Tohidul: does Seasol prime gene expression
Mark Ziemann
2022-02-10
Source codes: https://github.com/markziemann/tohidul_rnaseq
Background
Here we have n=6 control (control “H”) and n=6 seaweed (SW). We have separate leaf and root samples.
Reads underwent quality trimming using Skewer (Jiang et al, 2014). I mapped the reads to the Arabidopsis transcriptome (TAIR10/Ensembl47) using Kallisto (Bray et al, 2016). Expression counts were loaded into R and then DE analysis was performed with DESeq2 (Love et al, 2014). Enrichment analysis was performed using Plant Reactome genesets with the Mitch package (Kaspi & Ziemann 2020).
suppressPackageStartupMessages({
library("reshape2")
library("gplots")
library("DESeq2")
library("mitch")
library("kableExtra")
library("eulerr")
library("UpSetR")
library("vioplot")
library(ggplot2)
})Load data
Here we load the data in from the aligner. Take note that the columns are arranged in order.
tmp <- read.table("3col.tsv.gz")
x <- as.data.frame(acast(tmp, V2~V1, value.var="V3"))
x$gene <- sapply(strsplit(rownames(x),"\\."),"[[",1)
xx <- aggregate(. ~ gene, x, sum)
rownames(xx) <- xx$gene
xx$gene = NULL
xx <- xx[,order(colnames(xx))]
gn <- read.table("../../ref/Arabidopsis_thaliana.TAIR10.46.geneaccession2symbol.tsv")
rownames(gn)<-gn$V1
gn$V1=NULL
xn<-merge(gn,xx,by=0)
rownames(xn) <- paste(xn$Row.names,xn$V2)
xn[,1:2]=NULL
xx <- xn
write.table(xx,file="seasol_2021-03_genecounts.tsv",sep="\t",quote=FALSE)Sample sheet
The sample sheet is read in and put in order as well.
ss <- read.table("samplesheet.tsv",header=TRUE,sep="\t")
ss <- ss[order(ss$sample),]MDS
MDS is just like PCA. The more similar (correlated) the data sets are the closer they will appear on the scatterplot.
cols <- as.numeric(factor(ss$tissue))
cols <- gsub(1,"pink",cols)
cols <- gsub(2,"lightblue",cols)
plot(cmdscale(dist(t(xx))), xlab="Coordinate 1", ylab="Coordinate 2",
col=cols, cex=4 , pch=19, main="MDS plot all samples",bty="n")
plot(cmdscale(dist(t(xx))), xlab="Coordinate 1", ylab="Coordinate 2",
col=cols, cex=4 , pch=19, main="MDS plot all samples",bty="n")
text(cmdscale(dist(t(xx))), labels=colnames(xx) )
leaf <- xx[,grep("-L",colnames(xx))]
ssl <- subset(ss,tissue=="leaf")
cols <- as.numeric(factor(ssl$treatment))
cols <- gsub(1,"pink",cols)
cols <- gsub(2,"lightblue",cols)
plot(cmdscale(dist(t(leaf))), xlab="Coordinate 1", ylab="Coordinate 2",
col=cols, cex=4 , main="MDS plot leaf samples",pch=19,bty="n")
text(cmdscale(dist(t(leaf))), labels=colnames(leaf) )
root <- xx[,grep("-R",colnames(xx))]
ssr <- subset(ss,tissue=="root")
cols <- as.numeric(factor(ssr$treatment))
cols <- gsub(1,"pink",cols)
cols <- gsub(2,"lightblue",cols)
plot(cmdscale(dist(t(root))), xlab="Coordinate 1", ylab="Coordinate 2",
col=cols, cex=4 , main="MDS plot root samples",pch=19,bty="n")
text(cmdscale(dist(t(root))), labels=colnames(root) )
colfunc <- colorRampPalette(c("white","blue"))
heatmap.2(cor(xx,method="pearson"),col=colfunc(25),trace="none",
scale="none",margin=c(10,10),main="Pearson correlation all samples")
heatmap.2(cor(xx,method="spearman"),col=colfunc(25),trace="none",
scale="none",margin=c(10,10),main="Spearman correlation all samples")
heatmap.2(cor(leaf,method="pearson"),col=colfunc(25),trace="none",
scale="none",margin=c(10,10),main="Pearson correlation leaf samples")
heatmap.2(cor(leaf,method="spearman"),col=colfunc(25),trace="none",
scale="none",margin=c(10,10),main="Spearman correlation leaf samples")
heatmap.2(cor(root,method="pearson"),col=colfunc(25),trace="none",
scale="none",margin=c(10,10),main="Pearson correlation root samples")
heatmap.2(cor(root,method="spearman"),col=colfunc(25),trace="none",
scale="none",margin=c(10,10),main="Spearman correlation root samples")
Functions
run_de <- function(ss,xx){
xx <- xx[which(rowMeans(xx)>10),]
y <- round(xx)
# MDS
mds <- cmdscale(dist(t(y)))
XMAX=max(mds[,1])*1.1
XMIN=min(mds[,1])*1.1
plot( mds , xlab="Coordinate 1", ylab="Coordinate 2",
type = "n" , xlim=c(XMIN,XMAX),main="MDS plot",bty="n")
text(mds, labels=colnames(y) )
# DE
dds <- DESeqDataSetFromMatrix(countData=y, colData = ss, design = ~ trt)
dds <- DESeq(dds)
de <- DESeq2::results(dds)
de <- de[order(de$pvalue),]
up <- rownames(subset(de, log2FoldChange>0 & padj<0.05 ))
dn <- rownames(subset(de, log2FoldChange<0 & padj<0.05 ))
str(up)
str(dn)
# MA plot
sig <-subset(de, padj < 0.05 )
GENESUP <- length(up)
GENESDN <- length(dn)
SUBHEADER = paste(GENESUP, "up, ", GENESDN, "down")
ns <-subset(de, padj > 0.05 )
plot(log2(de$baseMean),de$log2FoldChange,
xlab="log2 basemean", ylab="log2 foldchange",
pch=19, cex=0.5, col="dark gray",
main="smear plot")
points(log2(sig$baseMean),sig$log2FoldChange,
pch=19, cex=0.5, col="red")
mtext(SUBHEADER)
# heatmap
yn <- y/colSums(y)*1000000
yf <- yn[which(rownames(yn) %in% rownames(de)[1:50]),]
mycols <- gsub("0","yellow",ss$trt)
mycols <- gsub("1","orange",mycols)
colfunc <- colorRampPalette(c("blue", "white", "red"))
heatmap.2( as.matrix(yf), col=colfunc(25),scale="row",
ColSideColors =mycols ,trace="none",
margin = c(10,20), cexRow=0.8, cexCol=0.8 , main="Top 50 genes by p-val")
mtext("yellow=ctrl, orange=trt")
return(de)
}
mitch_barplot <- function(res){
sig <- res$enrichment_result
sig <- head( sig[order(sig$pANOVA),] ,30)
sig <- sig[order(sig$s.dist),]
par(mar=c(3,25,1,1)); barplot(sig$s.dist,horiz=TRUE,las=2,cex.names = 0.6,cex.axis = 0.6,
names.arg=sig$set,main="Enrichment score") ;grid()
}
mitch_bubbleplot <- function(res,n) {
top <- head(res$enrichment_result,n)
top <- top[order(top$s.dist),]
top$set <- factor(top$set, levels = top$set[order(top$s.dist)])
ggplot(top, aes(s.dist, set, size = setSize)) + geom_point(aes(colour=-log10(top$p.adjustANOVA)))
}Split data into contrast groups
l3 <- leaf[,grep("3D",colnames(leaf))]
ssl3 <- subset(ssl,days==3)
ssl3$trt <- as.numeric(ssl3$treatment == "seaweed")
l5 <- leaf[,grep("5D",colnames(leaf))]
ssl5 <- subset(ssl,days==5)
ssl5$trt <- as.numeric(ssl5$treatment == "seaweed")
r3 <- root[,grep("3D",colnames(root))]
ssr3 <- subset(ssr,days==3)
ssr3$trt <- as.numeric(ssr3$treatment == "seaweed")
r5 <- root[,grep("5D",colnames(root))]
ssr5 <- subset(ssr,days==5)
ssr5$trt <- as.numeric(ssr5$treatment == "seaweed")DE
Here, were using DESeq2 to perform differential expression analysis to understand gene expression changes caused by seaweed treatment. Enrichment analysis is performed with mitch.
del3 <- run_de(ssl3,l3)## converting counts to integer mode## the design formula contains one or more numeric variables with integer values,
## specifying a model with increasing fold change for higher values.
## did you mean for this to be a factor? if so, first convert
## this variable to a factor using the factor() function## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## chr [1:518] "AT1G80315 AT1G80315" "AT2G47880 GRXC13" "AT2G02780 AT2G02780" ...
## chr [1:731] "AT4G02720 AT4G02720" "AT1G80890 AT1G80890" ...
del5 <- run_de(ssl5,l5)## converting counts to integer mode## the design formula contains one or more numeric variables with integer values,
## specifying a model with increasing fold change for higher values.
## did you mean for this to be a factor? if so, first convert
## this variable to a factor using the factor() function## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## chr [1:1944] "AT2G47880 GRXC13" "AT5G48485 DIR1" "AT1G25530 AT1G25530" ...
## chr [1:1838] "AT5G38910 AT5G38910" "AT5G38200 AT5G38200" ...
der3 <- run_de(ssr3,r3)## converting counts to integer mode## the design formula contains one or more numeric variables with integer values,
## specifying a model with increasing fold change for higher values.
## did you mean for this to be a factor? if so, first convert
## this variable to a factor using the factor() function## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## chr [1:1179] "AT1G01580 FRO2" "AT5G43780 APS4" "AT2G28160 FIT" ...
## chr [1:1239] "AT5G38910 AT5G38910" "AT4G19810 ChiC" "AT5G39100 GLP6" ...
der5 <- run_de(ssr5,r5)## converting counts to integer mode## the design formula contains one or more numeric variables with integer values,
## specifying a model with increasing fold change for higher values.
## did you mean for this to be a factor? if so, first convert
## this variable to a factor using the factor() function## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## chr [1:1748] "AT4G11310 RDL4" "AT5G43780 APS4" "AT4G40070 ATL32" ...
## chr [1:2207] "AT4G31330 AT4G31330" "AT5G38910 AT5G38910" "AT5G48850 SDI1" ...
del3_top <- head(as.data.frame(del3),40)
kbl(del3_top[order(del3_top$log2FoldChange),]) %>% kable_paper("hover", full_width = F)| baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | |
|---|---|---|---|---|---|---|
| AT4G02720 AT4G02720 | 66.28442 | -24.4055896 | 3.0036038 | -8.125436 | 0e+00 | 0.0000000 |
| AT5G24640 AT5G24640 | 55.61835 | -1.5123467 | 0.3039779 | -4.975186 | 7e-07 | 0.0003389 |
| AT1G19840 AT1G19840 | 291.76199 | -1.4406186 | 0.2427865 | -5.933684 | 0e+00 | 0.0000069 |
| AT5G47450 TIP2-3 | 276.17074 | -1.2829556 | 0.2439539 | -5.259009 | 1e-07 | 0.0001209 |
| AT1G23100 AT1G23100 | 85.06663 | -1.2205963 | 0.2136810 | -5.712236 | 0e+00 | 0.0000200 |
| AT1G17180 GSTU25 | 68.70081 | -1.1543346 | 0.2254434 | -5.120286 | 3e-07 | 0.0002079 |
| AT2G32190 AT2G32190 | 267.13594 | -1.1035412 | 0.2200884 | -5.014081 | 5e-07 | 0.0002959 |
| AT3G20470 GRP5 | 1080.03869 | -1.0493829 | 0.1991533 | -5.269223 | 1e-07 | 0.0001191 |
| AT4G23680 AT4G23680 | 1267.27525 | -1.0245152 | 0.1681644 | -6.092344 | 0e+00 | 0.0000033 |
| AT5G13210 AT5G13210 | 278.40913 | -0.9337214 | 0.1860677 | -5.018180 | 5e-07 | 0.0002959 |
| AT4G36900 RAP2-10 | 1747.05112 | -0.7127586 | 0.1351643 | -5.273276 | 1e-07 | 0.0001191 |
| AT5G57290 RPP3B | 3367.21007 | -0.5132475 | 0.0922677 | -5.562590 | 0e+00 | 0.0000370 |
| AT3G62130 LCD | 1534.20090 | -0.4672862 | 0.0859577 | -5.436234 | 1e-07 | 0.0000631 |
| AT1G67870 AT1G67870 | 19999.60151 | -0.4606123 | 0.0899859 | -5.118714 | 3e-07 | 0.0002079 |
| AT2G47690 AT2G47690 | 1511.67072 | -0.4518912 | 0.0800378 | -5.645974 | 0e+00 | 0.0000264 |
| AT1G80890 AT1G80890 | 641.55772 | -0.4461059 | 0.0711002 | -6.274325 | 0e+00 | 0.0000013 |
| AT1G76010 AT1G76010 | 5053.16066 | -0.4197083 | 0.0758145 | -5.535992 | 0e+00 | 0.0000404 |
| AT4G34265 AT4G34265 | 1692.51837 | -0.4115476 | 0.0770769 | -5.339441 | 1e-07 | 0.0001024 |
| AT1G74230 RBG5 | 3898.86721 | -0.3937941 | 0.0743613 | -5.295690 | 1e-07 | 0.0001178 |
| AT1G19600 AT1G19600 | 1838.47855 | -0.3569930 | 0.0682954 | -5.227188 | 2e-07 | 0.0001381 |
| AT3G06210 AT3G06210 | 1470.82316 | -0.2635968 | 0.0515054 | -5.117844 | 3e-07 | 0.0002079 |
| AT5G08100 AT5G08100 | 1346.99889 | -0.2542344 | 0.0506153 | -5.022875 | 5e-07 | 0.0002959 |
| AT1G71070 AT1G71070 | 1062.94542 | 0.2706976 | 0.0538302 | 5.028727 | 5e-07 | 0.0002959 |
| AT2G02780 AT2G02780 | 636.58620 | 0.4510758 | 0.0718314 | 6.279646 | 0e+00 | 0.0000013 |
| AT2G20110 AT2G20110 | 117.73248 | 0.6813811 | 0.1359518 | 5.011933 | 5e-07 | 0.0002959 |
| AT2G22860 PSK2 | 161.84427 | 0.8072783 | 0.1592426 | 5.069487 | 4e-07 | 0.0002522 |
| AT1G52800 AT1G52800 | 469.21434 | 0.8951727 | 0.1751122 | 5.111996 | 3e-07 | 0.0002079 |
| AT5G01600 FER1 | 32738.16957 | 0.9111937 | 0.1659004 | 5.492414 | 0e+00 | 0.0000487 |
| AT3G03910 GSH3 | 109.72718 | 1.1727545 | 0.2287562 | 5.126658 | 3e-07 | 0.0002079 |
| AT2G47880 GRXC13 | 786.20819 | 1.5068047 | 0.2379736 | 6.331814 | 0e+00 | 0.0000013 |
| AT3G46130 ATMYB48 | 370.67769 | 1.5505231 | 0.2923370 | 5.303889 | 1e-07 | 0.0001178 |
| AT2G16660 AT2G16660 | 2088.61339 | 1.8583295 | 0.3726677 | 4.986560 | 6e-07 | 0.0003289 |
| AT3G15270 SPL5 | 90.77205 | 1.9225486 | 0.3639272 | 5.282783 | 1e-07 | 0.0001191 |
| AT4G31355 AT4G31355 | 51.16141 | 1.9689334 | 0.3450022 | 5.707016 | 0e+00 | 0.0000200 |
| AT3G04200 AT3G04200 | 21.61730 | 2.2994837 | 0.4478093 | 5.134962 | 3e-07 | 0.0002079 |
| AT4G34950 AT4G34950 | 1829.91697 | 2.4090065 | 0.4291117 | 5.613939 | 0e+00 | 0.0000295 |
| AT1G19250 FMO1 | 217.09868 | 2.8345488 | 0.4887518 | 5.799567 | 0e+00 | 0.0000139 |
| AT4G28755 AT4G28755 | 954.49009 | 2.9529213 | 0.4977916 | 5.932043 | 0e+00 | 0.0000069 |
| AT4G39250 RL1 | 36.27994 | 3.3242302 | 0.5306020 | 6.265016 | 0e+00 | 0.0000013 |
| AT1G80315 AT1G80315 | 84.38164 | 24.0736723 | 3.0035242 | 8.015142 | 0e+00 | 0.0000000 |
del5_top <- head(as.data.frame(del5),40)
kbl(del5_top[order(del5_top$log2FoldChange),]) %>% kable_paper("hover", full_width = F)| baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | |
|---|---|---|---|---|---|---|
| AT5G38910 AT5G38910 | 303.58343 | -4.5031520 | 0.2307041 | -19.51916 | 0 | 0 |
| AT1G12030 AT1G12030 | 89.44473 | -3.5543185 | 0.3373152 | -10.53708 | 0 | 0 |
| AT1G73120 AT1G73120 | 1037.13677 | -3.3342276 | 0.2492811 | -13.37537 | 0 | 0 |
| AT5G48850 SDI1 | 3421.87881 | -3.2716802 | 0.3001879 | -10.89877 | 0 | 0 |
| AT3G05400 SUGTL5 | 846.71267 | -3.0674992 | 0.2460183 | -12.46858 | 0 | 0 |
| AT2G26695 AT2G26695 | 693.69282 | -2.8330305 | 0.1786367 | -15.85917 | 0 | 0 |
| AT3G49580 LSU1 | 4091.10177 | -2.7414330 | 0.2162405 | -12.67771 | 0 | 0 |
| AT1G78000 SULTR1;2 | 1864.03228 | -2.6870625 | 0.1789000 | -15.01991 | 0 | 0 |
| AT4G35720 AT4G35720 | 254.92627 | -2.6053282 | 0.2417786 | -10.77568 | 0 | 0 |
| AT3G08860 PYD4 | 7392.19603 | -2.5855746 | 0.1813214 | -14.25962 | 0 | 0 |
| AT5G38200 AT5G38200 | 1193.03428 | -2.2035942 | 0.1267627 | -17.38361 | 0 | 0 |
| AT4G34710 ADC2 | 56721.65201 | -2.2012682 | 0.2079808 | -10.58400 | 0 | 0 |
| AT3G49570 LSU3 | 1329.58400 | -2.1730786 | 0.1960074 | -11.08672 | 0 | 0 |
| AT1G23730 BCA3 | 1054.47982 | -2.1510868 | 0.1876288 | -11.46459 | 0 | 0 |
| AT3G50400 AT3G50400 | 875.51630 | -1.9573587 | 0.1529599 | -12.79655 | 0 | 0 |
| AT4G04830 MSRB5 | 3054.06777 | -1.9498782 | 0.1376807 | -14.16232 | 0 | 0 |
| AT2G31980 CYS2 | 302.03468 | -1.9037167 | 0.1658399 | -11.47924 | 0 | 0 |
| AT1G22500 ATL15 | 1331.09522 | -1.8170234 | 0.1276018 | -14.23980 | 0 | 0 |
| AT5G13900 VAS | 335.52898 | -1.7284904 | 0.1216908 | -14.20395 | 0 | 0 |
| AT5G13580 ABCG6 | 1077.75810 | -1.5823121 | 0.1505561 | -10.50978 | 0 | 0 |
| AT4G39675 AT4G39675 | 214.81777 | -1.5382484 | 0.1102498 | -13.95239 | 0 | 0 |
| AT1G70170 2MMP | 201.97607 | -1.4922090 | 0.1413324 | -10.55815 | 0 | 0 |
| AT5G50260 CEP1 | 414.67241 | -1.3750005 | 0.0997691 | -13.78183 | 0 | 0 |
| AT5G12930 AT5G12930 | 337.72142 | -1.3707290 | 0.0906339 | -15.12381 | 0 | 0 |
| AT1G56320 AT1G56320 | 212.37001 | -1.3622810 | 0.1261849 | -10.79591 | 0 | 0 |
| AT5G51200 AT5G51200 | 5514.01859 | -1.2352164 | 0.1178039 | -10.48536 | 0 | 0 |
| AT5G19600 SULTR3;5 | 1088.54267 | -1.1949236 | 0.1148836 | -10.40117 | 0 | 0 |
| AT2G40390 AT2G40390 | 323.13292 | -1.1353012 | 0.1088910 | -10.42603 | 0 | 0 |
| AT5G11090 AT5G11090 | 4250.91742 | -1.0331719 | 0.0718836 | -14.37285 | 0 | 0 |
