.63-1
[57] ggridges_0.5.1 Rcpp_1.0.2
[59] plyr_1.8.4 zlibbioc_1.30.0
[61] purrr_0.3.2 RCurl_1.95-4.12
[63] densityClust_0.3 pbapply_1.4-1
[65] viridis_0.5.1 zoo_1.8-6
[67] ggrepel_0.8.1 fs_1.3.1
[69] magrittr_1.5 data.table_1.12.4
[71] lmtest_0.9-37 RANN_2.6.1
[73] whisker_0.3-2 fitdistrplus_1.0-14
[75] lsei_1.2-0 evaluate_0.14
[77] xtable_1.8-4 sparsesvd_0.1-4
[79] gridExtra_2.3 HSMMSingleCell_1.4.0
[81] compiler_3.6.0 scater_1.12.2
[83] tibble_2.1.3 KernSmooth_2.23-15
[85] crayon_1.3.4 R.oo_1.22.0
[87] htmltools_0.4.0 tidyr_0.8.3
[89] DBI_1.0.0 tweenr_1.0.1
[91] MASS_7.3-51.4 R.methodsS3_1.7.1
[93] gdata_2.18.0 metap_1.1
[95] igraph_1.2.4.1 pkgconfig_2.0.3
[97] bigmemory.sri_0.1.3 plotly_4.9.0
[99] foreach_1.4.7 vipor_0.4.5
[101] dqrng_0.2.1 XVector_0.24.0
[103] bibtex_0.4.2 stringr_1.4.0
[105] digest_0.6.21 sctransform_0.2.0
[107] RcppAnnoy_0.0.12 tsne_0.1-3
[109] rmarkdown_1.14 DelayedMatrixStats_1.6.0
[111] gtools_3.8.1 nlme_3.1-141
[113] jsonlite_1.6 BiocNeighbors_1.2.0
[115] viridisLite_0.3.0 pillar_1.4.2
[117] lattice_0.20-38 httr_1.4.1
[119] survival_2.44-1.1 glue_1.3.1
[121] qlcMatrix_0.9.7 FNN_1.1.3
[123] png_0.1-7 iterators_1.0.12
[125] bit_1.1-14 ggforce_0.3.0
[127] stringi_1.4.3 blob_1.2.0
[129] BiocSingular_1.0.0 caTools_1.17.1.2
[131] memoise_1.1.0 future.apply_1.3.0
[133] ape_5.3