| AT4G33740 AT4G33740 | 2819.37270 | -0.6083600 | 0.0548784 | -11.08560 | 0 | 0 |
| AT4G12290 AT4G12290 | 11744.16318 | 0.6054930 | 0.0518641 | 11.67460 | 0 | 0 |
| AT3G20390 AT3G20390 | 6799.89789 | 0.9992839 | 0.0967066 | 10.33315 | 0 | 0 |
| AT5G43780 APS4 | 4091.27211 | 1.1228877 | 0.0972577 | 11.54548 | 0 | 0 |
| AT1G70260 AT1G70260 | 1138.62042 | 1.5113740 | 0.1350037 | 11.19505 | 0 | 0 |
| AT2G47880 GRXC13 | 845.56622 | 1.6210896 | 0.1006440 | 16.10716 | 0 | 0 |
| AT1G25530 AT1G25530 | 599.90207 | 1.6355270 | 0.1383917 | 11.81810 | 0 | 0 |
| AT3G54600 DJ1F | 3892.54924 | 1.9623217 | 0.1883099 | 10.42071 | 0 | 0 |
| AT4G13770 CYP83A1 | 17917.62554 | 2.2936056 | 0.2032137 | 11.28667 | 0 | 0 |
| AT5G07690 MYB29 | 467.97777 | 2.8190840 | 0.2748185 | 10.25798 | 0 | 0 |
| AT5G48485 DIR1 | 151.52175 | 10.6950494 | 0.8890387 | 12.02990 | 0 | 0 |
der3_top <- head(as.data.frame(der3),40)
kbl(der3_top[order(der3_top$log2FoldChange),]) %>% kable_paper("hover", full_width = F)| baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | |
|---|---|---|---|---|---|---|
| AT5G38910 AT5G38910 | 7603.14501 | -4.133033 | 0.1812878 | -22.79819 | 0 | 0 |
| AT3G49580 LSU1 | 601.11046 | -3.835374 | 0.2618020 | -14.64991 | 0 | 0 |
| AT5G39110 AT5G39110 | 282.59697 | -3.337531 | 0.2331867 | -14.31270 | 0 | 0 |
| AT2G26695 AT2G26695 | 386.78641 | -3.073131 | 0.2057175 | -14.93860 | 0 | 0 |
| AT2G27120 POL2B | 209.55241 | -3.020735 | 0.2278894 | -13.25527 | 0 | 0 |
| AT2G13810 ALD1 | 522.81463 | -2.878087 | 0.2032517 | -14.16021 | 0 | 0 |
| AT3G49570 LSU3 | 516.86182 | -2.797929 | 0.1897873 | -14.74244 | 0 | 0 |
| AT5G48850 SDI1 | 1998.59372 | -2.597973 | 0.1923928 | -13.50348 | 0 | 0 |
| AT2G02120 PDF2.1 | 284.20442 | -2.284459 | 0.2002009 | -11.41083 | 0 | 0 |
| AT5G39100 GLP6 | 1315.83169 | -2.199664 | 0.1418550 | -15.50642 | 0 | 0 |
| AT5G39120 AT5G39120 | 418.40320 | -2.182977 | 0.1541968 | -14.15708 | 0 | 0 |
| AT4G10500 DLO1 | 1170.26209 | -2.155743 | 0.1833811 | -11.75553 | 0 | 0 |
| AT2G46750 GULLO2 | 3234.51724 | -1.977838 | 0.1279011 | -15.46381 | 0 | 0 |
| AT2G20180 PIF1 | 639.73485 | -1.948559 | 0.1461721 | -13.33058 | 0 | 0 |
| AT4G31330 AT4G31330 | 564.09191 | -1.933556 | 0.1460151 | -13.24217 | 0 | 0 |
| AT2G18480 PLT3 | 3131.96461 | -1.894502 | 0.1630323 | -11.62041 | 0 | 0 |
| AT4G19810 ChiC | 3582.96863 | -1.834233 | 0.1047471 | -17.51106 | 0 | 0 |
| AT2G43590 AT2G43590 | 2204.61655 | -1.787978 | 0.1291326 | -13.84606 | 0 | 0 |
| AT1G19960 AT1G19960 | 1119.33110 | -1.652725 | 0.1488139 | -11.10598 | 0 | 0 |
| AT1G05340 AT1G05340 | 1343.33248 | -1.581242 | 0.1347783 | -11.73217 | 0 | 0 |
| AT4G34710 ADC2 | 39857.45038 | -1.497121 | 0.1032508 | -14.49984 | 0 | 0 |
| AT1G04770 AT1G04770 | 1509.35348 | -1.455235 | 0.1314361 | -11.07181 | 0 | 0 |
| AT4G02360 AT4G02360 | 354.41975 | -1.438273 | 0.1103522 | -13.03348 | 0 | 0 |
| AT2G26560 PLP2 | 1508.96850 | -1.311989 | 0.1108288 | -11.83798 | 0 | 0 |
| AT1G18100 MFT | 2796.46836 | -1.240233 | 0.1079974 | -11.48392 | 0 | 0 |
| AT5G64810 WRKY51 | 804.15443 | -1.221177 | 0.0988675 | -12.35165 | 0 | 0 |
| AT2G26700 PID2 | 768.95328 | -1.057281 | 0.0924989 | -11.43020 | 0 | 0 |
| AT5G19600 SULTR3;5 | 2588.71314 | -1.044640 | 0.0739189 | -14.13225 | 0 | 0 |
| AT4G23680 AT4G23680 | 12991.20760 | -1.013475 | 0.0909145 | -11.14756 | 0 | 0 |
| AT5G06860 PGIP1 | 9575.63931 | -1.006640 | 0.0903015 | -11.14754 | 0 | 0 |
| AT2G19060 AT2G19060 | 727.39414 | 1.173108 | 0.0965347 | 12.15218 | 0 | 0 |
| AT2G28160 FIT | 1329.02207 | 1.178656 | 0.0849199 | 13.87963 | 0 | 0 |
| AT4G15920 SWEET17 | 1097.19206 | 1.280599 | 0.1084333 | 11.81002 | 0 | 0 |
| AT5G43780 APS4 | 30279.47827 | 1.363587 | 0.0951731 | 14.32744 | 0 | 0 |
| AT4G19690 IRT1 | 4514.17013 | 2.447128 | 0.2002441 | 12.22072 | 0 | 0 |
| AT4G11310 RDL4 | 262.57723 | 2.593505 | 0.1899565 | 13.65315 | 0 | 0 |
| AT1G08090 NRT2.1 | 3090.95060 | 2.658760 | 0.2176852 | 12.21378 | 0 | 0 |
| AT4G31940 CYP82C4 | 1443.81255 | 2.731164 | 0.2301616 | 11.86629 | 0 | 0 |
| AT1G01580 FRO2 | 4176.79051 | 3.004503 | 0.1840404 | 16.32524 | 0 | 0 |
| AT3G12900 AT3G12900 | 70.86432 | 4.577151 | 0.4122334 | 11.10330 | 0 | 0 |
der5_top <- head(as.data.frame(der5),40)
kbl(der5_top[order(der5_top$log2FoldChange),]) %>% kable_paper("hover", full_width = F)| baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | |
|---|---|---|---|---|---|---|
| AT3G49580 LSU1 | 999.06743 | -4.6223573 | 0.3420175 | -13.51497 | 0 | 0 |
| AT5G38910 AT5G38910 | 10989.77686 | -3.7457317 | 0.1685360 | -22.22512 | 0 | 0 |
| AT5G48850 SDI1 | 1807.77877 | -3.1512533 | 0.1429119 | -22.05032 | 0 | 0 |
| AT3G49570 LSU3 | 587.88452 | -2.9992048 | 0.2010912 | -14.91465 | 0 | 0 |
| AT5G39120 AT5G39120 | 909.88853 | -2.8085250 | 0.1564968 | -17.94622 | 0 | 0 |
| AT3G05400 SUGTL5 | 108.95117 | -2.6443691 | 0.2097146 | -12.60937 | 0 | 0 |
| AT5G39100 GLP6 | 2796.63690 | -2.6104690 | 0.1372406 | -19.02111 | 0 | 0 |
| AT4G31330 AT4G31330 | 1110.73716 | -2.5305698 | 0.1094513 | -23.12051 | 0 | 0 |
| AT2G04050 DTX3 | 159.15440 | -2.5277994 | 0.2030504 | -12.44912 | 0 | 0 |
| AT5G39150 AT5G39150 | 838.94083 | -2.3449548 | 0.1555361 | -15.07659 | 0 | 0 |
| AT4G19760 AT4G19760 | 390.67651 | -2.3142296 | 0.1727126 | -13.39931 | 0 | 0 |
| AT2G30670 AT2G30670 | 96.05757 | -2.2548926 | 0.1484052 | -15.19416 | 0 | 0 |
| AT2G18480 PLT3 | 4362.06174 | -2.2457372 | 0.1500708 | -14.96451 | 0 | 0 |
| AT5G26220 GGCT2;1 | 692.96994 | -2.2001335 | 0.1677848 | -13.11283 | 0 | 0 |
| AT4G19810 ChiC | 4036.56636 | -2.1582913 | 0.1036906 | -20.81472 | 0 | 0 |
| AT4G10500 DLO1 | 1373.57422 | -2.0489456 | 0.1314500 | -15.58726 | 0 | 0 |
| AT2G46750 GULLO2 | 3670.90327 | -1.9608351 | 0.1207412 | -16.23999 | 0 | 0 |
| AT2G43570 CHI | 920.22091 | -1.8373215 | 0.1288913 | -14.25482 | 0 | 0 |
| AT2G43590 AT2G43590 | 1330.71989 | -1.7947046 | 0.1148597 | -15.62519 | 0 | 0 |
| AT1G01190 CYP78A8 | 2901.18061 | -1.6264979 | 0.1116772 | -14.56427 | 0 | 0 |
| AT3G16530 AT3G16530 | 1869.04592 | -1.5760701 | 0.1149547 | -13.71036 | 0 | 0 |
| AT2G20180 PIF1 | 473.78274 | -1.5407592 | 0.1044088 | -14.75698 | 0 | 0 |
| AT1G02920 GSTF7 | 6141.93661 | -1.5056203 | 0.1007818 | -14.93940 | 0 | 0 |
| AT1G04770 AT1G04770 | 1359.55279 | -1.3825699 | 0.0700132 | -19.74728 | 0 | 0 |
| AT2G15220 AT2G15220 | 1912.67513 | -1.3724258 | 0.0926413 | -14.81440 | 0 | 0 |
| AT4G37370 CYP81D8 | 369.05553 | -1.3569486 | 0.0979670 | -13.85108 | 0 | 0 |
| AT4G11650 OSM34 | 9292.46080 | -1.3407292 | 0.0926703 | -14.46773 | 0 | 0 |
| AT3G49120 PER34 | 11433.68627 | -1.3335607 | 0.0725850 | -18.37240 | 0 | 0 |
| AT5G06860 PGIP1 | 11082.34057 | -1.1602616 | 0.0802059 | -14.46604 | 0 | 0 |
| AT1G45201 ATTLL1 | 7954.53845 | -1.1525844 | 0.0680798 | -16.92990 | 0 | 0 |
| AT1G18100 MFT | 2482.37673 | -1.1412525 | 0.0686029 | -16.63563 | 0 | 0 |
| AT3G04070 NAC047 | 1138.70580 | -1.1236719 | 0.0758509 | -14.81423 | 0 | 0 |
| AT1G75280 AT1G75280 | 6891.41198 | -1.0048794 | 0.0675767 | -14.87021 | 0 | 0 |
| AT4G21990 APR3 | 8702.31605 | -0.8852739 | 0.0640951 | -13.81188 | 0 | 0 |
| AT5G57350 AHA3 | 3675.64143 | -0.8486650 | 0.0554210 | -15.31306 | 0 | 0 |
| AT5G38200 AT5G38200 | 3178.71589 | -0.7432135 | 0.0557160 | -13.33932 | 0 | 0 |
| AT4G30960 CIPK6 | 26787.72836 | -0.6194731 | 0.0486827 | -12.72471 | 0 | 0 |
| AT4G40070 ATL32 | 979.91640 | 1.4004369 | 0.1051780 | 13.31492 | 0 | 0 |
| AT5G43780 APS4 | 27359.76718 | 1.6806048 | 0.1192601 | 14.09193 | 0 | 0 |
| AT4G11310 RDL4 | 286.90624 | 2.5769697 | 0.1661997 | 15.50526 | 0 | 0 |
write.table(del3,file="del3.tsv",quote=FALSE,sep="\t")
write.table(del5,file="del5.tsv",quote=FALSE,sep="\t")
write.table(der3,file="der3.tsv",quote=FALSE,sep="\t")
write.table(der5,file="der5.tsv",quote=FALSE,sep="\t")
del3_up <- rownames(subset(del3,padj<0.05&log2FoldChange>0))
del3_dn <- rownames(subset(del3,padj<0.05&log2FoldChange<0))
del5_up <- rownames(subset(del5,padj<0.05&log2FoldChange>0))
del5_dn <- rownames(subset(del5,padj<0.05&log2FoldChange<0))
der3_up <- rownames(subset(der3,padj<0.05&log2FoldChange>0))
der3_dn <- rownames(subset(der3,padj<0.05&log2FoldChange<0))
der5_up <- rownames(subset(der5,padj<0.05&log2FoldChange>0))
der5_dn <- rownames(subset(der5,padj<0.05&log2FoldChange<0))
up <- sapply(list(del3_up,del5_up,der3_up,der5_up),length)
dn <- sapply(list(del3_dn,del5_dn,der3_dn,der5_dn),length)
res_summary <- data.frame(up,dn,row.names=c("L3","L5","R3","R5"))
res_summary$de <- c("Leaf 3d","Leaf 5d","Root 3d","Root 5d")
kbl(res_summary) %>% kable_paper("hover", full_width = F)| up | dn | de | |
|---|---|---|---|
| L3 | 518 | 731 | Leaf 3d |
| L5 | 1944 | 1838 | Leaf 5d |
| R3 | 1179 | 1239 | Root 3d |
| R5 | 1748 | 2207 | Root 5d |
barplot(res_summary$up,ylim=c(-2500,2500), axes=TRUE, main="number of DEGs up/down")
barplot(-res_summary$dn, add = TRUE, names.arg = rownames(res_summary), axes = FALSE)
Venn diagram plots of overlap
# upregulated genes
v1 <- list("leaf 3d up"=del3_up, "leaf 5d up"=del5_up,
"root 3d up" =der3_up , "root 5d up"=der5_up)
plot(euler(v1),quantities = TRUE)
intersect(del3_up,del5_up)## [1] "AT2G47880 GRXC13" "AT4G39250 RL1" "AT4G31355 AT4G31355"
## [4] "AT4G34950 AT4G34950" "AT5G01600 FER1" "AT3G46130 ATMYB48"
## [7] "AT3G15270 SPL5" "AT3G04200 AT3G04200" "AT3G03910 GSH3"
## [10] "AT1G52800 AT1G52800" "AT2G16660 AT2G16660" "AT3G04480 AT3G04480"
## [13] "AT1G12320 AT1G12320" "AT1G73890 AT1G73890" "AT5G07690 MYB29"
## [16] "AT2G24120 RPOT3" "AT4G31354 AT4G31354" "AT2G28210 ATACA2"
## [19] "AT5G24270 CBL4" "AT1G29720 RFK1" "AT2G25220 AT2G25220"
## [22] "AT1G05630 AT5PTASE13" "AT2G01023 AT2G01023" "AT5G45650 SBT5.6"
## [25] "AT4G22730 AT4G22730" "AT1G29270 AT1G29270" "AT1G53160 SPL4"
## [28] "AT1G66600 WRKY63" "AT2G40300 FER4" "AT4G37080 AT4G37080"
## [31] "AT4G00140 EDA34" "AT3G26700 AT3G26700" "AT2G01910 MAP65-6"
## [34] "AT3G20110 CYP705A20" "AT5G23020 MAM3" "AT5G23010 MAM1"
## [37] "AT2G30460 UXT2" "AT5G07700 MYB76" "AT3G49160 PKP4"
## [40] "AT1G08810 MYB60" "AT1G72930 TIR" "AT3G05290 PNC1"
## [43] "AT1G68585 AT1G68585" "AT1G67865 AT1G67865" "AT5G45550 MOB1A"
## [46] "AT2G42880 MPK20" "AT1G08180 SMR2" "AT4G00950 MEE47"
## [49] "AT4G23130 CRK5" "AT2G44210 AT2G44210" "AT2G21650 RL2"
## [52] "AT3G47500 CDF3" "AT3G29810 COBL3" "AT5G63950 CHR24"
## [55] "AT2G23610 MES3" "AT1G16640 AT1G16640" "AT3G56480 SCAB3"
## [58] "AT3G54600 DJ1F" "AT3G55520 FKBP20-1" "AT1G49620 KRP7"
## [61] "AT5G55490 GEX1" "AT2G19900 NADP-ME1" "AT1G12330 AT1G12330"
## [64] "AT3G25500 FH1" "AT3G19720 ARC5" "AT4G00670 AT4G00670"
## [67] "AT3G23570 AT3G23570" "AT4G19410 AT4G19410" "AT5G41140 AT5G41140"
## [70] "AT1G29660 AT1G29660" "AT1G13650 AT1G13650" "AT2G18328 RL4"
## [73] "AT1G25530 AT1G25530" "AT3G19710 BCAT4" "AT1G30490 ATHB-9"
## [76] "AT1G31690 AT1G31690" "AT4G32790 AT4G32790" "AT1G08090 NRT2.1"
## [79] "AT4G12140 AT4G12140" "AT3G26820 AT3G26820" "AT3G05900 AT3G05900"
## [82] "AT2G43100 IPMI2" "AT3G61310 AHL11" "AT1G72500 AT1G72500"
## [85] "AT1G02220 NAC003" "AT5G57123 AT5G57123" "AT1G72610 GLP1"
## [88] "AT5G65730 XTH6" "AT3G06450 BOR3" "AT2G19780 AT2G19780"
## [91] "AT1G12450 AT1G12450" "AT1G09510 AT1G09510" "AT4G36570 ATRL3"
## [94] "AT1G22690 GASA9" "AT2G42380 BZIP34" "AT3G26670 AT3G26670"
## [97] "AT4G13770 CYP83A1" "AT4G12030 BASS5" "AT1G10120 BHLH74"
## [100] "AT5G17270 AT5G17270" "AT3G11570 TBL8" "AT1G52240 ROPGEF11"
## [103] "AT3G05910 PAE12" "AT1G54040 ESP" "AT4G14070 AAE15"
## [106] "AT2G24300 AT2G24300" "AT5G43910 AT5G43910" "AT1G04160 XI-B"
## [109] "AT2G15050 LTP7" "AT4G25350 PHO1-H4" "AT5G01500 TAAC"
## [112] "AT1G60730 AT1G60730" "AT4G03050 AOP3" "AT3G60320 NRG2"
## [115] "AT3G09920 PIP5K9" "AT4G12290 AT4G12290" "AT4G38770 PRP4"
## [118] "AT2G21080 AT2G21080" "AT5G66560 AT5G66560" "AT4G38950 KIN7F"
## [121] "AT5G26000 TGG1" "AT1G16410 CYP79F1" "AT3G23690 BHLH77"
## [124] "AT3G14020 NFYA6" "AT5G33370 AT5G33370" "AT4G08760 AT4G08760"
## [127] "AT4G23060 IQD22" "AT4G14040 SBP2" "AT3G62960 GRXC14"
## [130] "AT1G73060 LPA3" "AT5G49680 KIP" "AT5G21105 AT5G21105"
## [133] "AT1G33030 AT1G33030" "AT3G08040 DTX43" "AT5G49215 AT5G49215"
## [136] "AT3G28930 AIG2A" "AT2G30010 TBL45" "AT3G03190 GSTF11"
## [139] "AT5G53930 AT5G53930" "AT1G70940 PIN3" "AT2G04190 AT2G04190"
## [142] "AT4G39950 CYP79B2" "AT4G11820 HMGS" "AT3G62630 AT3G62630"
## [145] "AT5G04160 UUAT1" "AT5G60920 COB" "AT4G18760 RLP51"
## [148] "AT4G21590 ENDO3" "AT5G16570 GLN1-4" "AT3G59010 PME35"
## [151] "AT3G04210 AT3G04210" "AT1G69700 HVA22C" "AT3G47450 ATNOS1"
## [154] "AT3G04810 NEK2" "AT4G19020 CMT2" "AT1G27840 ATCSA-1"
## [157] "AT3G24140 FAMA" "AT2G05760 NAT1" "AT5G14200 IMDH3"
## [160] "AT1G70210 CYCD1-1" "AT3G21950 AT3G21950" "AT3G24480 LRX4"
## [163] "AT1G75250 ATRL6" "AT3G07990 SCPL27" "AT5G46420 AT5G46420"
## [166] "AT5G09300 AT5G09300" "AT4G01440 AT4G01440" "AT4G27730 OPT6"
## [169] "AT1G58025 AT1G58025" "AT2G43020 PAO2" "AT3G02020 AK3"
## [172] "AT4G32410 CESA1" "AT2G22330 CYP79B3" "AT5G04130 GYRBM"
## [175] "AT3G47930 GLDH" "AT4G25230 RIN2" "AT1G10020 AT1G10020"
## [178] "AT2G01830 AHK4" "AT3G23820 GAE6" "AT3G20390 AT3G20390"
## [181] "AT3G01930 AT3G01930" "AT2G18890 AT2G18890" "AT1G17600 AT1G17600"
## [184] "AT4G29400 AT4G29400" "AT1G16400 CYP79F2" "AT4G14750 IQD19"
## [187] "AT1G17920 HDG12" "AT4G18030 AT4G18030" "AT4G35900 FD"
## [190] "AT1G70260 AT1G70260" "AT1G79720 AT1G79720" "AT1G21440 AT1G21440"
## [193] "AT1G60060 AT1G60060" "AT4G32710 PERK14" "AT4G05120 ENT3"
## [196] "AT5G18690 AGP25" "AT4G03820 AT4G03820" "AT1G13270 MAP1B"
## [199] "AT2G25450 GSL-OH" "AT2G36380 ABCG34" "AT4G05090 AT4G05090"
## [202] "AT5G17390 AT5G17390" "AT5G61950 AT5G61950" "AT4G40070 ATL32"
## [205] "AT2G23600 ACL" "AT3G58990 IPMI1" "AT1G23170 AT1G23170"
## [208] "AT1G66940 AT1G66940" "AT5G55720 AT5G55720" "AT1G23180 AT1G23180"
## [211] "AT4G16980 AT4G16980" "AT3G53100 AT3G53100" "AT2G44740 CYCU4-1"
## [214] "AT2G18910 AT2G18910" "AT4G01430 AT4G01430" "AT5G10250 DOT3"
## [217] "AT5G40830 AT5G40830" "AT5G64560 MRS2-2" "AT1G65860 FMOGS-OX1"
## [220] "AT1G19920 APS2" "AT5G51100 FSD2" "AT5G25130 CYP71B12"intersect(der3_up,der3_up)## [1] "AT1G01580 FRO2" "AT5G43780 APS4" "AT2G28160 FIT"
## [4] "AT4G11310 RDL4" "AT4G19690 IRT1" "AT1G08090 NRT2.1"
## [7] "AT2G19060 AT2G19060" "AT4G31940 CYP82C4" "AT4G15920 SWEET17"
## [10] "AT3G12900 AT3G12900" "AT5G02180 AVT1D" "AT5G24270 CBL4"
## [13] "AT5G40780 LHT1" "AT3G46280 AT3G46280" "AT2G25260 HPAT2"
## [16] "AT3G18450 PCR5" "AT5G26300 AT5G26300" "AT1G35240 ARF20"
## [19] "AT3G52190 PHF1" "AT4G25350 PHO1-H4" "AT3G27950 AT3G27950"
## [22] "AT5G38100 AT5G38100" "AT3G08040 DTX43" "AT3G10720 PME25"
## [25] "AT1G50590 AT1G50590" "AT3G61830 ARF18" "AT1G78120 TPR12"
## [28] "AT3G02610 AT3G02610" "AT3G24290 AMT1-5" "AT3G07195 AT3G07195"
## [31] "AT1G34047 AT1G34047" "AT5G62865 AT5G62865" "AT5G14650 AT5G14650"
## [34] "AT5G67450 AZF1" "AT5G40590 AT5G40590" "AT5G16570 GLN1-4"
## [37] "AT3G01190 PER27" "AT1G73270 SCPL6" "AT2G35270 AHL21"
## [40] "AT5G46050 NPF5.2" "AT3G58060 MTPC3" "AT3G55700 UGT76F1"
## [43] "AT3G23000 CIPK7" "AT3G14280 AT3G14280" "AT2G36690 AT2G36690"
## [46] "AT4G20260 PCAP1" "AT5G48485 DIR1" "AT4G15393 CYP702A5"
## [49] "AT2G39200 MLO12" "AT1G55940 CYP708A1" "AT3G58810 MTPA2"
## [52] "AT2G38390 PER23" "AT1G54010 GLL23" "AT4G12090 AT4G12090"
## [55] "AT3G24300 AMT1-3" "AT1G49320 USPL1" "AT1G07690 AT1G07690"
## [58] "AT3G55150 ATEXO70H1" "AT2G32270 ZIP3" "AT4G13510 AMT1-1"
## [61] "AT5G25810 TINY" "AT3G14225 GLIP4" "AT5G20470 AT5G20470"
## [64] "AT3G12820 AtMYB10" "AT4G30120 HMA3" "AT1G11540 AT1G11540"
## [67] "AT3G46130 ATMYB48" "AT1G21210 WAK4" "AT1G69900 AT1G69900"
## [70] "AT4G26050 PIRL8" "AT2G24010 scpl23" "AT5G48430 AT5G48430"
## [73] "AT4G00670 AT4G00670" "AT5G67520 APK4" "AT4G19925 AT4G19925"
## [76] "AT5G67080 MAPKKK19" "AT1G21230 WAK5" "AT1G49030 PCR6"
## [79] "AT4G40070 ATL32" "AT3G63360 AT3G63360" "AT1G19450 AT1G19450"
## [82] "AT3G50350 AT3G50350" "AT3G24503 ALDH2C4" "AT4G18940 AT4G18940"
## [85] "AT1G01360 PYL9" "AT3G51350 AT3G51350" "AT1G47840 HXK3"
## [88] "AT5G11610 AT5G11610" "AT5G14130 AT5G14130" "AT5G43590 AT5G43590"
## [91] "AT3G61400 AT3G61400" "AT5G50200 NRT3.1" "AT5G64000 SAL2"
## [94] "AT4G33720 AT4G33720" "AT4G20450 AT4G20450" "AT4G33820 AT4G33820"
## [97] "AT5G19040 IPT5" "AT3G20110 CYP705A20" "AT3G23510 AT3G23510"
## [100] "AT1G15670 AT1G15670" "AT3G60090 AT3G60090" "AT1G14210 AT1G14210"
## [103] "AT1G35242 AT1G35242" "AT5G33355 AT5G33355" "AT3G16390 NSP3"
## [106] "AT4G22460 AT4G22460" "AT4G04955 ALN" "AT5G54680 ILR3"
## [109] "AT1G34040 TAR3" "AT1G73120 AT1G73120" "AT4G17680 AT4G17680"
## [112] "AT5G43910 AT5G43910" "AT1G78860 AT1G78860" "AT1G30840 PUP4"
## [115] "AT1G08100 NRT2.2" "AT2G28460 AT2G28460" "AT1G05250 PER2"
## [118] "AT2G19800 MIOX2" "AT1G29240 AT1G29240" "AT5G46040 NPF5.3"
## [121] "AT1G24485 AT1G24485" "AT3G26590 DTX29" "AT1G14550 PER5"
## [124] "AT5G45280 PAE11" "AT3G59580 NLP9" "AT1G76990 ACR3"
## [127] "AT4G35040 BZIP19" "AT3G61380 AT3G61380" "AT2G11810 MGD3"
## [130] "AT5G56840 AT5G56840" "AT3G61880 CYP78A9" "AT2G30010 TBL45"
## [133] "AT2G28210 ATACA2" "AT5G54590 CRLK1" "AT4G08300 AT4G08300"
## [136] "AT3G56970 ORG2" "AT5G45380 DUR3" "AT5G45470 AT5G45470"
## [139] "AT5G19200 TSC10B" "AT5G05440 PYL5" "AT3G25730 ARF14"
## [142] "AT4G17870 PYR1" "AT5G51310 AT5G51310" "AT1G17300 AT1G17300"
## [145] "AT4G37520 PER50" "AT3G47980 AT3G47980" "AT5G03570 IREG2"
## [148] "AT5G40210 AT5G40210" "AT1G54950 AT1G54950" "AT1G66930 LRK10L-2.7"
## [151] "AT4G26220 AT4G26220" "AT5G24230 AT5G24230" "AT5G65320 BHLH99"
## [154] "AT1G30370 AT1G30370" "AT3G19680 AT3G19680" "AT3G51340 AT3G51340"
## [157] "AT3G23800 SBP3" "AT3G09922 IPS1" "AT5G60350 AT5G60350"
## [160] "AT5G62730 NPF4.7" "AT1G49310 AT1G49310" "AT2G02020 NPF8.4"
## [163] "AT3G54030 BSK6" "AT5G49850 JAL46" "AT1G38131 OFUT11"
## [166] "AT3G49860 ARL8D" "AT2G29995 PSY3" "AT4G25110 AMC2"
## [169] "AT2G38310 PYL4" "AT4G26060 AT4G26060" "AT5G56080 NAS2"
## [172] "AT2G28140 AT2G28140" "AT2G40330 PYL6" "AT1G49100 AT1G49100"
## [175] "AT1G24170 GATL8" "AT5G62420 AT5G62420" "AT1G22220 AT1G22220"
## [178] "AT1G27210 TOR1L4" "AT3G07000 AT3G07000" "AT1G54890 AT1G54890"
## [181] "AT2G43140 AT2G43140" "AT5G01220 SQD2" "AT3G56980 ORG3"
## [184] "AT1G14540 PER4" "AT5G46600 ALMT13" "AT4G36920 AP2"
## [187] "AT1G01420 UGT72B3" "AT5G66595 AT5G66595" "AT4G35060 HIPP25"
## [190] "AT3G29430 AT3G29430" "AT4G14780 AT4G14780" "AT4G30280 XTH18"
## [193] "AT2G36255 AT2G36255" "AT1G12330 AT1G12330" "AT5G20400 AT5G20400"
## [196] "AT1G29180 AT1G29180" "AT3G46810 AT3G46810" "AT3G49845 AT3G49845"
## [199] "AT2G42600 PPC2" "AT3G07720 AT3G07720" "AT5G01610 AT5G01610"
## [202] "AT1G57680 AT1G57680" "AT5G38940 AT5G38940" "AT1G78020 FLZ6"
## [205] "AT1G23110 AT1G23110" "AT2G21880 RABG2" "AT4G01750 RGXT2"
## [208] "AT2G39530 AT2G39530" "AT3G46710 RPP13L2" "AT3G46800 AT3G46800"
## [211] "AT5G54790 VUP4" "AT4G36990 HSFB1" "AT3G23090 AT3G23090"
## [214] "AT1G06640 AT1G06640" "AT4G33790 FAR3" "AT2G19190 SIRK"
## [217] "AT3G56060 AT3G56060" "AT5G41180 AT5G41180" "AT5G28630 AT5G28630"
## [220] "AT3G47110 AT3G47110" "AT1G21200 AT1G21200" "AT3G05950 AT3G05950"
## [223] "AT5G38820 AT5G38820" "AT2G23960 GGP4" "AT1G51790 AT1G51790"
## [226] "AT5G67210 IRX15-L" "AT4G18340 AT4G18340" "AT2G30990 AT2G30990"
## [229] "AT1G35580 CINV1" "AT1G80450 VQ11" "AT5G16900 AT5G16900"
## [232] "AT5G24100 AT5G24100" "AT5G60060 AT5G60060" "AT3G50160 AT3G50160"
## [235] "AT3G10870 MES17" "AT1G44170 ALDH3H1" "AT4G05120 ENT3"
## [238] "AT1G28570 AT1G28570" "AT5G45730 AT5G45730" "AT2G17710 AT2G17710"
## [241] "AT1G05300 ZIP5" "AT4G01480 PPA5" "AT5G06200 CASP4"
## [244] "AT1G03457 AT1G03457" "AT2G20142 AT2G20142" "AT1G19390 WAKL11"
## [247] "AT3G25110 FATA" "AT3G23730 XTH16" "AT1G53940 GLIP2"
## [250] "AT5G63450 CYP94B1" "AT1G05805 BHLH128" "AT3G02580 STE1"
## [253] "AT1G29025 AT1G29025" "AT5G66690 UGT72E2" "AT2G28080 UGT86A2"
## [256] "AT2G29750 UGT71C1" "AT1G48500 TIFY6A" "AT1G22160 FLZ5"
## [259] "AT1G17090 AT1G17090" "AT4G25420 GA20OX1" "AT1G51800 IOS1"
## [262] "AT2G47550 PME20" "AT5G46260 AT5G46260" "AT3G59970 MTHFR1"
## [265] "AT3G07940 AGD11" "AT5G10520 RBK1" "AT4G00880 AT4G00880"
## [268] "AT1G76090 SMT3" "AT2G35155 AT2G35155" "AT5G46330 FLS2"
## [271] "AT2G19990 PR-1-LIKE" "AT3G13610 F6'H1" "AT4G06534 AT4G06534"
## [274] "AT4G13130 AT4G13130" "AT3G13435 AT3G13435" "AT4G31860 AT4G31860"
## [277] "AT4G15160 AT4G15160" "AT2G25680 MOT1" "AT3G10980 AT3G10980"
## [280] "AT1G21140 AT1G21140" "AT2G27660 AT2G27660" "AT5G52830 WRKY27"
## [283] "AT2G02610 AT2G02610" "AT4G17880 MYC4" "AT3G14680 CYP72A14"
## [286] "AT5G10290 AT5G10290" "AT5G64120 PER71" "AT3G13790 CWINV1"
## [289] "AT5G03355 AT5G03355" "AT3G07390 AIR12" "AT1G78290 SRK2C"
## [292] "AT4G08360 AT4G08360" "AT4G32800 ERF043" "AT5G03995 AT5G03995"
## [295] "AT2G19880 AT2G19880" "AT1G12520 CCS" "AT4G12290 AT4G12290"
## [298] "AT4G07820 AT4G07820" "AT4G32940 GAMMA-VPE" "AT3G61680 PLIP1"
## [301] "AT3G09220 LAC7" "AT4G34500 AT4G34500" "AT5G65200 PUB38"
## [304] "AT2G39890 PROT1" "AT2G04090 DTX5" "AT2G38940 PHT1-4"
## [307] "AT3G04480 AT3G04480" "AT4G23010 UTR2" "AT2G27000 CYP705A8"
## [310] "AT4G33030 SQD1" "AT5G24410 PGL4" "AT2G18450 SDH1-2"
## [313] "AT2G28250 NCRK" "AT3G26450 AT3G26450" "AT3G51560 AT3G51560"
## [316] "AT4G25310 AT4G25310" "AT3G63270 ALP1" "AT1G60680 AGD2"
## [319] "AT4G21250 AT4G21250" "AT2G27550 CEN" "AT3G47210 AT3G47210"
## [322] "AT2G01670 NUDT17" "AT2G38400 AGT3" "AT1G56360 PAP6"
## [325] "AT2G37780 AT2G37780" "AT1G16420 AMC8" "AT4G01970 AtSTS"
## [328] "AT2G25410 ATL22" "AT2G42980 AT2G42980" "AT1G29179 AT1G29179"
## [331] "AT2G22240 IPS2" "AT3G61260 AT3G61260" "AT4G23070 RBL7"
## [334] "AT4G39640 GGT1" "AT3G26330 CYP71B37" "AT4G26010 AT4G26010"
## [337] "AT5G44610 PCAP2" "AT5G02800 PBL7" "AT1G44050 AT1G44050"
## [340] "AT5G53820 AT5G53820" "AT5G65687 AT5G65687" "AT5G43300 GDPD3"
## [343] "AT3G01810 AT3G01810" "AT5G52260 AtMYB19" "AT3G62280 AT3G62280"
## [346] "AT2G25000 WRKY60" "AT1G72360 HRE1" "AT3G02620 AT3G02620"
## [349] "AT2G46860 PPA3" "AT3G22800 LRX6" "AT1G51850 AT1G51850"
## [352] "AT2G40150 TBL28" "AT5G44020 AT5G44020" "AT3G04370 CRRSP39"
## [355] "AT5G63600 FLS5" "AT3G49370 CRK6" "AT2G45220 PME17"
## [358] "AT4G17100 AT4G17100" "AT4G20780 CML42" "AT5G65040 IRM1"
## [361] "AT1G33612 AT1G33612" "AT2G42060 AT2G42060" "AT5G63410 AT5G63410"
## [364] "AT5G43370 PHT1-2" "AT5G39430 AT5G39430" "AT2G34070 TBL37"
## [367] "AT5G45500 AT5G45500" "AT1G16160 WAKL5" "AT3G45440 AT3G45440"
## [370] "AT2G26640 KCS11" "AT5G09220 AAP2" "AT2G21045 HAC1"
## [373] "AT1G25530 AT1G25530" "AT1G79030 AT1G79030" "AT5G46780 AT5G46780"
## [376] "AT5G07220 BAG3" "AT4G32790 AT4G32790" "AT1G68150 WRKY9"
## [379] "AT4G30080 ARF16" "AT3G47220 PLC9" "AT4G37340 CYP81D3"
## [382] "AT5G01560 LECRK64" "AT5G04680 AT5G04680" "AT4G02410 LECRK43"
## [385] "AT1G24320 GCS2" "AT3G19553 AT3G19553" "AT2G23620 MES1"
## [388] "AT1G72220 ATL54" "AT1G12940 NRT2.5" "AT5G06510 NFYA10"
## [391] "AT1G61930 AT1G61930" "AT1G77690 LAX3" "AT4G18950 AT4G18950"
## [394] "AT2G30540 GRXS9" "AT2G18640 GGPP4" "AT3G05320 OFUT23"
## [397] "AT5G11790 NDL2" "AT5G64100 PER69" "AT1G29280 WRKY65"
## [400] "AT4G16400 AT4G16400" "AT3G16690 SWEET16" "AT1G44020 AT1G44020"
## [403] "AT3G50470 HR3" "AT1G68470 GT17" "AT5G63570 GSA1"
## [406] "AT3G28345 ABCB15" "AT5G60300 LECRK19" "AT3G10300 AT3G10300"
## [409] "AT1G47480 CXE2" "AT1G05850 CTL1" "AT3G05860 AT3G05860"
## [412] "AT3G62960 GRXC14" "AT5G15860 ICME" "AT4G11230 RBOHI"
## [415] "AT5G46790 PYL1" "AT1G05810 ARA" "AT1G34750 AT1G34750"
## [418] "AT4G12730 FLA2" "AT5G60920 COB" "AT1G10020 AT1G10020"
## [421] "AT1G66440 AT1G66440" "AT5G18500 AT5G18500" "AT2G44490 BGLU26"
## [424] "AT2G43120 AT2G43120" "AT1G64400 LACS3" "AT3G20935 CYP705A28"
## [427] "AT1G56520 AT1G56520" "AT1G14080 FUT6" "AT1G25580 SOG1"
## [430] "AT3G18460 PCR4" "AT3G44940 AT3G44940" "AT5G53110 AT5G53110"
## [433] "AT2G18650 ATL49" "AT4G04930 DES-1-LIKE" "AT4G11530 CRK34"
## [436] "AT1G30900 VSR6" "AT1G23140 CAR8" "AT3G12240 SCPL15"
## [439] "AT4G10530 AT4G10530" "AT4G28850 XTH26" "AT5G04150 BHLH101"
## [442] "AT1G61740 AT1G61740" "AT5G36870 CALS4" "AT3G58000 VQ25"
## [445] "AT5G07475 AT5G07475" "AT5G45440 AT5G45440" "AT4G21400 CRK28"
## [448] "AT3G02140 AFP4" "AT1G34200 AT1G34200" "AT2G25240 AT2G25240"
## [451] "AT4G36570 ATRL3" "AT5G25640 AT5G25640" "AT2G35730 AT2G35730"
## [454] "AT5G41700 UBC8" "AT4G01700 AT4G01700" "AT1G44608 AT1G44608"
## [457] "AT2G03360 AT2G03360" "AT1G10550 XTH33" "AT1G28310 AT1G28310"
## [460] "AT2G32390 GLR3.5" "AT4G35900 FD" "AT5G47950 AT5G47950"
## [463] "AT5G23510 AT5G23510" "AT2G43220 AT2G43220" "AT5G40510 AT5G40510"
## [466] "AT5G25050 AT5G25050" "AT3G60720 PDLP8" "AT1G62262 SLAH4"
## [469] "AT4G02630 AT4G02630" "AT1G77530 AT1G77530" "AT5G53160 PYL8"
## [472] "AT5G67430 AT5G67430" "AT5G07780 FH19" "AT5G20410 MGD2"
## [475] "AT1G55390 AT1G55390" "AT1G67110 CYP735A2" "AT1G73330 ATDR4"
## [478] "AT3G20850 AT3G20850" "AT5G37420 AT5G37420" "AT4G21410 CRK29"
## [481] "AT1G22740 RABG3B" "AT1G64780 AMT1-2" "AT1G13640 PI4KG6"
## [484] "AT1G47740 AT1G47740" "AT1G13970 AT1G13970" "AT5G09480 AT5G09480"
## [487] "AT1G02575 AT1G02575" "AT2G21650 RL2" "AT3G29034 AT3G29034"
## [490] "AT5G13810 AT5G13810" "AT5G45490 AT5G45490" "AT1G27420 AT1G27420"
## [493] "AT2G18730 DGK3" "AT1G28170 SOT7" "AT5G41590 AT5G41590"
## [496] "AT5G60770 NRT2.4" "AT5G19770 TUBA3" "AT5G07070 CIPK2"
## [499] "AT2G04430 NUDT5" "AT1G74210 GDPD5" "AT5G44910 AT5G44910"
## [502] "AT4G02330 PME41" "AT5G45340 CYP707A3" "AT1G33870 AT1G33870"
## [505] "AT2G44581 AT2G44581" "AT1G52420 AT1G52420" "AT2G35612 CEP4"
## [508] "AT5G56300 GAMT2" "AT1G65310 ATXTH17" "AT4G07960 CSLC12"
## [511] "AT3G51330 AT3G51330" "AT1G27960 ECT9" "AT3G50620 AT3G50620"
## [514] "AT3G20340 AT3G20340" "AT5G43420 ATL16" "AT1G18330 RVE7"
## [517] "AT4G25970 PSD3" "AT5G46140 AT5G46140" "AT3G63280 ATNEK4"
## [520] "AT5G36250 AT5G36250" "AT4G25090 RBOHG" "AT3G57740 AT3G57740"
## [523] "AT3G03260 HDG8" "AT3G59930 AT3G59930" "AT3G13480 AT3G13480"
## [526] "AT3G07010 AT3G07010" "AT2G31020 ORP1A" "AT2G17700 STY8"
## [529] "AT5G14340 AtMYB40" "AT1G56160 ATMYB72" "AT1G10350 AT1G10350"
## [532] "AT1G02360 AT1G02360" "AT1G03970 GBF4" "AT2G42140 VQ17"
## [535] "AT4G23000 AT4G23000" "AT3G50460 HR2" "AT3G61440 CYSC1"
## [538] "AT1G75360 AT1G75360" "AT1G24620 CML25" "AT4G13770 CYP83A1"
## [541] "AT1G74940 FLZ13" "AT4G26790 AT4G26790" "AT5G61290 AT5G61290"
## [544] "AT2G36630 AT2G36630" "AT5G19930 PGR" "AT5G52710 AT5G52710"
## [547] "AT3G07570 AT3G07570" "AT5G06390 FLA17" "AT3G01870 AT3G01870"
## [550] "AT4G21960 PER42" "AT2G32295 AT2G32295" "AT5G04840 AT5G04840"
## [553] "AT4G25160 PUB35" "AT3G14610 CYP72A7" "AT4G02270 RHS13"
## [556] "AT3G43600 AAO2" "AT4G25030 AT4G25030" "AT1G08930 ERD6"
## [559] "AT2G03450 PAP9" "AT5G67400 PER73" "AT4G00300 AT4G00300"
## [562] "AT1G72430 SAUR78" "AT3G48346 AT3G48346" "AT2G44160 MTHFR2"
## [565] "AT1G75680 AtGH9B7" "AT1G77525 AT1G77525" "AT2G46660 CYP78A6"
## [568] "AT3G46330 MEE39" "AT1G21360 GLTP2" "AT2G04410 AT2G04410"
## [571] "AT5G66420 AT5G66420" "AT4G20700 AT4G20700" "AT4G12360 AT4G12360"
## [574] "AT5G17820 AT5G17820" "AT5G37600 GLN1-1" "AT3G17440 NPSN13"
## [577] "AT5G24180 AT5G24180" "AT5G63910 FLCY" "AT1G77145 AT1G77145"
## [580] "AT1G60110 AT1G60110" "AT1G51940 LYK3" "AT5G61570 AT5G61570"
## [583] "AT3G07340 BHLH62" "AT5G23810 AAP7" "AT1G70900 AT1G70900"
## [586] "AT2G40540 POT2" "AT3G18170 AT3G18170" "AT3G02250 OFUT21"
## [589] "AT5G45480 AT5G45480" "AT3G28050 AT3G28050" "AT3G48840 AT3G48840"
## [592] "AT1G43650 AT1G43650" "AT1G33170 AT1G33170" "AT2G39410 AT2G39410"
## [595] "AT2G02800 PBL3" "AT4G11820 HMGS" "AT3G15510 NAC056"
## [598] "AT5G43170 AZF3" "AT3G16180 NPF1.1" "AT1G60095 AT1G60095"
## [601] "AT1G11580 ATPMEPCRA" "AT3G09940 MDAR3" "AT3G62210 EDA32"
## [604] "AT3G50560 AT3G50560" "AT5G59450 SCL11" "AT5G06610 AT5G06610"
## [607] "AT4G31550 WRKY11" "AT4G08040 ACS11" "AT3G29360 UGD2"
## [610] "AT5G07150 AT5G07150" "AT1G03445 BSU1" "AT5G10820 AT5G10820"
## [613] "AT5G04470 SIM" "AT1G53635 AT1G53635" "AT3G46720 UGT76E5"
## [616] "AT3G47000 AT3G47000" "AT4G15360 CYP705A3" "AT5G09470 PUMP6"
## [619] "AT5G45370 AT5G45370" "AT3G27190 UKL2" "AT5G64500 AT5G64500"
## [622] "AT3G06145 AT3G06145" "AT3G02290 AT3G02290" "AT2G23990 ENODL11"
## [625] "AT2G03730 ACR5" "AT1G80050 APT2" "AT4G15350 CYP705A2"
## [628] "AT3G21260 GLTP3" "AT5G58780 AT5G58780" "AT2G43200 AT2G43200"
## [631] "AT5G20640 AT5G20640" "AT5G17590 AT5G17590" "AT4G25070 AT4G25070"
## [634] "AT3G01690 AT3G01690" "AT2G44340 VQ18" "AT2G19160 AT2G19160"
## [637] "AT4G23060 IQD22" "AT3G14470 RPPL1" "AT5G37690 AT5G37690"
## [640] "AT4G12450 AT4G12450" "AT1G09400 AT1G09400" "AT2G35880 WDL4"
## [643] "AT3G18780 ACT2" "AT1G11680 CYP51G1" "AT3G62390 TBL6"
## [646] "AT4G24240 WRKY7" "AT1G16750 AT1G16750" "AT1G26200 AT1G26200"
## [649] "AT2G32260 CCT1" "AT1G76430 PHT1-9" "AT1G30910 AT1G30910"
## [652] "AT3G51670 PATL6" "AT4G33770 ITPK2" "AT1G76160 sks5"
## [655] "AT2G19050 AT2G19050" "AT2G35930 PUB23" "AT3G23870 AT3G23870"
## [658] "AT1G63550 CRRSP9" "AT1G72160 PATL3" "AT1G70110 LECRK51"
## [661] "AT4G03460 AT4G03460" "AT4G35920 MCA1" "AT1G58330 ZW2"
## [664] "AT5G36940 CAT3" "AT1G52200 PCR8" "AT1G01430 TBL25"
## [667] "AT4G01720 WRKY47" "AT3G58190 LBD29" "AT2G43020 PAO2"
## [670] "AT2G38120 AUX1" "AT2G42320 AT2G42320" "AT1G31420 FEI1"
## [673] "AT4G16490 AT4G16490" "AT4G27430 CIP7" "AT5G56340 ATCRT1"
## [676] "AT1G05990 CML7" "AT3G53840 WAKL15" "AT2G28850 CYP710A3"
## [679] "AT3G02885 GASA5" "AT5G42010 AT5G42010" "AT4G16600 PGSIP7"
## [682] "AT1G34670 AtMYB93" "AT2G45360 AT2G45360" "AT5G66920 sks17"
## [685] "AT1G22280 PAPP2C" "AT1G03210 AT1G03210" "AT4G30910 AT4G30910"
## [688] "AT2G04190 AT2G04190" "AT3G25030 AT3G25030" "AT5G07240 IQD24"
## [691] "AT5G48780 AT5G48780" "AT5G06930 AT5G06930" "AT5G43540 AT5G43540"
## [694] "AT5G01840 OFP1" "AT5G23360 AT5G23360" "AT2G36570 PXC1"
## [697] "AT4G14980 AT4G14980" "AT4G37850 BHLH25" "AT2G01900 AT2G01900"
## [700] "AT1G19920 APS2" "AT5G40230 AT5G40230" "AT1G65840 PAO4"
## [703] "AT1G49390 AT1G49390" "AT5G02230 AT5G02230" "AT2G13900 AT2G13900"
## [706] "AT5G44690 AT5G44690" "AT1G64405 AT1G64405" "AT5G58900 AT5G58900"
## [709] "AT1G12290 AT1G12290" "AT3G26820 AT3G26820" "AT3G25930 AT3G25930"
## [712] "AT2G30070 POT1" "AT1G31885 NIP3-1" "AT3G02870 VTC4"
## [715] "AT5G61340 AT5G61340" "AT1G47603 ATPUP19" "AT5G25240 AT5G25240"
## [718] "AT4G11090 TBL23" "AT5G58560 FOLK" "AT1G66800 AT1G66800"
## [721] "AT2G25220 AT2G25220" "AT5G43920 WDS" "AT2G38630 AT2G38630"
## [724] "AT4G04700 CPK27" "AT1G13710 CYP78A5" "AT4G10390 AT4G10390"
## [727] "AT5G05170 CESA3" "AT3G49050 AT3G49050" "AT5G25250 FLOT1"
## [730] "AT5G59700 AT5G59700" "AT5G33280 CLC-G" "AT5G01040 LAC8"
## [733] "AT5G65683 WAVH2" "AT2G38320 TBL34" "AT4G33120 AT4G33120"
## [736] "AT2G29670 AT2G29670" "AT2G46530 ARF11" "AT1G49570 PER10"
## [739] "AT4G24310 DMP3" "AT3G47420 ATPS3" "AT1G69690 TCP15"
## [742] "AT1G34050 AT1G34050" "AT2G13950 AT2G13950" "AT4G37400 CYP81F3"
## [745] "AT5G19080 LUL3" "AT1G19360 RRA3" "AT2G26040 PYL2"
## [748] "AT5G33290 XGD1" "AT3G03760 LBD20" "AT1G29020 AT1G29020"
## [751] "AT1G61950 CPK19" "AT5G45840 AT5G45840" "AT3G02630 S-ACP-DES5"
## [754] "AT1G13500 AT1G13500" "AT4G30640 FBL19" "AT5G46540 ABCB7"
## [757] "AT2G45890 ROPGEF4" "AT1G05660 AT1G05660" "AT3G23410 FAO3"
## [760] "AT2G41240 BHLH100" "AT3G20380 AT3G20380" "AT1G22882 SUN3"
## [763] "AT1G48300 AT1G48300" "AT3G47380 PMEI11" "AT2G05260 AT2G05260"
## [766] "AT2G34000 AT2G34000" "AT3G29400 ATEXO70E1" "AT2G23530 AT2G23530"
## [769] "AT1G29230 CIPK18" "AT2G28120 AT2G28120" "AT1G49240 ACT8"
## [772] "AT5G26280 AT5G26280" "AT5G14480 AT5G14480" "AT1G63500 BSK7"
## [775] "AT1G30110 NUDT25" "AT4G23980 ARF9" "AT1G59780 AT1G59780"
## [778] "AT1G07620 ATOBGM" "AT1G55120 CWINV3" "AT3G05690 UNE8"
## [781] "AT5G26660 MYB86" "AT3G26935 PAT07" "AT1G12090 ELP"
## [784] "AT3G23190 AT3G23190" "AT5G67190 ERF010" "AT3G14370 WAG2"
## [787] "AT3G23340 CKL10" "AT5G11540 GULLO3" "AT5G60280 LECRK18"
## [790] "AT4G00550 DGD2" "AT1G13440 GAPC2" "AT3G02880 AT3G02880"
## [793] "AT2G46890 AT2G46890" "AT5G03040 iqd2" "AT3G58620 TTL4"
## [796] "AT5G49720 KOR" "AT1G15600 AT1G15600" "AT3G09790 UBQ8"
## [799] "AT3G13760 AT3G13760" "AT3G26700 AT3G26700" "AT4G20460 AT4G20460"
## [802] "AT5G39000 AT5G39000" "AT4G14570 AT4G14570" "AT1G67560 LOX6"
## [805] "AT1G23030 PUB11" "AT2G01570 RGA" "AT1G14600 AT1G14600"
## [808] "AT1G79760 DTA4" "AT3G08600 AT3G08600" "AT4G11290 PER39"
## [811] "AT1G58100 TCP8" "AT1G28340 AtRLP4" "AT2G45590 AT2G45590"
## [814] "AT4G25300 AT4G25300" "AT2G44500 OFUT20" "AT5G28010 AT5G28010"
## [817] "AT5G08750 AT5G08750" "AT1G55365 AT1G55365" "AT1G13420 SOT8"
## [820] "AT4G35310 CPK5" "AT2G28930 APK1B" "AT3G63080 GPX5"
## [823] "AT3G02240 RGF7" "AT1G54000 GLL22" "AT5G64410 OPT4"
## [826] "AT1G05700 AT1G05700" "AT1G01300 APF2" "AT5G18670 BAM9"
## [829] "AT3G20540 POLGAMMA1" "AT2G03090 EXPA15" "AT1G01750 ADF11"
## [832] "AT2G26410 Iqd4" "AT1G20260 VHA-B3" "AT1G48640 AT1G48640"
## [835] "AT1G59960 AT1G59960" "AT3G60320 NRG2" "AT2G20562 AT2G20562"
## [838] "AT2G33710 AT2G33710" "AT4G21230 CRK27" "AT2G34470 UREG"
## [841] "AT5G05840 AT5G05840" "AT1G70450 AT1G70450" "AT1G50580 UGT79B5"
## [844] "AT2G43910 ATHOL1" "AT2G03720 MRH6" "AT1G47670 AATL1"
## [847] "AT5G37250 AT5G37250" "AT1G33780 AT1G33780" "AT4G16110 ARR2"
## [850] "AT5G24880 AT5G24880" "AT1G72880 AT1G72880" "AT4G12520 AT4G12520"
## [853] "AT1G69810 WRKY36" "AT2G39740 HESO1" "AT5G13820 TRP4"
## [856] "AT2G30930 AT2G30930" "AT4G37430 CYP81F1" "AT1G67270 AT1G67270"
## [859] "AT1G19900 AT1G19900" "AT5G64550 AT5G64550" "AT1G10400 UGT90A2"
## [862] "AT1G65560 AT1G65560" "AT5G26320 AT5G26320" "AT5G52670 AT5G52670"
## [865] "AT3G13437 AT3G13437" "AT3G07270 GCH1" "AT1G77420 AT1G77420"
## [868] "AT2G42490 AT2G42490" "AT4G25230 RIN2" "AT1G56720 AT1G56720"
## [871] "AT5G05460 ENGASE1" "AT1G79410 OCT5" "AT1G53310 PPC1"
## [874] "AT1G51480 AT1G51480" "AT4G01140 AT4G01140" "AT1G04040 AT1G04040"
## [877] "AT3G48080 EDS1B" "AT2G43620 AT2G43620" "AT3G46240 AT3G46240"
## [880] "AT3G05490 RALFL22" "AT5G41140 AT5G41140" "AT5G44920 TIK"
## [883] "AT1G59580 MPK2" "AT4G10550 AT4G10550" "AT5G01050 LAC9"
## [886] "AT5G60310 LECRK110" "AT5G26780 SHM2" "AT1G74460 AT1G74460"
## [889] "AT4G03330 SYP123" "AT3G21510 AHP1" "AT1G17040 SHA"
## [892] "AT3G20360 AT3G20360" "AT3G63260 ATMRK1" "AT1G65590 HEXO3"
## [895] "AT5G22050 AT5G22050" "AT1G01440 AT1G01440" "AT4G40050 AT4G40050"
## [898] "AT1G06120 AT1G06120" "AT2G23790 AT2G23790" "AT5G13760 AT5G13760"
## [901] "AT3G60550 CYCU2-2" "AT5G63990 SAL3" "AT4G11300 AT4G11300"
## [904] "AT2G30100 AT2G30100" "AT5G14920 GASA14" "AT3G06150 AT3G06150"
## [907] "AT3G59130 AT3G59130" "AT5G44585 AT5G44585" "AT2G23810 TET8"
## [910] "AT4G04340 OSCA1" "AT4G22756 SMO1-2" "AT2G46710 ROPGAP3"
## [913] "AT4G22640 AT4G22640" "AT1G04010 PSAT" "AT2G31310 LBD14"
## [916] "AT4G36220 CYP84A1" "AT5G16530 PIN5" "AT1G51630 MSR2"
## [919] "AT1G66110 AT1G66110" "AT3G44820 AT3G44820" "AT4G15210 BAM5"
## [922] "AT1G80870 AT1G80870" "AT3G59730 LECRK56" "AT4G27850 AT4G27850"
## [925] "AT3G29140 AT3G29140" "AT5G41260 BSK8" "AT1G69340 AT1G69340"
## [928] "AT1G01640 AT1G01640" "AT3G02750 AT3G02750" "AT5G14330 AT5G14330"
## [931] "AT1G19110 AT1G19110" "AT1G09430 ACLA-3" "AT3G43890 AT3G43890"
## [934] "AT1G19000 AT1G19000" "AT3G05150 AT3G05150" "AT5G56660 ILL2"
## [937] "AT4G29740 CKX4" "AT5G02200 FHL" "AT2G30490 CYP73A5"
## [940] "AT2G45510 CYP704A2" "AT5G14200 IMDH3" "AT1G69580 AT1G69580"
## [943] "AT1G73310 SCPL4" "AT5G12200 PYD2" "AT4G15417 ATRTL1"
## [946] "AT1G52660 AT1G52660" "AT4G33020 ZIP9" "AT5G10410 AT5G10410"
## [949] "AT1G08650 PPCK1" "AT3G57510 ADPG1" "AT4G02860 AT4G02860"
## [952] "AT1G55535 AT1G55535" "AT5G65158 PLAT3" "AT2G45720 AT2G45720"
## [955] "AT4G24170 KIN7I" "AT1G06830 GRXS11" "AT2G23780 AT2G23780"
## [958] "AT5G08170 AIH" "AT4G03940 AT4G03940" "AT1G29830 AT1G29830"
## [961] "AT1G22410 AT1G22410" "AT2G19970 AT2G19970" "AT5G45120 AT5G45120"
## [964] "AT3G23430 PHO1" "AT1G16150 WAKL4" "AT3G27390 AT3G27390"
## [967] "AT1G55430 AT1G55430" "AT4G21390 B120" "AT4G30520 AT4G30520"
## [970] "AT1G14350 MYB124" "AT2G25200 AT2G25200" "AT2G35840 SPP2"
## [973] "AT1G02810 PME7" "AT2G44110 MLO15" "AT5G17680 AT5G17680"
## [976] "AT1G33610 AT1G33610" "AT2G10930 AT2G10930" "AT4G13930 SHM4"
## [979] "AT2G26660 SPX2" "AT2G38290 AMT2" "AT5G55730 FLA1"
## [982] "AT3G14020 NFYA6" "AT1G01180 AT1G01180" "AT2G44790 UCC2"
## [985] "AT5G02400 PLL2" "AT3G32980 PER32" "AT5G16590 LRR1"
## [988] "AT3G27610 AT3G27610" "AT4G23650 CPK3" "AT1G22070 TGA3"
## [991] "AT1G34760 GRF11" "AT3G45210 AT3G45210" "AT2G44380 AT2G44380"
## [994] "AT3G11820 SYP121" "AT5G01330 PDC3" "AT3G03910 GSH3"
## [997] "AT2G36320 SAP4" "AT3G63350 HSFA7B" "AT3G08510 PLC2"
## [1000] "AT1G30730 AT1G30730" "AT3G04360 AT3G04360" "AT1G65960 GAD2"
## [1003] "AT5G44340 TUBB4" "AT4G36790 AT4G36790" "AT4G28260 AT4G28260"
## [1006] "AT5G15330 ATSPX4" "AT1G11130 SUB" "AT4G33080 AT4G33080"
## [1009] "AT4G31170 AT4G31170" "AT5G45220 AT5G45220" "AT4G29610 CDA6"
## [1012] "AT1G34520 AT1G34520" "AT1G70370 PGL3" "AT2G36724 AT2G36724"
## [1015] "AT1G06620 AT1G06620" "AT5G54780 AT5G54780" "AT5G42280 AT5G42280"
## [1018] "AT2G28840 XBAT31" "AT3G02430 DMP5" "AT1G79590 SYP52"
## [1021] "AT5G49820 RUS6" "AT4G30440 GAE1" "AT1G56280 ATDI19"
## [1024] "AT3G46830 RABA2C" "AT3G02860 AT3G02860" "AT2G42580 TTL3"
## [1027] "AT3G57650 LPAT2" "AT5G40250 ATL46" "AT5G22360 VAMP714"
## [1030] "AT4G00500 AT4G00500" "AT3G07490 CML3" "AT1G20560 AAE1"
## [1033] "AT5G43350 PHT1-1" "AT3G50710 AT3G50710" "AT5G44130 FLA13"
## [1036] "AT4G23870 AT4G23870" "AT2G24710 ATGLR2.3" "AT3G50060 MYB77"
## [1039] "AT4G24890 PAP24" "AT5G10280 MYB92" "AT1G01450 AT1G01450"
## [1042] "AT2G47370 AT2G47370" "AT3G58490 LPPD" "AT5G10430 AGP4"
## [1045] "AT5G40240 AT5G40240" "AT5G38340 AT5G38340" "AT5G09690 ATMGT7"
## [1048] "AT3G57420 STL2" "AT5G39490 AT5G39490" "AT5G02360 AT5G02360"
## [1051] "AT1G07520 AT1G07520" "AT3G52400 SYP122" "AT1G11920 AT1G11920"
## [1054] "AT2G33775 RALFL19" "AT1G10155 ATPP2-A10" "AT5G03520 RABE1D"
## [1057] "AT4G34950 AT4G34950" "AT4G35320 AT4G35320" "AT2G45910 PUB33"
## [1060] "AT3G45650 NAXT1" "AT5G15130 WRKY72" "AT4G34580 SFH1"
## [1063] "AT4G24100 AT4G24100" "AT1G58070 AT1G58070" "AT2G36310 URH1"
## [1066] "AT3G10210 AT3G10210" "AT1G02290 AT1G02290" "AT4G10840 KLCR1"
## [1069] "AT4G32420 CYP95" "AT5G27450 MVK" "AT5G23280 TCP7"
## [1072] "AT2G28890 PLL4" "AT4G14290 AT4G14290" "AT1G44160 AT1G44160"
## [1075] "AT5G58700 PLC4" "AT1G70990 AT1G70990" "AT3G23820 GAE6"
## [1078] "AT4G08770 PER37" "AT4G15540 AT4G15540" "AT2G17050 AT2G17050"
## [1081] "AT5G02580 AT5G02580" "AT1G80730 ZFP1" "AT4G22230 AT4G22230"
## [1084] "AT3G29180 AT3G29180" "AT1G76220 AT1G76220" "AT4G12420 SKU5"
## [1087] "AT3G19970 AT3G19970" "AT5G19230 AT5G19230" "AT3G09290 TAC1"
## [1090] "AT4G14365 XBAT34" "AT1G71692 AGL12" "AT2G16380 SFH7"
## [1093] "AT1G57570 JAL14" "AT2G02640 AT2G02640" "AT5G59930 AT5G59930"
## [1096] "AT3G50300 AT3G50300" "AT1G71015 AT1G71015" "AT4G28270 RMA2"
## [1099] "AT2G21540 SFH3" "AT1G25510 AT1G25510" "AT1G55440 AT1G55440"
## [1102] "AT3G03000 CML18" "AT3G27630 SMR7" "AT5G57940 CNGC5"
## [1105] "AT1G67940 ABCI17" "AT5G26010 AT5G26010" "AT1G03840 MGP"
## [1108] "AT4G39950 CYP79B2" "AT5G58860 CYP86A1" "AT5G49870 JAL48"
## [1111] "AT1G77280 AT1G77280" "AT1G60390 PGL2" "AT5G60660 PIP2-4"
## [1114] "AT5G44480 DUR" "AT4G22580 GT19" "AT1G29740 AT1G29740"
## [1117] "AT3G59680 AT3G59680" "AT3G15300 VQ19" "AT2G14510 AT2G14510"
## [1120] "AT4G00680 ADF8" "AT5G24655 LSU4" "AT4G11320 RDL5"
## [1123] "AT1G64070 RLM1A" "AT5G56610 AT5G56610" "AT3G42180 AT3G42180"
## [1126] "AT1G23980 ATL47" "AT4G15300 CYP702A2" "AT5G08260 SCPL35"
## [1129] "AT5G54160 OMT1" "AT1G65730 YSL7" "AT4G32650 KAT3"
## [1132] "AT4G04450 WRKY42" "AT5G16190 ATCSLA11" "AT3G59690 IQD13"
## [1135] "AT1G78530 AT1G78530" "AT2G26510 NAT3" "AT5G59020 AT5G59020"
## [1138] "AT5G01520 AIRP2" "AT1G55450 AT1G55450" "AT2G28970 AT2G28970"
## [1141] "AT3G17650 YSL5" "AT1G72950 AT1G72950" "AT5G60490 FLA12"
## [1144] "AT3G18215 AT3G18215" "AT2G37280 PDR5" "AT1G02980 CUL2"
## [1147] "AT5G64740 CESA6" "AT5G40440 MKK3" "AT1G15125 AT1G15125"
## [1150] "AT3G12020 AT3G12020" "AT3G21770 PER30" "AT1G18670 IBS1"
## [1153] "AT1G17060 CYP72C1" "AT5G17090 AT5G17090" "AT4G06536 AT4G06536"
## [1156] "AT5G15290 CASP5" "AT3G01760 AT3G01760" "AT5G01060 AT5G01060"
## [1159] "AT5G55960 AT5G55960" "AT2G44210 AT2G44210" "AT1G34060 TAR4"
## [1162] "AT2G36330 AT2G36330" "AT3G59760 OASC" "AT3G13360 WIP3"
## [1165] "AT3G01930 AT3G01930" "AT3G01720 SERGT1" "AT4G32020 AT4G32020"
## [1168] "AT5G26720 AT5G26720" "AT2G39518 AT2G39518" "AT1G67750 AT1G67750"
## [1171] "AT1G79420 AT1G79420" "AT2G29740 UGT71C2" "AT3G52370 FLA15"
## [1174] "AT5G06250 AT5G06250" "AT4G08450 AT4G08450" "AT3G09540 AT3G09540"
## [1177] "AT5G15150 HAT7" "AT1G64330 AT1G64330" "AT5G28960 AT5G28960"# downregulated genes
v2 <- list("leaf 3d dn"=del3_dn, "leaf 5d dn"=del5_dn,
"root 3d dn" =der3_dn , "root 5d dn"=der5_dn)
plot(euler(v2),quantities = TRUE)
intersect(del3_dn,del5_dn)## [1] "AT4G02720 AT4G02720" "AT4G23680 AT4G23680" "AT1G19840 AT1G19840"
## [4] "AT3G62130 LCD" "AT1G19600 AT1G19600" "AT1G17180 GSTU25"
## [7] "AT2G32190 AT2G32190" "AT3G16770 RAP2-3" "AT5G17330 GAD1"
## [10] "AT1G34180 anac016" "AT4G28720 YUC8" "AT3G16420 PBP1"
## [13] "AT5G62150 AT5G62150" "AT2G33840 AT2G33840" "AT5G50760 AT5G50760"
## [16] "AT3G62730 AT3G62730" "AT5G26731 AT5G26731" "AT1G53830 PME2"
## [19] "AT1G49000 AT1G49000" "AT4G30180 BHLH146" "AT4G30190 HA2"
## [22] "AT2G27830 AT2G27830" "AT1G68500 AT1G68500" "AT5G46240 KAT1"
## [25] "AT1G16120 WAKL1" "AT2G37360 ABCG2" "AT2G05510 AT2G05510"
## [28] "AT1G18970 GLP1" "AT2G47560 ATL64" "AT3G22240 AT3G22240"
## [31] "AT4G30960 CIPK6" "AT4G29700 AT4G29700" "AT4G13420 POT5"
## [34] "AT2G02230 PP2B1" "AT3G49570 LSU3" "AT1G20990 AT1G20990"
## [37] "AT3G62270 BOR2" "AT1G23150 AT1G23150" "AT1G70170 2MMP"
## [40] "AT1G77400 AT1G77400" "AT5G07570 AT5G07570" "AT1G05000 AT1G05000"
## [43] "AT1G65690 NHL6" "AT2G47870 GRXC12" "AT3G09400 PLL3"
## [46] "AT4G33960 AT4G33960" "AT3G05880 RCI2A" "AT3G52450 PUB22"
## [49] "AT5G47550 CYS5" "AT5G13900 VAS" "AT1G77180 SKIP"
## [52] "AT4G19200 AT4G19200" "AT5G19410 AT5G19410" "AT4G35720 AT4G35720"
## [55] "AT5G66170 STR18" "AT5G47590 AT5G47590" "AT5G43980 CRRSP56"
## [58] "AT4G39190 AT4G39190" "AT4G30670 AT4G30670" "AT4G29340 PRO3"
## [61] "AT4G18280 AT4G18280" "AT4G14819 AT4G14819" "AT1G01190 CYP78A8"
## [64] "AT3G60520 AT3G60520" "AT5G14000 anac084" "AT2G23150 NRAMP3"
## [67] "AT3G23325 AT3G23325" "AT1G64370 AT1G64370" "AT5G14730 AT5G14730"
## [70] "AT2G39700 EXPA4" "AT5G64260 EXL2" "AT1G19830 AT1G19830"
## [73] "AT2G18480 PLT3" "AT4G21990 APR3" "AT3G15150 MMS21"
## [76] "AT2G31200 ADF6" "AT2G02120 PDF2.1" "AT1G77760 NIA1"
## [79] "AT5G12930 AT5G12930" "AT5G58570 AT5G58570" "AT3G49940 LBD38"
## [82] "AT1G70300 POT6" "AT3G19030 AT3G19030" "AT2G47485 AT2G47485"
## [85] "AT5G39590 AT5G39590" "AT1G64170 CHX16" "AT1G77590 LACS9"
## [88] "AT1G18980 AT1G18980" "AT4G23860 AT4G23860" "AT2G36270 ABI5"
## [91] "AT3G26140 AT3G26140" "AT5G51200 AT5G51200" "AT2G42360 ATL41"
## [94] "AT3G58930 AT3G58930" "AT4G17215 AT4G17215" "AT2G02010 GAD4"
## [97] "AT3G62830 UXS2" "AT1G07780 PAI1" "AT5G65010 ASN2"
## [100] "AT3G60330 AHA7" "AT5G59990 AT5G59990" "AT2G35820 AT2G35820"
## [103] "AT1G62480 AT1G62480" "AT4G14630 GLP9" "AT5G45350 AT5G45350"
## [106] "AT5G11100 SYTD" "AT5G22890 STOP2" "AT1G30560 AT1G30560"
## [109] "AT5G40670 AT5G40670" "AT1G56320 AT1G56320" "AT3G50770 CML41"
## [112] "AT5G12940 AT5G12940" "AT2G31980 CYS2" "AT5G19970 AT5G19970"
## [115] "AT1G62422 AT1G62422" "AT1G22500 ATL15" "AT2G37570 SLT1"
## [118] "AT1G03820 AT1G03820" "AT5G06210 S-RBP11" "AT4G18550 AT4G18550"
## [121] "AT4G34881 AT4G34881" "AT3G07350 AT3G07350" "AT4G04830 MSRB5"
## [124] "AT2G37330 ALS3" "AT2G16760 AT2G16760" "AT1G60450 GOLS7"
## [127] "AT5G57567 AT5G57567" "AT1G23730 BCA3" "AT3G18140 LST8-1"
## [130] "AT1G12110 NPF6.3" "AT5G40010 AATP1" "AT1G70800 CAR6"
## [133] "AT3G05200 ATL6" "AT5G10580 AT5G10580" "AT4G33740 AT4G33740"
## [136] "AT4G39300 AT4G39300" "AT2G38170 CAX1" "AT5G18290 SIP1-2"
## [139] "AT1G21550 CML44" "AT5G12140 CYS1" "AT5G66658 AT5G66658"
## [142] "AT1G13480 AT1G13480" "AT5G01180 NPF8.2" "AT1G78400 AT1G78400"
## [145] "AT1G19190 CXE1" "AT3G61630 CRF6" "AT2G34690 ACD11"
## [148] "AT4G17340 TIP2-2" "AT1G66180 AT1G66180" "AT2G45280 ATRAD51C"
## [151] "AT1G68620 CXE6" "AT3G55646 AT3G55646" "AT1G44750 PUP11"
## [154] "AT4G20820 AT4G20820" "AT5G07440 GDH2" "AT3G62990 AT3G62990"
## [157] "AT5G55190 RAN3" "AT5G09520 PELPK2" "AT3G27025 AT3G27025"
## [160] "AT5G47530 AT5G47530" "AT5G62490 HVA22B" "AT1G14870 PCR2"
## [163] "AT5G66650 AT5G66650" "AT2G39350 ABCG1" "AT1G55240 AT1G55240"
## [166] "AT1G20190 EXPA11" "AT1G53170 ERF8" "AT1G48750 AT1G48750"
## [169] "AT4G24420 AT4G24420" "AT1G36370 SHM7" "AT4G29820 CFIS1"
## [172] "AT4G05200 CRK25" "AT1G28400 AT1G28400" "AT3G49580 LSU1"
## [175] "AT1G31835 AT1G31835" "AT4G03540 AT4G03540" "AT1G24575 AT1G24575"
## [178] "AT5G57350 AHA3" "AT5G61890 ERF114" "AT3G56130 AT3G56130"
## [181] "AT3G07870 AT3G07870" "AT4G21110 AT4G21110" "AT3G18560 AT3G18560"
## [184] "AT3G03650 EDA5" "AT5G47920 AT5G47920" "AT1G20693 HMGB2"
## [187] "AT5G41590 AT5G41590" "AT1G12030 AT1G12030" "AT1G51830 AT1G51830"
## [190] "AT4G23670 AT4G23670" "AT4G31140 AT4G31140" "AT5G28520 JAL40"
## [193] "AT4G20320 AT4G20320" "AT2G06040 AT2G06040" "AT2G23120 AT2G23120"
## [196] "AT4G39675 AT4G39675" "AT2G23540 AT2G23540" "AT2G18160 BZIP2"
## [199] "AT2G37170 PIP2B" "AT2G41800 AT2G41800" "AT5G02480 AT5G02480"
## [202] "AT3G46190 AT3G46190" "AT3G01200 RP2" "AT2G02955 MEE12"
## [205] "AT4G01360 AT4G01360" "AT1G66830 AT1G66830" "AT1G68350 AT1G68350"
## [208] "AT1G32928 AT1G32928" "AT5G13580 ABCG6" "AT3G30725 GDU6"
## [211] "AT1G78650 POLD3" "AT2G17840 ERD7" "AT3G22910 ACA13"
## [214] "AT1G49840 AT1G49840" "AT4G14030 SBP1" "AT5G47130 AT5G47130"
## [217] "AT4G31910 BAT1" "AT5G06090 GPAT7" "AT1G70670 PXG4"
## [220] "AT4G17280 AT4G17280" "AT5G38200 AT5G38200" "AT3G08030 AT3G08030"
## [223] "AT5G37740 AT5G37740" "AT1G09870 AT1G09870" "AT1G60610 AT1G60610"
## [226] "AT5G42980 TRX3" "AT4G11070 WRKY41" "AT2G35770 SCPL28"
## [229] "AT5G09530 PELPK1" "AT1G31750 AT1G31750" "AT3G16730 CAPH2"
## [232] "AT2G36930 AT2G36930" "AT4G24130 AT4G24130" "AT2G30360 CIPK11"
## [235] "AT3G50400 AT3G50400" "AT2G40400 RER5" "AT2G37440 IP5P8"
## [238] "AT1G54540 AT1G54540" "AT4G18630 AT4G18630" "AT5G40460 SMR6"
## [241] "AT4G28703 AT4G28703" "AT3G29575 AFP3" "AT1G61480 AT1G61480"
## [244] "AT5G46370 TPK2" "AT3G16410 NSP4" "AT4G21650 SBT3.13"
## [247] "AT2G23070 CKA4" "AT5G11090 AT5G11090" "AT5G15960 KIN1"
## [250] "AT1G62420 AT1G62420" "AT3G56240 CCH" "AT4G31330 AT4G31330"
## [253] "AT5G22310 AT5G22310" "AT3G44550 FAR5" "AT3G12520 SULTR4;2"
## [256] "AT4G15960 AT4G15960" "AT1G70690 CRRSP2" "AT1G52980 NUG2"
## [259] "AT1G45145 TRX5" "AT1G26450 AT1G26450" "AT1G75390 BZIP44"
## [262] "AT2G41200 AT2G41200" "AT3G49760 AtbZIP5" "AT5G62680 NPF2.11"
## [265] "AT4G35640 SAT4" "AT5G02260 EXPA9" "AT2G15620 NIR1"
## [268] "AT5G19600 SULTR3;5" "AT1G18870 ICS2" "AT1G74000 SSL11"
## [271] "AT5G46140 AT5G46140" "AT1G75440 UBC16" "AT2G01580 AT2G01580"
## [274] "AT4G28230 AT4G28230" "AT1G15310 SRP-54A" "AT1G27200 AT1G27200"
## [277] "AT2G41410 CML35" "AT1G59660 NUP98B" "AT3G22600 AT3G22600"
## [280] "AT5G53700 AT5G53700" "AT2G22080 AT2G22080" "AT2G39800 P5CSA"
## [283] "AT4G32920 AT4G32920" "AT3G21710 VUP1" "AT1G75280 AT1G75280"
## [286] "AT3G59850 AT3G59850" "AT1G27670 AT1G27670" "AT5G37980 AT5G37980"
## [289] "AT3G03341 AT3G03341" "AT1G51340 DTX42" "AT2G41480 PER25"
## [292] "AT1G19230 RBOHE" "AT2G18340 AT2G18340" "AT5G52390 AT5G52390"
## [295] "AT3G48510 AT3G48510" "AT3G09270 GSTU8" "AT2G47200 AT2G47200"
## [298] "AT3G50260 ERF011" "AT5G63030 GRXC1" "AT2G42350 ATL40"
## [301] "AT4G25670 AT4G25670" "AT1G04770 AT1G04770" "AT1G64140 AT1G64140"
## [304] "AT3G56200 AVT6C" "AT5G49350 AT5G49350" "AT1G70440 SRO3"
## [307] "AT3G21480 AT3G21480" "AT3G61900 AT3G61900" "AT1G05450 AT1G05450"
## [310] "AT1G02400 GA2OX6" "AT1G65220 AT1G65220" "AT4G32480 AT4G32480"
## [313] "AT3G05165 AT3G05165" "AT1G66530 AT1G66530" "AT1G51840 AT1G51840"
## [316] "AT2G25690 FLZ11" "AT3G14560 AT3G14560" "AT3G52790 AT3G52790"intersect(der3_dn,der3_dn)## [1] "AT5G38910 AT5G38910" "AT4G19810 ChiC" "AT5G39100 GLP6"
## [4] "AT2G46750 GULLO2" "AT2G26695 AT2G26695" "AT3G49570 LSU3"
## [7] "AT3G49580 LSU1" "AT4G34710 ADC2" "AT5G39110 AT5G39110"
## [10] "AT2G13810 ALD1" "AT5G39120 AT5G39120" "AT5G19600 SULTR3;5"
## [13] "AT2G43590 AT2G43590" "AT5G48850 SDI1" "AT2G20180 PIF1"
## [16] "AT2G27120 POL2B" "AT4G31330 AT4G31330" "AT4G02360 AT4G02360"
## [19] "AT5G64810 WRKY51" "AT2G26560 PLP2" "AT4G10500 DLO1"
## [22] "AT1G05340 AT1G05340" "AT2G18480 PLT3" "AT1G18100 MFT"
## [25] "AT2G26700 PID2" "AT2G02120 PDF2.1" "AT4G23680 AT4G23680"
## [28] "AT5G06860 PGIP1" "AT1G19960 AT1G19960" "AT1G04770 AT1G04770"
## [31] "AT5G39150 AT5G39150" "AT4G04830 MSRB5" "AT3G08860 PYD4"
## [34] "AT2G04050 DTX3" "AT3G16530 AT3G16530" "AT3G62040 AT3G62040"
## [37] "AT1G62710 bVPE" "AT5G28520 JAL40" "AT1G36370 SHM7"
## [40] "AT4G01870 AT4G01870" "AT3G51895 SULTR3;1" "AT5G24030 SLAH3"
## [43] "AT1G01190 CYP78A8" "AT2G04070 DTX4" "AT4G21990 APR3"
## [46] "AT5G38200 AT5G38200" "AT3G11930 AT3G11930" "AT5G57350 AHA3"
## [49] "AT3G12520 SULTR4;2" "AT1G01140 CIPK9" "AT3G12700 NANA"
## [52] "AT5G18170 GDH1" "AT4G11650 OSM34" "AT2G24260 BHLH66"
## [55] "AT3G05400 SUGTL5" "AT3G62730 AT3G62730" "AT1G17840 ABCG11"
## [58] "AT1G68620 CXE6" "AT1G66180 AT1G66180" "AT1G15830 AT1G15830"
## [61] "AT1G15380 AT1G15380" "AT4G12580 AT4G12580" "AT1G71050 HIPP20"
## [64] "AT2G43570 CHI" "AT5G06730 PER54" "AT3G15500 NAC055"
## [67] "AT1G51340 DTX42" "AT2G18660 EGC2" "AT5G13080 WRKY75"
## [70] "AT4G33666 AT4G33666" "AT3G47580 AT3G47580" "AT3G13433 AT3G13433"
## [73] "AT4G18350 NCED2" "AT5G22390 AT5G22390" "AT5G59540 AT5G59540"
## [76] "AT1G20180 AT1G20180" "AT3G04070 NAC047" "AT5G10180 SULTR2;1"
## [79] "AT1G60470 GOLS4" "AT4G19760 AT4G19760" "AT1G08430 ALMT1"
## [82] "AT1G29670 AT1G29670" "AT1G51330 AT1G51330" "AT1G48750 AT1G48750"
## [85] "AT4G09120 ATL36" "AT4G15490 UGT84A3" "AT3G47480 CML47"
## [88] "AT2G47560 ATL64" "AT1G78000 SULTR1;2" "AT2G37330 ALS3"
## [91] "AT5G59220 SAG113" "AT1G24130 AT1G24130" "AT2G32487 AT2G32487"
## [94] "AT4G14630 GLP9" "AT3G52970 CYP76G1" "AT3G14990 DJ1A"
## [97] "AT5G07050 AT5G07050" "AT2G46680 ATHB-7" "AT4G30960 CIPK6"
## [100] "AT5G64210 AOX2" "AT2G45135 AT2G45135" "AT1G15825 AT1G15825"
## [103] "AT3G61890 ATHB-12" "AT4G13420 POT5" "AT3G30210 ATMYB121"
## [106] "AT5G28510 BGLU24" "AT5G12930 AT5G12930" "AT5G40010 AATP1"
## [109] "AT1G70830 MLP28" "AT3G25882 NIMIN-2" "AT1G09080 MED37B"
## [112] "AT4G19700 BOI" "AT4G35640 SAT4" "AT1G75900 EXL3"
## [115] "AT5G07560 GRP20" "AT1G74590 GSTU10" "AT2G43510 ATTI1"
## [118] "AT3G24310 MYB305" "AT5G63350 AT5G63350" "AT3G50970 XERO2"
## [121] "AT5G24640 AT5G24640" "AT2G40460 NPF5.1" "AT1G02310 MAN1"
## [124] "AT4G21200 GA2OX8" "AT4G25700 BETA-OHASE" "AT2G36780 UGT73C3"
## [127] "AT1G22900 DIR11" "AT4G04570 CRK40" "AT1G66760 DTX9"
## [130] "AT2G17640 SAT2" "AT1G65690 NHL6" "AT3G49120 PER34"
## [133] "AT4G19750 AT4G19750" "AT1G22430 AT1G22430" "AT1G18870 ICS2"
## [136] "AT4G00070 AT4G00070" "AT4G36880 CP1" "AT5G13330 ERF113"
## [139] "AT4G33070 PDC1" "AT3G62990 AT3G62990" "AT5G39520 AT5G39520"
## [142] "AT5G66650 AT5G66650" "AT2G25690 FLZ11" "AT5G01300 AT5G01300"
## [145] "AT5G24660 LSU2" "AT2G15220 AT2G15220" "AT5G14780 FDH1"
## [148] "AT3G48510 AT3G48510" "AT1G45201 ATTLL1" "AT2G32510 MAPKKK17"
## [151] "AT1G17615 AT1G17615" "AT4G17340 TIP2-2" "AT3G28510 AT3G28510"
## [154] "AT3G21090 ABCG15" "AT4G37050 PLP3" "AT1G51500 ABCG12"
## [157] "AT5G64250 AT5G64250" "AT3G60415 AT3G60415" "AT1G13520 AT1G13520"
## [160] "AT2G16005 ROSY1" "AT3G06210 AT3G06210" "AT1G74010 AT1G74010"
## [163] "AT4G13250 NYC1" "AT1G02920 GSTF7" "AT5G13170 SWEET15"
## [166] "AT2G39450 MTP11" "AT5G67340 PUB2" "AT4G19740 AT4G19740"
## [169] "AT3G45730 AT3G45730" "AT3G55090 ABCG16" "AT1G28010 ABCB14"
## [172] "AT1G72970 HTH" "AT5G11210 GLR2.5" "AT4G37370 CYP81D8"
## [175] "AT5G13320 PBS3" "AT4G38810 AT4G38810" "AT5G50260 CEP1"
## [178] "AT2G44460 BGLU28" "AT2G16890 UGT90A1" "AT2G30140 UGT87A2"
## [181] "AT3G55790 AT3G55790" "AT3G16330 AT3G16330" "AT4G33550 AT4G33550"
## [184] "AT1G73260 KTI1" "AT2G23150 NRAMP3" "AT1G52890 NAC019"
## [187] "AT5G01720 FBL3" "AT5G23050 AAE17" "AT1G07720 KCS3"
## [190] "AT1G68880 BZIP8" "AT1G02205 CER1" "AT5G06905 CYP712A2"
## [193] "AT4G27410 RD26" "AT5G47050 AT5G47050" "AT5G50360 AT5G50360"
## [196] "AT5G47240 atnudt8" "AT5G26340 STP13" "AT1G26450 AT1G26450"
## [199] "AT3G22740 HMT3" "AT2G34610 AT2G34610" "AT4G19230 CYP707A1"
## [202] "AT5G47450 TIP2-3" "AT1G24600 AT1G24600" "AT1G74458 AT1G74458"
## [205] "AT1G27200 AT1G27200" "AT2G43000 JUB1" "AT2G39800 P5CSA"
## [208] "AT5G62350 AT5G62350" "AT4G13480 AtMYB79" "AT4G25960 ABCB2"
## [211] "AT1G22640 MYB3" "AT1G31050 AT1G31050" "AT5G26220 GGCT2;1"
## [214] "AT1G71140 DTX14" "AT2G29380 HAI3" "AT2G20720 AT2G20720"
## [217] "AT2G28270 AT2G28270" "AT5G59320 LTP3" "AT2G41190 AVT1A"
## [220] "AT4G31140 AT4G31140" "AT1G07430 AIP1" "AT3G53470 AT3G53470"
## [223] "AT4G03420 AT4G03420" "AT4G32210 SDH3-1" "AT2G36640 ECP63"
## [226] "AT2G36270 ABI5" "AT1G73810 AT1G73810" "AT4G24510 CER2"
## [229] "AT3G20470 GRP5" "AT1G73390 AT1G73390" "AT1G56600 GOLS2"
## [232] "AT5G11650 AT5G11650" "AT5G18470 AT5G18470" "AT3G46650 AT3G46650"
## [235] "AT1G44180 AT1G44180" "AT3G11410 PP2CA" "AT1G70440 SRO3"
## [238] "AT4G05380 AT4G05380" "AT4G12430 TPPF" "AT4G37870 PCKA"
## [241] "AT3G28320 AT3G28320" "AT3G55310 AT3G55310" "AT4G10860 AT4G10860"
## [244] "AT1G32870 ANAC13" "AT4G35190 LOG5" "AT1G76470 AT1G76470"
## [247] "AT5G61820 AT5G61820" "AT3G57540 REM4.1" "AT1G49200 ATL75"
## [250] "AT1G05560 UGT1" "AT1G15310 SRP-54A" "AT4G23700 CHX17"
## [253] "AT5G62530 ALDH12A1" "AT2G31980 CYS2" "AT1G26410 FOX4"
## [256] "AT1G77450 NAC032" "AT4G39330 CAD9" "AT1G70640 AT1G70640"
## [259] "AT4G19200 AT4G19200" "AT5G02480 AT5G02480" "AT1G77760 NIA1"
## [262] "AT3G16370 APG" "AT2G30750 CYP71A12" "AT1G56580 SVB"
## [265] "AT4G33220 PME44" "AT2G39490 AT2G39490" "AT1G19750 AT1G19750"
## [268] "AT3G28290 AT14A" "AT3G28300 AT14A" "AT5G22500 FAR1"
## [271] "AT5G43580 AT5G43580" "AT1G55240 AT1G55240" "AT3G22370 AOX1A"
## [274] "AT4G30460 AT4G30460" "AT1G69260 AFP1" "AT4G37060 PLP5"
## [277] "AT3G46190 AT3G46190" "AT1G32940 SBT3.5" "AT5G53700 AT5G53700"
## [280] "AT4G16220 AT4G16220" "AT4G28703 AT4G28703" "AT5G66260 AT5G66260"
## [283] "AT5G24220 AT5G24220" "AT5G45950 AT5G45950" "AT1G80820 CCR2"
## [286] "AT4G15550 UGT75D1" "AT3G19100 CRK2" "AT1G09180 ATSAR1"
## [289] "AT5G25460 AT5G25460" "AT1G78230 AT1G78230" "AT1G02230 NAC004"
## [292] "AT1G36622 AT1G36622" "AT4G24010 CSLG1" "AT3G56400 WRKY70"
## [295] "AT1G04180 YUC9" "AT3G50260 ERF011" "AT3G09390 MT2A"
## [298] "AT4G28840 SPEAR3" "AT4G34320 AT4G34320" "AT5G41740 AT5G41740"
## [301] "AT2G42250 CYP712A1" "AT2G35300 LEA18" "AT4G30270 XTH24"
## [304] "AT1G73805 SARD1" "AT3G56240 CCH" "AT5G06320 NHL3"
## [307] "AT5G17460 AT5G17460" "AT3G57260 BGL2" "AT5G27350 SFP1"
## [310] "AT1G73880 UGT89B1" "AT1G12110 NPF6.3" "AT2G38823 AT2G38823"
## [313] "AT5G17650 AT5G17650" "AT3G02480 AT3G02480" "AT4G23860 AT4G23860"
## [316] "AT3G48850 MPT2" "AT3G08870 AT3G08870" "AT3G48520 CYP94B3"
## [319] "AT5G24080 AT5G24080" "AT1G75210 AT1G75210" "AT5G39090 AT5G39090"
## [322] "AT5G61650 CYCU4-3" "AT5G50760 AT5G50760" "AT4G29340 PRO3"
## [325] "AT1G68530 CUT1" "AT4G04610 APR1" "AT5G49130 DTX55"
## [328] "AT4G25860 ORP4A" "AT5G39030 AT5G39030" "AT3G01970 WRKY45"
## [331] "AT1G62280 SLAH1" "AT1G16850 AT1G16850" "AT1G07900 LBD1"
## [334] "AT1G04560 AT1G04560" "AT2G29460 GSTU4" "AT3G23450 AT3G23450"
## [337] "AT3G22550 FLZ8" "AT1G46768 RAP2-1" "AT4G33467 AT4G33467"
## [340] "AT3G22830 HSFA6B" "AT4G28040 AT4G28040" "AT4G00305 AT4G00305"
## [343] "AT3G61630 CRF6" "AT2G24180 CYP71B6" "AT5G43840 HSFA6A"
## [346] "AT4G21750 ATML1" "AT2G38540 LTP1" "AT5G07010 SOT15"
## [349] "AT5G66400 RAB18" "AT4G28490 RLK5" "AT2G05510 AT2G05510"
## [352] "AT1G70740 AT1G70740" "AT5G43180 AT5G43180" "AT4G16146 AT4G16146"
## [355] "AT4G21440 ATMYB102" "AT1G02850 BGLU11" "AT1G68020 TPS6"
## [358] "AT2G16720 MYB7" "AT5G11090 AT5G11090" "AT5G58330 AT5G58330"
## [361] "AT5G17430 BBM" "AT3G46230 HSP17.4A" "AT4G00430 PIP1.4"
## [364] "AT1G68500 AT1G68500" "AT5G65790 ATMYB68" "AT4G23880 AT4G23880"
## [367] "AT1G13480 AT1G13480" "AT3G14690 CYP72A15" "AT3G27250 AT3G27250"
## [370] "AT1G78850 AT1G78850" "AT2G02060 AT2G02060" "AT4G31830 AT4G31830"
## [373] "AT5G59520 ZIP2" "AT5G44567 AT5G44567" "AT1G32350 AOX3"
## [376] "AT4G12735 AT4G12735" "AT2G32660 AtRLP22" "AT1G07400 HSP17.8"
## [379] "AT4G37730 AtbZIP7" "AT4G04490 CRK36" "AT5G53990 UGT79B9"
## [382] "AT3G12910 AT3G12910" "AT4G30470 AT4G30470" "AT5G38980 AT5G38980"
## [385] "AT5G13370 AT5G13370" "AT4G36040 ATJ11" "AT1G53625 AT1G53625"
## [388] "AT3G05165 AT3G05165" "AT2G37870 AT2G37870" "AT4G26120 AT4G26120"
## [391] "AT5G39190 GLP5A" "AT4G34250 KCS16" "AT3G52720 ACA1"
## [394] "AT1G53470 MSL4" "AT4G26080 ABI1" "AT4G37790 HAT22"
## [397] "AT3G14440 NCED3" "AT5G14550 AT5G14550" "AT3G47600 MYB94"
## [400] "AT1G57943 PUP17" "AT2G31945 AT2G31945" "AT5G54165 AT5G54165"
## [403] "AT1G69526 AT1G69526" "AT3G57160 AT3G57160" "AT5G24380 YSL2"
## [406] "AT4G17740 CTPA2" "AT1G53170 ERF8" "AT2G41730 AT2G41730"
## [409] "AT1G05330 AT1G05330" "AT1G69570 CDF5" "AT1G12200 AT1G12200"
## [412] "AT1G19850 ARF5" "AT1G49470 AT1G49470" "AT5G38900 AT5G38900"
## [415] "AT5G52310 RD29A" "AT1G26420 FOX5" "AT3G22240 AT3G22240"
## [418] "AT2G27830 AT2G27830" "AT5G52320 CYP96A4" "AT4G33905 AT4G33905"
## [421] "AT1G80770 PDE318" "AT4G33420 AT4G33420" "AT5G04370 NAMT1"
## [424] "AT2G31070 TCP10" "AT4G15260 AT4G15260" "AT4G28460 PIP1"
## [427] "AT4G23920 UGE2" "AT1G77920 TGA7" "AT2G42840 PDF1"
## [430] "AT4G32540 YUC" "AT1G73930 AT1G73930" "AT4G20820 AT4G20820"
## [433] "AT1G17020 SRG1" "AT2G15580 AT2G15580" "AT1G01720 NAC002"
## [436] "AT4G32380 AT4G32380" "AT3G25710 BHLH32" "AT2G25625 AT2G25625"
## [439] "AT3G22100 BHLH117" "AT1G05100 MAPKKK18" "AT3G57830 AT3G57830"
## [442] "AT5G17760 AT5G17760" "AT1G69120 AP1" "AT5G03210 AT5G03210"
## [445] "AT5G13400 NPF6.1" "AT2G15490 UGT73B4" "AT3G27820 MDAR4"
## [448] "AT1G12030 AT1G12030" "AT5G57660 COL5" "AT2G37760 AKR4C8"
## [451] "AT2G26690 NPF6.2" "AT2G16700 ADF5" "AT1G77990 SULTR2;2"
## [454] "AT5G52570 BETA-OHASE" "AT4G22070 WRKY31" "AT5G23660 SWEET12"
## [457] "AT4G12350 MYB42" "AT2G38530 LTP2" "AT2G23170 GH3.3"
## [460] "AT3G49130 AT3G49130" "AT5G42900 COR27" "AT3G62090 PIF6"
## [463] "AT5G17850 CCX2" "AT1G80110 PP2B11" "AT3G28007 SWEET4"
## [466] "AT3G03660 WOX11" "AT2G47020 AT2G47020" "AT2G40390 AT2G40390"
## [469] "AT4G17470 AT4G17470" "AT2G21130 CYP19-2" "AT4G28410 AT4G28410"
## [472] "AT1G52000 JAL5" "AT3G18440 ALMT9" "AT5G48400 GLR1.2"
## [475] "AT5G39050 PMAT1" "AT4G37150 MES9" "AT4G11655 AT4G11655"
## [478] "AT3G11660 NHL1" "AT3G63060 EDL3" "AT3G20300 AT3G20300"
## [481] "AT1G06130 GLX2-4" "AT5G59190 AT5G59190" "AT3G10430 AT3G10430"
## [484] "AT3G01500 BCA1" "AT2G30310 AT2G30310" "AT2G30580 DRIP2"
## [487] "AT5G05410 DREB2A" "AT1G78950 AT1G78950" "AT1G79470 IMPDH"
## [490] "AT3G26460 AT3G26460" "AT5G59310 LTP4" "AT2G38920 RF178"
## [493] "AT4G25850 ORP4B" "AT5G02020 SIS" "AT1G11300 AT1G11300"
## [496] "AT4G16233 AT4G16233" "AT3G08590 AT3G08590" "AT5G52550 AT5G52550"
## [499] "AT2G41480 PER25" "AT1G55110 IDD7" "ATCG01020 RPL32"
## [502] "AT1G54100 ALDH7B4" "AT5G14570 NRT2.7" "AT1G26390 FOX2"
## [505] "AT1G05680 UGT74E2" "AT2G16060 AHB1" "AT1G64110 AT1G64110"
## [508] "AT2G30670 AT2G30670" "AT2G23120 AT2G23120" "AT3G62270 BOR2"
## [511] "AT5G06760 LEA46" "AT1G04778 AT1G04778" "AT3G17520 AT3G17520"
## [514] "AT3G50030 AT3G50030" "AT5G19855 RBCX2" "AT3G21352 AT3G21352"
## [517] "AT4G08250 SCL26" "AT3G29575 AFP3" "AT4G25670 AT4G25670"
## [520] "AT1G52827 CDT1" "AT5G43980 CRRSP56" "AT4G11910 SGR2"
## [523] "AT3G60520 AT3G60520" "AT4G31520 AT4G31520" "AT5G53970 AT5G53970"
## [526] "AT5G15960 KIN1" "AT3G27690 LHCB2.4" "AT1G62580 AT1G62580"
## [529] "AT5G36700 PGLP1A" "AT4G35480 ATL45" "AT2G31280 CPUORF7"
## [532] "AT1G62180 APR2" "AT1G58300 HO4" "AT5G57050 ABI2"
## [535] "AT2G32690 GRP23" "AT1G52400 BGLU18" "AT5G39610 NAC92"
## [538] "AT4G29050 AT4G29050" "AT5G22290 NAC089" "AT3G63380 ACA12"
## [541] "AT1G55230 AT1G55230" "AT5G13490 AAC2" "AT3G56200 AVT6C"
## [544] "AT5G06870 PGIP2" "AT2G47810 NFYB5" "AT3G30725 GDU6"
## [547] "AT1G30620 MUR4" "AT5G06900 CYP93D1" "AT5G60850 DOF5.4"
## [550] "AT1G07470 AT1G07470" "AT4G21650 SBT3.13" "AT3G62590 PLIP3"
## [553] "AT5G24770 VSP2" "AT2G16630 AT2G16630" "AT1G02770 AT1G02770"
## [556] "AT1G54740 AT1G54740" "AT2G33150 PED1" "AT1G14240 APY3"
## [559] "AT2G30500 NET4B" "AT5G18290 SIP1-2" "AT5G65710 HSL2"
## [562] "AT1G54160 NFYA5" "AT5G66480 AT5G66480" "AT1G64620 DOF1.8"
## [565] "AT1G60190 PUB19" "AT1G66600 WRKY63" "AT1G47960 C/VIF1"
## [568] "AT5G62470 MYB96" "AT2G25215 AT2G25215" "AT5G52720 AT5G52720"
## [571] "AT1G20450 ERD10" "AT3G61450 SYP73" "AT1G68750 PPC4"
## [574] "AT2G03530 UPS2" "AT5G40370 AT5G40370" "AT2G47770 TSPO"
## [577] "AT5G38410 AT5G38410" "AT4G13290 CYP71A19" "AT1G04500 AT1G04500"
## [580] "AT2G16500 ADC1" "AT3G62690 ATL5" "AT2G38240 ANS"
## [583] "AT1G35190 AT1G35190" "AT4G09600 GASA3" "AT3G05880 RCI2A"
## [586] "AT5G52420 AT5G52420" "AT4G23190 CRK11" "AT5G47920 AT5G47920"
## [589] "AT4G04620 ATG8B" "AT1G64370 AT1G64370" "AT5G49420 AT5G49420"
## [592] "AT3G02100 UGT83A1" "AT4G27460 CBSX5" "AT5G06530 ABCG22"
## [595] "AT2G44480 BGLU17" "AT2G02930 GSTF3" "AT5G24160 SQE6"
## [598] "AT1G53610 AT1G53610" "AT3G55730 MYB109" "AT3G13672 AT3G13672"
## [601] "AT2G32190 AT2G32190" "AT4G25900 AT4G25900" "AT3G21690 DTX40"
## [604] "AT4G31290 GGCT2;2" "AT5G14940 NPF5.8" "AT2G38250 GT-3B"
## [607] "AT5G65990 AVT3A" "AT1G72770 HAB1" "AT1G05000 AT1G05000"
## [610] "AT1G03790 SOM" "AT4G33740 AT4G33740" "AT2G36120 DOT1"
## [613] "AT1G64900 CYP89A2" "AT1G08920 ESL1" "AT2G42950 AT2G42950"
## [616] "AT2G30770 CYP71A13" "AT1G70810 CAR7" "AT4G29020 AT4G29020"
## [619] "AT5G59430 TRP1" "AT5G45630 AT5G45630" "AT5G09640 SCPL19"
## [622] "AT4G08570 HIPP24" "AT2G42540 COR15A" "AT2G41870 REM4.2"
## [625] "AT2G21990 AT2G21990" "AT2G20880 ERF053" "AT5G52390 AT5G52390"
## [628] "AT1G72760 AT1G72760" "AT3G28910 MYB30" "AT1G64670 BDG1"
## [631] "AT3G25870 AT3G25870" "AT1G52690 LEA7" "AT4G37490 CYCB1-1"
## [634] "AT3G13080 ABCC3" "AT1G66950 ABCG39" "AT1G17550 HAB2"
## [637] "AT4G18280 AT4G18280" "AT5G59200 PCMP-E41" "AT1G29920 LHCB1.1"
## [640] "AT5G36970 NHL25" "AT2G30550 AT2G30550" "AT4G37030 AT4G37030"
## [643] "AT2G47950 AT2G47950" "AT2G01430 ATHB-17" "AT5G54230 MYB49"
## [646] "AT1G23730 BCA3" "AT3G23325 AT3G23325" "AT3G52820 PAP22"
## [649] "AT5G53710 AT5G53710" "AT1G78915 AT1G78915" "AT2G39510 AT2G39510"
## [652] "AT5G04250 AT5G04250" "AT1G63750 AT1G63750" "AT3G62800 DBR4"
## [655] "AT2G18050 HIS1-3" "AT4G21930 AT4G21930" "AT3G26280 CYP71B4"
## [658] "AT1G67148 AT1G67148" "AT4G21620 AT4G21620" "AT5G25610 RD22"
## [661] "AT1G48405 AT1G48405" "AT5G59570 BOA" "AT1G52790 AT1G52790"
## [664] "AT2G21640 AT2G21640" "AT4G04890 PDF2" "AT2G46320 AT2G46320"
## [667] "AT5G55135 AT5G55135" "AT2G01150 RHA2B" "AT1G01600 CYP86A4"
## [670] "AT5G37840 AT5G37840" "AT2G41380 AT2G41380" "AT4G25690 AT4G25690"
## [673] "AT5G23060 CAS" "AT2G30360 CIPK11" "AT4G39190 AT4G39190"
## [676] "AT5G07440 GDH2" "AT4G34680 GATA3" "AT5G05220 AT5G05220"
## [679] "AT5G35735 AT5G35735" "AT2G33380 PXG3" "AT5G22460 AT5G22460"
## [682] "AT1G32080 PLGG1" "AT1G79900 BAC2" "AT2G25297 AT2G25297"
## [685] "AT4G22610 AT4G22610" "AT4G33560 AT4G33560" "AT1G74020 SSL12"
## [688] "AT1G11190 ENDO1" "AT1G02660 PLIP2" "AT1G68320 MYB62"
## [691] "AT1G27950 LTPG1" "AT2G33080 AtRLP28" "AT5G39130 AT5G39130"
## [694] "AT2G47260 WRKY23" "AT3G04010 AT3G04010" "AT2G39330 JAL23"
## [697] "AT2G41720 EMB2654" "AT5G53730 NHL26" "AT3G61550 ATL68"
## [700] "AT3G58680 MBF1B" "AT5G26250 STP8" "AT1G24575 AT1G24575"
## [703] "AT5G20350 PAT24" "AT2G03760 SOT12" "AT1G62290 APA2"
## [706] "AT1G78170 AT1G78170" "AT2G20920 AT2G20920" "AT1G07985 AT1G07985"
## [709] "AT1G17147 VQ1" "AT5G03500 AT5G03500" "AT1G50740 FAX5"
## [712] "AT1G73480 AT1G73480" "AT1G21890 AT1G21890" "AT2G43610 AT2G43610"
## [715] "AT4G25434 ATNUDT10" "AT5G47560 TDT" "AT1G80160 AT1G80160"
## [718] "AT2G31083 CLE5" "AT2G40400 RER5" "AT1G51090 AT1G51090"
## [721] "AT5G10770 AT5G10770" "AT5G57840 AT5G57840" "AT5G48480 AT5G48480"
## [724] "AT1G52820 AT1G52820" "AT5G47600 HSP14.7" "AT1G06150 EMB1444"
## [727] "AT1G69480 PHO1-H10" "AT1G48000 MYB112" "AT5G57390 AIL5"
## [730] "AT3G63160 AT3G63160" "AT5G48175 AT5G48175" "AT4G15760 MO1"
## [733] "AT1G27100 AT1G27100" "AT3G53040 AT3G53040" "AT5G57785 AT5G57785"
## [736] "AT2G05540 AT2G05540" "AT1G72740 AT1G72740" "AT1G21670 AT1G21670"
## [739] "AT1G69880 TRX8" "AT3G18250 AT3G18250" "AT5G47800 AT5G47800"
## [742] "AT3G50980 XERO1" "AT5G53420 AT5G53420" "AT3G06500 INVC"
## [745] "AT1G20440 COR47" "AT2G26740 ATSEH" "AT1G52040 MBP1"
## [748] "AT1G10360 GSTU18" "AT3G09400 PLL3" "AT5G49740 FRO7"
## [751] "AT1G20070 AT1G20070" "AT3G52810 PAP21" "AT2G32830 PHT1-5"
## [754] "AT1G62570 FMOGS-OX4" "AT1G70420 AT1G70420" "AT1G05160 KAO1"
## [757] "AT1G63720 AT1G63720" "AT5G22040 AT5G22040" "AT3G16210 AT3G16210"
## [760] "AT1G14870 PCR2" "AT5G07000 SOT14" "AT2G48090 AT2G48090"
## [763] "AT2G02390 ATGSTZ1" "AT5G12340 AT5G12340" "AT2G17840 ERD7"
## [766] "AT5G66130 RAD17" "AT2G36950 HIPP05" "AT2G47600 MHX"
## [769] "AT1G60950 FD2" "AT5G49700 AHL17" "AT1G78390 NCED9"
## [772] "AT1G33811 AT1G33811" "AT5G37490 PUB21" "AT1G12820 AFB3"
## [775] "AT2G47190 ATMYB2" "AT5G54170 AT5G54170" "AT1G21520 AT1G21520"
## [778] "AT1G54260 AT1G54260" "AT5G22570 WRKY38" "AT3G28920 ZHD9"
## [781] "AT2G38830 AT2G38830" "AT5G01445 AT5G01445" "AT5G40670 AT5G40670"
## [784] "AT5G49665 WAV3" "AT5G39590 AT5G39590" "AT1G30700 AT1G30700"
## [787] "AT2G23270 AT2G23270" "AT4G06746 RAP2-9" "AT1G35710 AT1G35710"
## [790] "AT2G46640 AT2G46640" "AT3G16170 AAE13" "AT1G07180 NDA1"
## [793] "AT4G18980 AtS40-3" "AT2G16990 AT2G16990" "AT4G01360 AT4G01360"
## [796] "AT3G12510 AT3G12510" "AT1G75270 DHAR2" "AT3G55290 AT3G55290"
## [799] "AT1G76680 OPR1" "AT5G40880 ZFWD3" "AT3G22420 WNK2"
## [802] "AT3G23920 BAM1" "AT2G39470 PNSL1" "AT5G51750 SBT1.3"
## [805] "AT4G11370 RHA1A" "AT3G60470 AT3G60470" "AT3G53400 AT3G53400"
## [808] "AT1G75600 AT1G75600" "AT1G64170 CHX16" "AT4G39000 AtGH9B17"
## [811] "AT4G20070 AAH" "AT5G10300 HNL" "AT4G18550 AT4G18550"
## [814] "AT2G42720 AT2G42720" "AT5G63790 ANAC102" "AT1G49900 AT1G49900"
## [817] "AT1G62620 AT1G62620" "AT2G23030 SRK2J" "AT5G48330 AT5G48330"
## [820] "AT5G51440 HSP23.5" "AT5G54250 CNGC4" "AT5G08560 WDR26"
## [823] "AT2G44750 TPK2" "AT3G05820 INVH" "AT3G18950 AT3G18950"
## [826] "AT1G28430 CYP705A24" "AT4G18170 WRKY28" "AT2G34430 LHB1B1"
## [829] "AT1G78610 MSL6" "AT1G04710 KAT1" "AT1G09530 PIF3"
## [832] "AT4G02520 GSTF2" "AT4G34000 ABF3" "AT3G51750 AT3G51750"
## [835] "AT1G71080 AT1G71080" "AT2G18360 AT2G18360" "AT5G41410 BEL1"
## [838] "AT3G15670 LEA29" "AT5G25220 KNAT3" "AT5G54940 AT5G54940"
## [841] "AT1G70880 AT1G70880" "AT3G14770 SWEET2" "AT3G02990 HSFA1E"
## [844] "AT5G65870 PSK5" "AT3G19090 AT3G19090" "AT4G23990 CSLG3"
## [847] "AT4G11360 RHA1B" "AT5G01740 AT5G01740" "AT5G11110 SPS2"
## [850] "AT5G62480 GSTU9" "AT5G28020 CYSD2" "AT5G40405 PCMP-H14"
## [853] "AT4G25380 SAP10" "AT1G72870 AT1G72870" "AT4G22270 MRB1"
## [856] "AT1G62420 AT1G62420" "AT4G22240 PAP2" "AT4G28390 AAC3"
## [859] "AT3G14420 GLO1" "AT1G08280 GALT29A" "AT5G55620 AT5G55620"
## [862] "AT3G11580 AT3G11580" "AT1G25400 AT1G25400" "AT1G79360 OCT2"
## [865] "AT4G33960 AT4G33960" "AT3G02520 GRF7" "AT3G62260 AT3G62260"
## [868] "AT5G51810 GA20OX2" "AT4G18360 GLO5" "AT4G11960 PGRL1B"
## [871] "AT4G37070 PLP1" "AT2G40955 AT2G40955" "AT3G25570 SAMDC3"
## [874] "AT4G05200 CRK25" "AT5G53590 AT5G53590" "AT1G28190 AT1G28190"
## [877] "AT4G13840 CER26" "AT2G38820 AT2G38820" "AT1G79520 AT1G79520"
## [880] "AT4G24060 DOF4.6" "AT1G47890 AtRLP7" "AT3G03341 AT3G03341"
## [883] "AT3G52340 SPP2" "AT4G26520 AT4G26520" "AT1G54270 TIF4A-2"
## [886] "AT1G29070 RPL34" "AT4G37180 HHO5" "AT1G56120 AT1G56120"
## [889] "AT2G31940 AT2G31940" "AT4G13260 YUC2" "AT4G23160 CRK8"
## [892] "AT2G41090 CML10" "AT5G37740 AT5G37740" "AT2G17220 PIX13"
## [895] "AT5G42050 AT5G42050" "AT5G15970 KIN2" "AT1G64680 AT1G64680"
## [898] "AT5G61380 APRR1" "AT2G38340 DREB2E" "AT2G23680 AT2G23680"
## [901] "AT1G27300 AT1G27300" "AT3G48740 SWEET11" "AT2G41850 ADPG2"
## [904] "AT3G18610 NUCL2" "AT4G13345 MEE55" "AT2G15970 COR413PM1"
## [907] "AT3G16410 NSP4" "AT3G53540 AT3G53540" "AT3G04030 MYR2"
## [910] "AT4G35690 AT4G35690" "AT4G24040 TRE1" "AT4G35720 AT4G35720"
## [913] "AT3G43720 LTPG2" "AT1G66970 SVL2" "AT1G36730 AT1G36730"
## [916] "AT4G10955 AT4G10955" "AT4G16670 AT4G16670" "AT1G05780 AT1G05780"
## [919] "AT5G09660 PMDH2" "AT3G11180 AT3G11180" "AT2G44130 AT2G44130"
## [922] "AT4G10430 AT4G10430" "AT4G24450 GWD2" "AT3G16400 NSP1"
## [925] "AT5G14740 BCA2" "AT1G08230 GAT1" "AT4G00955 AT4G00955"
## [928] "AT5G57560 XTH22" "AT5G04140 GLU1" "AT3G46780 PTAC16"
## [931] "AT3G11840 PUB24" "AT4G27830 BGLU10" "AT4G22960 AT4G22960"
## [934] "AT1G77670 AT1G77670" "AT3G47510 AT3G47510" "AT5G48250 COL10"
## [937] "AT1G54290 AT1G54290" "AT1G14040 PHO1;H3" "AT5G50950 FUM2"
## [940] "ATCG00020 PSBA" "AT1G20630 CAT1" "AT3G49940 LBD38"
## [943] "AT2G47520 ERF071" "AT1G55260 AT1G55260" "AT5G54390 AHL"
## [946] "AT3G48920 AtMYB45" "AT3G25620 ABCG21" "AT1G60610 AT1G60610"
## [949] "AT1G62975 BHLH125" "AT1G26730 PHO1-H7" "AT3G14620 CYP72A8"
## [952] "AT4G31270 AT4G31270" "AT5G47650 ATNUDT2" "AT5G53870 ENODL1"
## [955] "AT1G07480 AT1G07480" "AT4G24960 HVA22D" "AT3G27210 Y-2"
## [958] "AT2G44970 AT2G44970" "AT1G09415 NIMIN-3" "AT2G21330 FBA1"
## [961] "AT2G34650 PID" "AT5G12890 UGT92A1" "AT5G47660 AT5G47660"
## [964] "AT2G32100 OFP16" "AT4G34230 CAD5" "AT3G26740 CCL"
## [967] "AT5G39080 AT5G39080" "AT5G57240 ORP4C" "AT4G28750 PSAE1"
## [970] "AT3G01120 CGS1" "AT5G03180 AT5G03180" "AT3G25910 AT3G25910"
## [973] "AT4G32295 AT4G32295" "AT2G02100 PDF2.2" "AT1G05690 BT3"
## [976] "AT3G63140 CSP41A" "AT2G47240 LACS1" "AT5G24210 AT5G24210"
## [979] "AT1G01680 PUB54" "AT4G37310 CYP81H1" "AT5G17370 AT5G17370"
## [982] "AT5G27750 AT5G27750" "AT4G38470 STY46" "AT5G13360 AT5G13360"
## [985] "AT1G66880 AT1G66880" "AT1G16500 AT1G16500" "AT5G65730 XTH6"
## [988] "AT1G02450 NIMIN-1" "AT1G49450 AT1G49450" "AT4G13180 AT4G13180"
## [991] "AT1G49840 AT1G49840" "AT2G29470 GSTU3" "AT4G24340 AT4G24340"
## [994] "AT2G40020 AT2G40020" "AT1G53670 MSRB1" "AT1G47510 IP5P11"
## [997] "AT1G65500 AT1G65500" "AT3G53235 AT3G53235" "AT5G02030 BLH9"
## [1000] "AT5G49450 BZIP1" "AT5G67245 AT5G67245" "AT1G53560 AT1G53560"
## [1003] "AT4G30630 AT4G30630" "AT3G61080 AT3G61080" "AT5G52300 LTI65"
## [1006] "AT1G76100 PETE1" "AT4G25100 FSD1" "AT5G12270 AT5G12270"
## [1009] "AT1G61440 AT1G61440" "AT1G54310 AT1G54310" "AT1G75280 AT1G75280"
## [1012] "ATCG00800 RPS3" "AT4G26490 AT4G26490" "AT2G18193 AT2G18193"
## [1015] "AT3G49160 PKP4" "AT5G14700 AT5G14700" "AT2G45760 BAP2"
## [1018] "AT4G08780 PER38" "AT5G23220 NIC3" "AT5G02790 GSTL3"
## [1021] "AT1G77220 AT1G77220" "AT5G66780 AT5G66780" "AT5G50160 FRO8"
## [1024] "AT5G38030 DTX30" "AT4G16760 ACX1" "AT1G02670 AT1G02670"
## [1027] "AT5G14590 AT5G14590" "AT2G32560 AT2G32560" "AT4G34135 UGT73B2"
## [1030] "AT5G48180 NSP5" "AT1G68540 TKPR2" "AT4G14930 AT4G14930"
## [1033] "AT3G45300 IVD" "AT1G72190 AT1G72190" "AT4G29270 AT4G29270"
## [1036] "AT2G05440 ATGRP9" "AT1G61480 AT1G61480" "AT4G14746 AT4G14746"
## [1039] "AT1G12780 UGE1" "AT2G26250 FDH" "AT4G30450 AT4G30450"
## [1042] "AT4G19870 AT4G19870" "AT5G19875 AT5G19875" "AT3G50820 PSBO2"
## [1045] "AT4G15765 AT4G15765" "AT3G08770 LTP6" "AT3G11900 ANT1"
## [1048] "AT1G18710 AtMYB47" "AT1G53640 AT1G53640" "AT2G35920 AT2G35920"
## [1051] "AT3G48690 CXE12" "AT5G24150 SQE5" "AT5G18310 AT5G18310"
## [1054] "AT3G44880 PAO" "AT5G19880 PER58" "AT3G27027 AT3G27027"
## [1057] "AT1G80590 WRKY66" "AT2G46270 GBF3" "AT4G15530 PPDK"
## [1060] "AT3G03670 PER28" "AT3G04720 HEL" "AT5G14410 AT5G14410"
## [1063] "AT1G70800 CAR6" "AT5G16040 AT5G16040" "AT2G37220 CP29B"
## [1066] "AT3G13310 AT3G13310" "AT3G20810 JMJ30" "AT1G51805 AT1G51805"
## [1069] "AT4G15630 AT4G15630" "AT2G30570 PSBW" "AT5G13550 SULTR4;1"
## [1072] "AT3G02150 TCP13" "AT2G13360 AGT1" "AT3G16910 AAE7"
## [1075] "AT1G66830 AT1G66830" "AT3G06490 MYB108" "AT5G54130 AT5G54130"
## [1078] "AT2G39850 SBT4.1" "AT1G33110 DTX21" "AT1G12860 SCRM2"
## [1081] "AT1G47610 AT1G47610" "AT4G00750 AT4G00750" "AT3G52870 IQM3"
## [1084] "AT1G56650 MYB75" "AT1G08125 AT1G08125" "AT1G28660 AT1G28660"
## [1087] "AT5G64220 CAMTA2" "AT4G05180 PSBQ2" "AT1G74710 EDS16"
## [1090] "AT5G33210 SRS8" "AT2G45770 CPFTSY" "AT3G59940 SKIP20"
## [1093] "AT2G21140 PRP2" "AT3G14780 AT3G14780" "AT3G14560 AT3G14560"
## [1096] "AT2G26150 HSFA2" "AT2G24430 ANAC038" "AT5G51990 DREB1D"
## [1099] "AT4G38970 FBA2" "AT3G03890 AT3G03890" "AT3G27880 AT3G27880"
## [1102] "AT3G20820 AT3G20820" "AT3G09360 AT3G09360" "AT2G34860 PSA2"
## [1105] "AT1G52230 PSAH2" "AT1G04310 ERS2" "AT3G20475 MSH5"
## [1108] "AT5G26000 TGG1" "AT1G45249 ABF2" "AT1G61660 BHLH112"
## [1111] "AT4G16900 AT4G16900" "AT1G71200 AT1G71200" "AT2G41660 MIZ1"
## [1114] "AT3G01470 HAT5" "AT2G05070 LHCB2.2" "AT4G22260 AOX4"
## [1117] "AT2G34600 TIFY" "AT5G06090 GPAT7" "AT2G18890 AT2G18890"
## [1120] "ATCG00780 RPL14" "AT5G23680 AT5G23680" "AT5G47060 AT5G47060"
## [1123] "AT3G52610 AT3G52610" "AT2G20570 GPRI1" "AT3G45160 AT3G45160"
## [1126] "AT2G27389 AT2G27389" "AT5G25630 AT5G25630" "AT1G12900 GAPA-2"
## [1129] "AT3G26180 CYP71B20" "AT5G62520 SRO5" "AT2G26550 HO2"
## [1132] "AT5G66670 AT5G66670" "AT3G62130 LCD" "AT5G28030 DES1"
## [1135] "AT1G08380 PSAO" "AT3G17611 RBL14" "AT5G58640 AT5G58640"
## [1138] "AT1G63370 AT1G63370" "AT4G16990 RLM3" "AT2G18500 OFP7"
## [1141] "AT3G03170 AT3G03170" "AT3G12230 SCPL14" "AT2G02061 AT2G02061"
## [1144] "AT1G18485 PCMP-H8" "AT5G01550 LECRKA4.2" "AT5G27920 AT5G27920"
## [1147] "AT5G64430 AT5G64430" "ATCG00790 RPL16" "AT2G40900 AT2G40900"
## [1150] "AT3G55800 SBPASE" "AT2G21150 XCT" "AT2G07180 PBL17"
## [1153] "AT4G28140 ERF054" "AT2G21180 AT2G21180" "AT1G42970 GAPB"
## [1156] "AT5G54300 AT5G54300" "AT1G66980 SNC4" "AT2G14610 PR1"
## [1159] "AT1G02750 DI19-2" "AT3G62100 IAA30" "AT3G47960 NPF2.10"
## [1162] "AT2G36080 ARF31" "AT5G59030 COPT1" "AT3G63190 RRF"
## [1165] "AT1G19200 FLZ12" "ATCG00830 rpl2-A" "ATCG01310 rpl2-A"
## [1168] "AT5G17860 CCX1" "AT1G04800 AT1G04800" "AT1G28470 NAC010"
## [1171] "AT3G59200 AT3G59200" "AT5G18270 ANAC087" "AT4G10960 UGE5"
## [1174] "AT1G20693 HMGB2" "AT1G54040 ESP" "ATCG00760 RPL36"
## [1177] "AT5G44400 AT5G44400" "AT3G08760 ATSIK" "AT1G63360 AT1G63360"
## [1180] "AT1G09910 AT1G09910" "AT2G38230 PDX11" "AT3G51730 AT3G51730"
## [1183] "AT4G12940 AT4G12940" "AT1G65660 SMP1" "ATCG00470 ATPE"
## [1186] "AT5G47000 PER65" "AT2G28400 AT2G28400" "AT5G12900 IRKI"
## [1189] "AT3G26220 CYP71B3" "AT5G39330 AT5G39330" "AT3G58550 AT3G58550"
## [1192] "AT3G46530 RPP13" "AT3G10040 AT3G10040" "AT5G10760 AED1"
## [1195] "AT2G48120 PAC" "AT1G68010 HPR" "AT2G25460 AT2G25460"
## [1198] "AT2G18720 AT2G18720" "AT5G67370 CGLD27" "AT1G32060 PRK"
## [1201] "AT3G48310 CYP71A22" "AT4G29930 BHLH27" "AT1G15640 AT1G15640"
## [1204] "AT1G30380 PSAK" "AT2G32230 PRORP1" "AT1G06645 AT1G06645"
## [1207] "AT2G04570 AT2G04570" "AT1G52220 CURT1C" "AT1G67090 RBCS-1A"
## [1210] "AT2G48100 AT2G48100" "AT5G48940 RCH1" "AT1G30610 EMB2279"
## [1213] "AT2G35820 AT2G35820" "AT5G54270 LHCB3" "AT5G15780 AT5G15780"
## [1216] "AT4G19730 AT4G19730" "AT1G64710 AT1G64710" "AT5G13210 AT5G13210"
## [1219] "AT2G26500 AT2G26500" "AT5G43450 AT5G43450" "AT4G12330 CYP706A7"
## [1222] "AT1G52720 AT1G52720" "AT4G00270 GEBP" "AT1G14700 PAP3"
## [1225] "AT3G58430 AT3G58430" "AT2G38170 CAX1" "AT5G26920 CBP60G"
## [1228] "AT3G26170 CYP71B19" "AT5G43750 PNSB5" "AT3G14490 TPS17"
## [1231] "AT4G35180 LHT7" "AT5G47550 CYS5" "AT1G52342 AT1G52342"
## [1234] "AT4G31370 FLA5" "AT4G20320 AT4G20320" "AT3G21780 UGT71B6"
## [1237] "AT4G13280 TPS12" "AT1G21790 AT1G21790" "AT2G46310 CRF5"DEG summary
Here is a heatmap of all the differentially expressed genes.
degs <- unique(c(del3_up, del3_dn,
del5_up, del5_dn,
der3_up, der3_dn,
der5_up, der5_dn))
xxx <- xx/colSums(xx)*1e6
deg_mx <- as.matrix(xxx[which(rownames(xxx) %in% degs),])
colfunc <- colorRampPalette(c("blue", "white", "red"))
heatmap.2(deg_mx,col=colfunc(25),cexCol=0.8,trace="none",scale="row",margin=c(10,10),main="all samples")
degs_leaf <- unique(c(del3_up, del3_dn, del5_up, del5_dn))
leafx <- leaf/colSums(leaf)*1e6
deg_mx <- as.matrix(leaf[which(rownames(leaf) %in% degs_leaf),])
colfunc <- colorRampPalette(c("blue", "white", "red"))
heatmap.2(deg_mx,col=colfunc(25),cexCol=0.8,trace="none",scale="row",margin=c(10,10),main="leaf samples")
degs_root <- unique(c(der3_up, der3_dn, der5_up, der5_dn))
rootx <- root/colSums(root)*1e6
deg_mx <- as.matrix(root[which(rownames(root) %in% degs_root),])
colfunc <- colorRampPalette(c("blue", "white", "red"))
heatmap.2(deg_mx,col=colfunc(25),cexCol=0.8,trace="none",scale="row",margin=c(10,10),main="root samples")
Pathway analysis
Mapman pathways last modified in 2012 and used in the previous RNA-seq analysis. First I’ll strt with unidimensional analysis.
# strip off gene symbols
rownames(del3) <- sapply(strsplit(rownames(del3)," "),"[[",1)
rownames(del5) <- sapply(strsplit(rownames(del5)," "),"[[",1)
rownames(der3) <- sapply(strsplit(rownames(der3)," "),"[[",1)
rownames(der5) <- sapply(strsplit(rownames(der5)," "),"[[",1)
genesets <- gmt_import("../../ref/Ath_AGI_LOCUS_TAIR10_Aug2012.txt.gmt")
gt <- read.table("../../ref/Arabidopsis_thaliana.TAIR10.46.geneaccession2symbol.tsv",
fill=TRUE)
gt$V1 <- sapply(strsplit(gt$V1,"\\."),"[[",1)
gt <- unique(gt)
m <- mitch_import(x=as.data.frame(del3), DEtype="deseq2")## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 20884## Note: no. genes in output = 20884## Note: estimated proportion of input genes in output = 1del3m <- mitch_calc(x=m,genesets=genesets,priority="effect",minsetsize=5)## Note: Enrichments with large effect sizes may not be
## statistically significant.mitch_barplot(del3m)
mitch_bubbleplot(del3m,30)
unlink("del3m_mitch.html")
capture.output(
mitch_report(del3m, outfile="del3m_mitch.html"),
file = "/dev/null", append = FALSE,
type = c("output", "message"), split = FALSE)## Dataset saved as " /tmp/RtmpshgKK6/del3m_mitch.rds ".##
##
## processing file: mitch.Rmd## Contour plot does not apply to unidimensional analysis.## output file: /mnt/bfx10/projects/tohidul_bfx10/296_DU_MTI/dge/mitch.knit.md##
## Output created: /tmp/RtmpshgKK6/mitch_report.html
m <- mitch_import(x=as.data.frame(del5),DEtype="deseq2")## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 20839## Note: no. genes in output = 20839## Note: estimated proportion of input genes in output = 1del5m <- mitch_calc(x=m,genesets=genesets,priority="effect",minsetsize=5)## Note: Enrichments with large effect sizes may not be
## statistically significant.mitch_barplot(del5m)
mitch_bubbleplot(del5m,30)
unlink("del5m_mitch.html")
capture.output(
mitch_report(del5m, outfile="del5m_mitch.html"),
file = "/dev/null", append = FALSE,
type = c("output", "message"), split = FALSE)## Dataset saved as " /tmp/RtmpshgKK6/del5m_mitch.rds ".##
##
## processing file: mitch.Rmd## Contour plot does not apply to unidimensional analysis.## output file: /mnt/bfx10/projects/tohidul_bfx10/296_DU_MTI/dge/mitch.knit.md##
## Output created: /tmp/RtmpshgKK6/mitch_report.html
m <- mitch_import(x=as.data.frame(der3),DEtype="deseq2")## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21102## Note: no. genes in output = 21102## Note: estimated proportion of input genes in output = 1der3m <- mitch_calc(x=m,genesets=genesets,priority="effect",minsetsize=5)## Note: Enrichments with large effect sizes may not be
## statistically significant.mitch_barplot(der3m)
mitch_bubbleplot(der3m,30)
unlink("der3m_mitch.html")
capture.output(
mitch_report(der3m, outfile="der3m_mitch.html"),
file = "/dev/null", append = FALSE,
type = c("output", "message"), split = FALSE)## Dataset saved as " /tmp/RtmpshgKK6/der3m_mitch.rds ".##
##
## processing file: mitch.Rmd## Contour plot does not apply to unidimensional analysis.## output file: /mnt/bfx10/projects/tohidul_bfx10/296_DU_MTI/dge/mitch.knit.md##
## Output created: /tmp/RtmpshgKK6/mitch_report.html
m <- mitch_import(x=as.data.frame(der5),DEtype="deseq2")## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 20891## Note: no. genes in output = 20891## Note: estimated proportion of input genes in output = 1der5m <- mitch_calc(x=m,genesets=genesets,priority="effect",minsetsize=5)## Note: Enrichments with large effect sizes may not be
## statistically significant.mitch_barplot(der5m)
mitch_bubbleplot(der5m,30)
unlink("der5m_mitch.html")
capture.output(
mitch_report(der5m, outfile="der5m_mitch.html"),
file = "/dev/null", append = FALSE,
type = c("output", "message"), split = FALSE)## Dataset saved as " /tmp/RtmpshgKK6/der5m_mitch.rds ".##
##
## processing file: mitch.Rmd## Contour plot does not apply to unidimensional analysis.## output file: /mnt/bfx10/projects/tohidul_bfx10/296_DU_MTI/dge/mitch.knit.md##
## Output created: /tmp/RtmpshgKK6/mitch_report.html
Next, multidimensional analysis with all data.
l <- list("del3"=del3,"del5"=del5,
"der3"=der3, "der5"=der5)
m <- mitch_import(x=l,DEtype="deseq2")## Note: Mean no. genes in input = 20929## Note: no. genes in output = 19618## Note: estimated proportion of input genes in output = 0.937# effect size
res <- mitch_calc(x=m,genesets=genesets,priority="effect",minsetsize=5)## Note: Enrichments with large effect sizes may not be
## statistically significant.top <- subset(res$enrichment_result,p.adjustMANOVA<0.05)
kbl(head(top,30)) %>% kable_paper("hover", full_width = F)| set | setSize | pMANOVA | s.del3 | s.del5 | s.der3 | s.der5 | p.del3 | p.del5 | p.der3 | p.der5 | s.dist | SD | p.adjustMANOVA | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 179 | transport.sulphate | 12 | 0.0000016 | -0.5699446 | -0.6027832 | -0.7421198 | -0.7539444 | 0.0006287 | 0.0002992 | 0.0000085 | 0.0000061 | 1.3443802 | 0.0944205 | 0.0000233 |
| 127 | protein.synthesis.ribosomal.protein.eukaryotic.60S.subunit.L41 | 5 | 0.0013862 | -0.9075919 | 0.0654362 | -0.4924591 | -0.5576811 | 0.0004398 | 0.7999707 | 0.0565193 | 0.0308032 | 1.1753847 | 0.4026302 | 0.0067283 |
| 23 | cell.wall.cellulose.synthesis | 12 | 0.0000742 | 0.4328097 | 0.4731035 | 0.6177956 | 0.7122224 | 0.0094283 | 0.0045417 | 0.0002105 | 0.0000193 | 1.1402120 | 0.1294041 | 0.0005468 |
| 9 | PS.calvin.cycle.rubisco.interacting | 6 | 0.0001275 | 0.4412095 | 0.8110171 | -0.4590217 | 0.2655177 | 0.0612659 | 0.0005804 | 0.0515184 | 0.2600511 | 1.0647136 | 0.5333516 | 0.0008456 |
| 103 | RNA.regulation.of.transcription.ARF..Auxin.Response.Factor.family | 14 | 0.0000215 | 0.5373393 | 0.1115662 | 0.4920935 | 0.7181260 | 0.0004987 | 0.4698445 | 0.0014316 | 0.0000033 | 1.0290974 | 0.2549216 | 0.0001946 |
| 4 | PS.lightreaction.photosystem.I.PSI.polypeptide.subunits | 16 | 0.0000000 | 0.0573730 | 0.6457568 | -0.7972082 | 0.0224276 | 0.6911426 | 0.0000077 | 0.0000000 | 0.8765774 | 1.0277828 | 0.5930301 | 0.0000000 |
| 1 | PS.lightreaction.photosystem.II.LHC.II | 15 | 0.0000000 | 0.0429424 | 0.5517693 | -0.8042272 | 0.1629444 | 0.7733940 | 0.0002153 | 0.0000001 | 0.2745723 | 0.9897605 | 0.5712803 | 0.0000000 |
| 22 | cell.wall.precursor.synthesis.GAE | 6 | 0.0047255 | 0.4492828 | 0.4757121 | 0.7202733 | 0.0658950 | 0.0566735 | 0.0435972 | 0.0022464 | 0.7798545 | 0.9753424 | 0.2703534 | 0.0199688 |
| 84 | Biodegradation.of.Xenobiotics.lactoylglutathione.lyase | 10 | 0.0000116 | 0.0060588 | 0.3886475 | -0.5866381 | -0.6439310 | 0.9735354 | 0.0333243 | 0.0013156 | 0.0004213 | 0.9538737 | 0.4950449 | 0.0001210 |
| 174 | transport.p..and.v.ATPases.H..transporting.two.sector.ATPase | 8 | 0.0000001 | -0.0246303 | 0.4074579 | 0.5572540 | -0.6316548 | 0.9039833 | 0.0459671 | 0.0063430 | 0.0019747 | 0.9360280 | 0.5330311 | 0.0000018 |
| 2 | PS.lightreaction.photosystem.II.PSII.polypeptide.subunits | 32 | 0.0000000 | -0.0021731 | 0.6191731 | -0.6297355 | -0.2938834 | 0.9830276 | 0.0000000 | 0.0000000 | 0.0040119 | 0.9307601 | 0.5300348 | 0.0000000 |
| 6 | PS.lightreaction.NADH.DH | 9 | 0.0000249 | -0.1621534 | 0.5220562 | -0.6333656 | -0.4022699 | 0.3996007 | 0.0066850 | 0.0009999 | 0.0366394 | 0.9283370 | 0.4992180 | 0.0002155 |
| 36 | cell.wall.pectin.esterases.acetyl.esterase | 11 | 0.0086775 | 0.4293318 | 0.4848871 | 0.4012992 | 0.5015973 | 0.0136759 | 0.0053564 | 0.0211861 | 0.0039670 | 0.9121854 | 0.0469223 | 0.0325920 |
| 28 | cell.wall.cell.wall.proteins.AGPs.AGP | 37 | 0.0000000 | 0.4821235 | 0.3729719 | 0.4986397 | 0.4109265 | 0.0000004 | 0.0000863 | 0.0000002 | 0.0000152 | 0.8882867 | 0.0592892 | 0.0000002 |
| 135 | protein.synthesis.ribosome.biogenesis.Pre.rRNA.processing.and.modifications.WD.repeat.proteins | 6 | 0.0000354 | -0.3769291 | 0.2448671 | -0.2001496 | 0.6684343 | 0.1098472 | 0.2989572 | 0.3958888 | 0.0045739 | 0.8299998 | 0.4692683 | 0.0002819 |
| 7 | PS.lightreaction.cyclic.electron.flow.chlororespiration | 9 | 0.0033734 | 0.0442824 | -0.0055473 | -0.6303625 | -0.5107009 | 0.8180679 | 0.9770110 | 0.0010568 | 0.0079747 | 0.8125047 | 0.3446651 | 0.0149179 |
| 3 | PS.lightreaction.photosystem.I.LHC.I | 6 | 0.0017566 | 0.0322252 | 0.6136889 | -0.4954620 | 0.1516588 | 0.8912757 | 0.0092325 | 0.0355769 | 0.5200308 | 0.8038255 | 0.4558208 | 0.0083227 |
| 75 | redox.peroxiredoxin | 5 | 0.0144705 | -0.3981339 | 0.4872992 | -0.2263091 | -0.4354969 | 0.1231422 | 0.0591567 | 0.3808494 | 0.0917167 | 0.7980254 | 0.4300640 | 0.0461742 |
| 150 | protein.assembly.and.cofactor.ligation | 21 | 0.0000000 | -0.3162948 | 0.3491521 | -0.4174570 | -0.4596938 | 0.0121002 | 0.0056070 | 0.0009265 | 0.0002652 | 0.7794474 | 0.3782990 | 0.0000010 |
| 170 | development.late.embryogenesis.abundant | 15 | 0.0107437 | -0.3304426 | -0.3434610 | -0.3771430 | -0.4637487 | 0.0267034 | 0.0212713 | 0.0114378 | 0.0018714 | 0.7644982 | 0.0600174 | 0.0381787 |
| 137 | protein.synthesis.ribosome.biogenesis.Pre.rRNA.processing.and.modifications.misc | 9 | 0.0027872 | -0.4713879 | -0.3674220 | -0.3968869 | 0.1244723 | 0.0143304 | 0.0562996 | 0.0392275 | 0.5178967 | 0.7281607 | 0.2717309 | 0.0126057 |
| 138 | protein.synthesis.ribosome.biogenesis.BRIX | 6 | 0.0013612 | -0.3775920 | -0.1895268 | -0.2140356 | 0.5439527 | 0.1092237 | 0.4214394 | 0.3639368 | 0.0210296 | 0.7212433 | 0.4107415 | 0.0067283 |
| 136 | protein.synthesis.ribosome.biogenesis.Pre.rRNA.processing.and.modifications.DExD.box.helicases | 14 | 0.0000051 | 0.3014837 | -0.0629973 | -0.1409261 | 0.6349870 | 0.0508065 | 0.6832013 | 0.3612790 | 0.0000388 | 0.7196734 | 0.3576653 | 0.0000676 |
| 181 | transport.metabolite.transporters.at.the.envelope.membrane | 21 | 0.0005374 | 0.1696688 | 0.3803036 | 0.4534732 | 0.3714441 | 0.1783254 | 0.0025520 | 0.0003210 | 0.0032107 | 0.7190459 | 0.1217190 | 0.0028901 |
| 25 | cell.wall.cellulose.synthesis.COBRA | 7 | 0.0165814 | 0.4085826 | 0.2004487 | 0.5383495 | -0.0465409 | 0.0612078 | 0.3584310 | 0.0136395 | 0.8311508 | 0.7064741 | 0.2556974 | 0.0499953 |
| 141 | protein.postranslational.modification.kinase | 17 | 0.0010058 | 0.4729621 | -0.0364777 | 0.2452006 | 0.4128871 | 0.0007343 | 0.7945754 | 0.0800700 | 0.0032039 | 0.6749984 | 0.2281088 | 0.0052671 |
| 132 | protein.synthesis.ribosome.biogenesis.export.from.nucleus | 7 | 0.0122970 | -0.4019683 | -0.3282779 | -0.2500565 | 0.2887374 | 0.0655214 | 0.1325718 | 0.2519423 | 0.1858786 | 0.6443930 | 0.3139409 | 0.0415697 |
| 55 | hormone.metabolism.ethylene.signal.transduction | 13 | 0.0000070 | 0.0187903 | -0.3166735 | 0.3355620 | -0.4444745 | 0.9066229 | 0.0480481 | 0.0361823 | 0.0055216 | 0.6409326 | 0.3509150 | 0.0000817 |
| 24 | cell.wall.cellulose.synthesis.cellulose.synthase | 21 | 0.0060513 | 0.3432620 | 0.3790886 | 0.3232589 | 0.1858861 | 0.0064656 | 0.0026343 | 0.0103335 | 0.1403249 | 0.6329194 | 0.0845411 | 0.0245756 |
| 53 | secondary.metabolism.simple.phenols | 16 | 0.0074963 | 0.0553069 | 0.1098549 | 0.5048146 | 0.3412024 | 0.7017219 | 0.4468103 | 0.0004717 | 0.0181290 | 0.6215978 | 0.2087767 | 0.0292504 |
rownames(top) <- top[,1]
top <- top[1:50,4:7]
colfunc <- colorRampPalette(c("blue", "white", "red"))
colnames(top) <- gsub("s\\.","",colnames(top))
heatmap.2( as.matrix(top), col=colfunc(25),
scale="none",Colv=FALSE,trace="none", dendrogram="row",
margins = c(5,25), cexCol=0.8 , cexRow=0.7, main="Top genes sets by effect size (FDR<0.05)")
unlink("mapman_report_eff.html")
capture.output(
mitch_report(res,outfile=paste("mapman_report_eff.html"))
, file = "/dev/null", append = FALSE,
type = c("output", "message"), split = FALSE)## Dataset saved as " /tmp/RtmpshgKK6/mapman_report_eff.rds ".##
##
## processing file: mitch.Rmd##
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output file: /mnt/bfx10/projects/tohidul_bfx10/296_DU_MTI/dge/mitch.knit.md
##
##
## Output created: /tmp/RtmpshgKK6/mitch_report.html
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## 2Mitch analysis leaf
Next, multidimensional analysis with all leaf samples
l <- list("del3"=del3,"del5"=del5)
m <- mitch_import(x=l,DEtype="deseq2")## Note: Mean no. genes in input = 20861.5## Note: no. genes in output = 20681## Note: estimated proportion of input genes in output = 0.991# effect size
res <- mitch_calc(x=m,genesets=genesets,priority="effect",minsetsize=5)## Note: Enrichments with large effect sizes may not be
## statistically significant.top <- subset(res$enrichment_result,p.adjustMANOVA<0.05)
top <- head(top,50)
kbl(head(top,30)) %>% kable_paper("hover", full_width = F)| set | setSize | pMANOVA | s.del3 | s.del5 | p.del3 | p.del5 | s.dist | SD | p.adjustMANOVA | |
|---|---|---|---|---|---|---|---|---|---|---|
| 10 | PS.calvin.cycle.rubisco.interacting | 6 | 0.0025879 | 0.4371141 | 0.8078194 | 0.0637086 | 0.0006101 | 0.9184993 | 0.2621283 | 0.0238793 |
| 129 | protein.synthesis.ribosomal.protein.eukaryotic.60S.subunit.L41 | 5 | 0.0003166 | -0.9090153 | 0.0554846 | 0.0004308 | 0.8298826 | 0.9107070 | 0.6820044 | 0.0045904 |
| 183 | transport.sulphate | 12 | 0.0001605 | -0.5724999 | -0.6058993 | 0.0005941 | 0.0002783 | 0.8335887 | 0.0236170 | 0.0027157 |
| 24 | cell.wall.cellulose.synthesis | 14 | 0.0011618 | 0.3945213 | 0.5384084 | 0.0105892 | 0.0004859 | 0.6674808 | 0.1017435 | 0.0131021 |
| 77 | redox.peroxiredoxin | 5 | 0.0057215 | -0.4017218 | 0.4806152 | 0.1197972 | 0.0627223 | 0.6263955 | 0.6239065 | 0.0475178 |
| 4 | PS.lightreaction.photosystem.I.PSI.polypeptide.subunits | 18 | 0.0000097 | 0.0073454 | 0.5926266 | 0.9569745 | 0.0000134 | 0.5926722 | 0.4138563 | 0.0002468 |
| 29 | cell.wall.cell.wall.proteins.AGPs.AGP | 38 | 0.0000013 | 0.4506816 | 0.3641964 | 0.0000015 | 0.0001021 | 0.5794419 | 0.0611543 | 0.0000435 |
| 2 | PS.lightreaction.photosystem.II.PSII.polypeptide.subunits | 45 | 0.0000000 | 0.0367642 | 0.5648123 | 0.6696183 | 0.0000000 | 0.5660075 | 0.3733864 | 0.0000000 |
| 1 | PS.lightreaction.photosystem.II.LHC.II | 15 | 0.0004190 | 0.0390464 | 0.5458628 | 0.7934597 | 0.0002514 | 0.5472575 | 0.3583733 | 0.0056700 |
| 105 | RNA.regulation.of.transcription.ARF..Auxin.Response.Factor.family | 14 | 0.0016545 | 0.5340536 | 0.1039960 | 0.0005398 | 0.5004982 | 0.5440849 | 0.3040966 | 0.0167930 |
| 143 | protein.postranslational.modification.kinase | 17 | 0.0005465 | 0.4695862 | -0.0423584 | 0.0008012 | 0.7623798 | 0.4714928 | 0.3619995 | 0.0068620 |
| 7 | PS.lightreaction.NADH.DH | 12 | 0.0023372 | -0.1388392 | 0.4478123 | 0.4049858 | 0.0072277 | 0.4688413 | 0.4148253 | 0.0225929 |
| 152 | protein.assembly.and.cofactor.ligation | 24 | 0.0000026 | -0.3074987 | 0.3294928 | 0.0091138 | 0.0052010 | 0.4506894 | 0.4504210 | 0.0000742 |
| 150 | protein.folding | 64 | 0.0000000 | -0.0573677 | 0.3763323 | 0.4274066 | 0.0000002 | 0.3806798 | 0.3066722 | 0.0000003 |
| 97 | RNA.processing.splicing | 53 | 0.0000248 | -0.0655914 | -0.3526147 | 0.4088199 | 0.0000089 | 0.3586633 | 0.2029561 | 0.0005043 |
| 141 | protein.synthesis.initiation | 79 | 0.0001494 | -0.2403269 | -0.2210342 | 0.0002215 | 0.0006824 | 0.3265167 | 0.0136420 | 0.0027157 |
| 169 | cell.vesicle.transport | 154 | 0.0000000 | 0.2479844 | -0.1165978 | 0.0000001 | 0.0125297 | 0.2740280 | 0.2577986 | 0.0000000 |
| 156 | signalling.MAP.kinases | 44 | 0.0005747 | 0.1680036 | -0.1901615 | 0.0538389 | 0.0290757 | 0.2537452 | 0.2532610 | 0.0068620 |
| 48 | secondary.metabolism.phenylpropanoids | 36 | 0.0030261 | -0.1633890 | 0.1856570 | 0.0897975 | 0.0538932 | 0.2473146 | 0.2468128 | 0.0267086 |
| 146 | protein.degradation.ubiquitin.E3.SCF.FBOX | 263 | 0.0000001 | -0.1615510 | -0.1841978 | 0.0000065 | 0.0000003 | 0.2450052 | 0.0160137 | 0.0000037 |
| 164 | cell.organisation | 345 | 0.0000003 | 0.1682442 | 0.1001254 | 0.0000001 | 0.0014012 | 0.1957836 | 0.0481673 | 0.0000140 |
| 100 | RNA.transcription | 83 | 0.0013672 | 0.0453161 | -0.1842020 | 0.4754737 | 0.0037205 | 0.1896943 | 0.1622938 | 0.0146079 |
| 142 | protein.postranslational.modification | 212 | 0.0000124 | 0.0818186 | -0.1185954 | 0.0400954 | 0.0029239 | 0.1440803 | 0.1417141 | 0.0002794 |
| 202 | not.assigned.no.ontology | 537 | 0.0002458 | 0.0283173 | -0.0769269 | 0.2619999 | 0.0023080 | 0.0819733 | 0.0744190 | 0.0038382 |
| 203 | not.assigned.unknown | 639 | 0.0058519 | -0.0638030 | 0.0068619 | 0.0059575 | 0.7674270 | 0.0641710 | 0.0499676 | 0.0475178 |
rownames(top) <- top[,1]
top <- top[,4:5]
colfunc <- colorRampPalette(c("blue", "white", "red"))
colnames(top) <- gsub("s\\.","",colnames(top))
heatmap.2( as.matrix(top), col=colfunc(25),
scale="none",Colv=FALSE,trace="none", dendrogram="row",
margins = c(5,25), cexCol=0.8 , cexRow=0.7, main="Top genes sets in leaf by effect size (FDR<0.05)")
unlink("mapman_report_eff_leaf.html")
capture.output(
mitch_report(res,outfile=paste("mapman_report_eff_leaf.html"))
, file = "/dev/null", append = FALSE,
type = c("output", "message"), split = FALSE)## Dataset saved as " /tmp/RtmpshgKK6/mapman_report_eff_leaf.rds ".##
##
## processing file: mitch.Rmd## output file: /mnt/bfx10/projects/tohidul_bfx10/296_DU_MTI/dge/mitch.knit.md##
## Output created: /tmp/RtmpshgKK6/mitch_report.html
mitch_plots(res, outfile = "mapman_eff_plots_leaf.pdf")## png
## 2Special scatterplot leaf
plot(res$enrichment_result$s.del3, res$enrichment_result$s.del5 ,
pch=19,col="gray",bty="none", cex=1.3,
xlab="ES: 3h", ylab="root 5hr ES",
main="pathway regulation in leaf")
abline(h=0,lty=2)
abline(v=0,lty=2)
sig <- subset(res$enrichment_result,p.adjustMANOVA<0.05)
points(sig$s.del3, sig$s.del5 , pch=19,col="red",cex=1.4)
tmpdf <- sig[grep("cell.wall",sig$set,ignore.case=TRUE),]
points(tmpdf$s.del3, tmpdf$s.del5 , pch=19,col="green",cex=2.5)
range <- 1:nrow(tmpdf)
text(tmpdf$s.del3, tmpdf$s.del5 , labels=range, cex=1.2)
tmp <- tmpdf
tmpdf <- sig[grep("sig",sig$set,ignore.case=TRUE),]
points(tmpdf$s.del3, tmpdf$s.del5 , pch=19,col="orange",cex=2.5)
range <- (range[length(range)]+1):(range[length(range)]+nrow(tmpdf))
text(tmpdf$s.del3, tmpdf$s.del5 , labels=range, cex=1.2)
tmp <- rbind(tmp,tmpdf)
tmpdf <- sig[grep("^PS.",sig$set,ignore.case=TRUE),]
points(tmpdf$s.del3, tmpdf$s.del5 , pch=19,col="deepskyblue",cex=2.5)
range <- (range[length(range)]+1):(range[length(range)]+nrow(tmpdf))
text(tmpdf$s.del3, tmpdf$s.del5 , labels=range, cex=1.2)
tmp <- rbind(tmp,tmpdf)
rownames(tmp) <- 1:nrow(tmp)
tmp %>%
kbl(row.names=TRUE) %>%
kable_paper("hover", full_width = F)| set | setSize | pMANOVA | s.del3 | s.del5 | p.del3 | p.del5 | s.dist | SD | p.adjustMANOVA | |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | cell.wall.cellulose.synthesis | 14 | 0.0011618 | 0.3945213 | 0.5384084 | 0.0105892 | 0.0004859 | 0.6674808 | 0.1017435 | 0.0131021 |
| 2 | cell.wall.cell.wall.proteins.AGPs.AGP | 38 | 0.0000013 | 0.4506816 | 0.3641964 | 0.0000015 | 0.0001021 | 0.5794419 | 0.0611543 | 0.0000435 |
| 3 | signalling.MAP.kinases | 44 | 0.0005747 | 0.1680036 | -0.1901615 | 0.0538389 | 0.0290757 | 0.2537452 | 0.2532610 | 0.0068620 |
| 4 | not.assigned.no.ontology | 537 | 0.0002458 | 0.0283173 | -0.0769269 | 0.2619999 | 0.0023080 | 0.0819733 | 0.0744190 | 0.0038382 |
| 5 | not.assigned.unknown | 639 | 0.0058519 | -0.0638030 | 0.0068619 | 0.0059575 | 0.7674270 | 0.0641710 | 0.0499676 | 0.0475178 |
| 6 | PS.calvin.cycle.rubisco.interacting | 6 | 0.0025879 | 0.4371141 | 0.8078194 | 0.0637086 | 0.0006101 | 0.9184993 | 0.2621283 | 0.0238793 |
| 7 | PS.lightreaction.photosystem.I.PSI.polypeptide.subunits | 18 | 0.0000097 | 0.0073454 | 0.5926266 | 0.9569745 | 0.0000134 | 0.5926722 | 0.4138563 | 0.0002468 |
| 8 | PS.lightreaction.photosystem.II.PSII.polypeptide.subunits | 45 | 0.0000000 | 0.0367642 | 0.5648123 | 0.6696183 | 0.0000000 | 0.5660075 | 0.3733864 | 0.0000000 |
| 9 | PS.lightreaction.photosystem.II.LHC.II | 15 | 0.0004190 | 0.0390464 | 0.5458628 | 0.7934597 | 0.0002514 | 0.5472575 | 0.3583733 | 0.0056700 |
| 10 | PS.lightreaction.NADH.DH | 12 | 0.0023372 | -0.1388392 | 0.4478123 | 0.4049858 | 0.0072277 | 0.4688413 | 0.4148253 | 0.0225929 |
Mitch analysis root
Next, multidimensional analysis with all root samples
l <- list("der3"=der3,"der5"=der5)
m <- mitch_import(x=l,DEtype="deseq2")## Note: Mean no. genes in input = 20996.5## Note: no. genes in output = 20771## Note: estimated proportion of input genes in output = 0.989# effect size
res <- mitch_calc(x=m,genesets=genesets,priority="effect",minsetsize=5)## Note: Enrichments with large effect sizes may not be
## statistically significant.top <- subset(res$enrichment_result,p.adjustMANOVA<0.05)
top <- head(top,50)
kbl(head(top,30)) %>% kable_paper("hover", full_width = F)| set | setSize | pMANOVA | s.der3 | s.der5 | p.der3 | p.der5 | s.dist | SD | p.adjustMANOVA | |
|---|---|---|---|---|---|---|---|---|---|---|
| 181 | transport.sulphate | 12 | 0.0000011 | -0.7468247 | -0.7565152 | 0.0000074 | 0.0000057 | 1.0630439 | 0.0068523 | 0.0000203 |
| 23 | cell.wall.cellulose.synthesis | 12 | 0.0000256 | 0.6027185 | 0.7060311 | 0.0002996 | 0.0000228 | 0.9283047 | 0.0730531 | 0.0003669 |
| 49 | secondary.metabolism.phenylpropanoids.lignin.biosynthesis.CCR1 | 5 | 0.0124980 | -0.5550612 | -0.7284985 | 0.0315968 | 0.0047841 | 0.9158619 | 0.1226387 | 0.0456747 |
| 103 | RNA.regulation.of.transcription.ARF..Auxin.Response.Factor.family | 15 | 0.0000028 | 0.5115565 | 0.7326909 | 0.0006021 | 0.0000009 | 0.8936029 | 0.1563657 | 0.0000462 |
| 180 | transport.ammonium | 7 | 0.0038501 | 0.6243086 | 0.6292071 | 0.0042288 | 0.0039388 | 0.8863762 | 0.0034638 | 0.0198427 |
| 84 | Biodegradation.of.Xenobiotics.lactoylglutathione.lyase | 10 | 0.0003914 | -0.5942777 | -0.6482828 | 0.0011362 | 0.0003848 | 0.8794525 | 0.0381874 | 0.0032206 |
| 176 | transport.p..and.v.ATPases.H..transporting.two.sector.ATPase | 8 | 0.0000001 | 0.5371815 | -0.6375042 | 0.0085085 | 0.0017920 | 0.8336520 | 0.8306283 | 0.0000030 |
| 1 | PS.lightreaction.photosystem.II.LHC.II | 15 | 0.0000000 | -0.8070020 | 0.1551359 | 0.0000001 | 0.2982200 | 0.8217782 | 0.6803342 | 0.0000000 |
| 7 | PS.lightreaction.cyclic.electron.flow.chlororespiration | 9 | 0.0019458 | -0.6370720 | -0.5163707 | 0.0009335 | 0.0073046 | 0.8200606 | 0.0853487 | 0.0115032 |
| 4 | PS.lightreaction.photosystem.I.PSI.polypeptide.subunits | 16 | 0.0000000 | -0.8000301 | 0.0142978 | 0.0000000 | 0.9211274 | 0.8001579 | 0.5758168 | 0.0000001 |
| 6 | PS.lightreaction.NADH.DH | 9 | 0.0033271 | -0.6402509 | -0.4088024 | 0.0008799 | 0.0336930 | 0.7596319 | 0.1636588 | 0.0180740 |
| 22 | cell.wall.precursor.synthesis.GAE | 6 | 0.0045813 | 0.7038446 | 0.0592343 | 0.0028277 | 0.8016142 | 0.7063327 | 0.4558083 | 0.0224594 |
| 2 | PS.lightreaction.photosystem.II.PSII.polypeptide.subunits | 32 | 0.0000000 | -0.6362288 | -0.3006835 | 0.0000000 | 0.0032406 | 0.7037029 | 0.2372664 | 0.0000002 |
| 135 | protein.synthesis.ribosome.biogenesis.Pre.rRNA.processing.and.modifications.WD.repeat.proteins | 6 | 0.0006643 | -0.2159724 | 0.6618669 | 0.3596066 | 0.0049888 | 0.6962125 | 0.6207261 | 0.0049454 |
| 136 | protein.synthesis.ribosome.biogenesis.Pre.rRNA.processing.and.modifications.DExD.box.helicases | 14 | 0.0000008 | -0.1559130 | 0.6287862 | 0.3124749 | 0.0000462 | 0.6478278 | 0.5548661 | 0.0000151 |
| 151 | protein.assembly.and.cofactor.ligation | 21 | 0.0001985 | -0.4281905 | -0.4659323 | 0.0006808 | 0.0002184 | 0.6328033 | 0.0266875 | 0.0019592 |
| 36 | cell.wall.pectin.esterases.acetyl.esterase | 11 | 0.0109122 | 0.3870906 | 0.4955246 | 0.0262107 | 0.0044283 | 0.6287955 | 0.0766745 | 0.0438672 |
| 28 | cell.wall.cell.wall.proteins.AGPs.AGP | 38 | 0.0000002 | 0.4899309 | 0.3932074 | 0.0000002 | 0.0000273 | 0.6282072 | 0.0683938 | 0.0000048 |
| 27 | cell.wall.hemicellulose.synthesis.glucuronoxylan | 9 | 0.0114997 | 0.5714928 | 0.2190112 | 0.0029872 | 0.2552381 | 0.6120212 | 0.2492421 | 0.0440488 |
| 53 | secondary.metabolism.simple.phenols | 16 | 0.0023862 | 0.4888762 | 0.3351963 | 0.0007092 | 0.0202639 | 0.5927533 | 0.1086681 | 0.0133230 |
| 138 | protein.synthesis.ribosome.biogenesis.BRIX | 6 | 0.0045180 | -0.2303235 | 0.5360302 | 0.3285736 | 0.0229744 | 0.5834186 | 0.5418939 | 0.0224594 |
| 183 | transport.metabolite.transporters.at.the.envelope.membrane | 22 | 0.0007073 | 0.4313286 | 0.3698798 | 0.0004608 | 0.0026692 | 0.5682037 | 0.0434508 | 0.0050772 |
| 70 | redox.ascorbate.and.glutathione | 17 | 0.0000007 | 0.2178800 | -0.5204383 | 0.1198771 | 0.0002028 | 0.5642054 | 0.5220699 | 0.0000146 |
| 21 | cell.wall.precursor.synthesis.UXS | 6 | 0.0144305 | 0.5420499 | -0.1063970 | 0.0214823 | 0.6517640 | 0.5523934 | 0.4585212 | 0.0493212 |
| 173 | development.squamosa.promoter.binding.like..SPL. | 14 | 0.0074471 | 0.2521628 | 0.4827081 | 0.1023418 | 0.0017634 | 0.5446037 | 0.1630201 | 0.0328947 |
| 9 | PS.calvin.cycle.rubisco.interacting | 6 | 0.0087133 | -0.4691388 | 0.2581588 | 0.0465827 | 0.2734875 | 0.5354784 | 0.5142770 | 0.0364871 |
| 141 | protein.postranslational.modification.kinase | 18 | 0.0050259 | 0.2706061 | 0.4377894 | 0.0468500 | 0.0013004 | 0.5146720 | 0.1182165 | 0.0234934 |
| 58 | hormone.metabolism.gibberelin.signal.transduction | 8 | 0.0111369 | 0.4768097 | -0.1056928 | 0.0195202 | 0.6046971 | 0.4883835 | 0.4118915 | 0.0438923 |
| 55 | hormone.metabolism.ethylene.signal.transduction | 15 | 0.0000701 | 0.2932228 | -0.3681185 | 0.0492684 | 0.0135660 | 0.4706281 | 0.4676389 | 0.0007827 |
| 122 | protein.aa.activation.pseudouridylate.synthase | 16 | 0.0001393 | -0.3215731 | 0.2965791 | 0.0259430 | 0.0399806 | 0.4374568 | 0.4370996 | 0.0014735 |
rownames(top) <- top[,1]
top <- top[,4:5]
colfunc <- colorRampPalette(c("blue", "white", "red"))
colnames(top) <- gsub("s\\.","",colnames(top))
heatmap.2( as.matrix(top), col=colfunc(25),
scale="none",Colv=FALSE,trace="none", dendrogram="row",
margins = c(5,25), cexCol=0.8 , cexRow=0.7, main="Top genes sets in root by effect size (FDR<0.05)")
unlink("mapman_report_eff_root.html")
capture.output(
mitch_report(res,outfile=paste("mapman_report_eff_root.html"))
, file = "/dev/null", append = FALSE,
type = c("output", "message"), split = FALSE)## Dataset saved as " /tmp/RtmpshgKK6/mapman_report_eff_root.rds ".##
##
## processing file: mitch.Rmd## output file: /mnt/bfx10/projects/tohidul_bfx10/296_DU_MTI/dge/mitch.knit.md##
## Output created: /tmp/RtmpshgKK6/mitch_report.html
mitch_plots(res, outfile = "mapman_eff_plots_root.pdf")## png
## 2Special scatterplot root
plot(res$enrichment_result$s.der3, res$enrichment_result$s.der5 ,
pch=19,col="gray",bty="none", cex=1.3,
xlab="ES: 3h", ylab="root 5hr ES",
main="pathway regulation in root")
abline(h=0,lty=2)
abline(v=0,lty=2)
sig <- subset(res$enrichment_result,p.adjustMANOVA<0.05)
points(sig$s.der3, sig$s.der5 , pch=19,col="red",cex=1.4)
tmpdf <- sig[grep("cell.wall",sig$set,ignore.case=TRUE),]
points(tmpdf$s.der3, tmpdf$s.der5 , pch=19,col="green",cex=2.5)
range <- 1:nrow(tmpdf)
text(tmpdf$s.der3, tmpdf$s.der5 , labels=range, cex=1.2)
tmp <- tmpdf
tmpdf <- sig[grep("sig",sig$set,ignore.case=TRUE),]
points(tmpdf$s.der3, tmpdf$s.der5 , pch=19,col="orange",cex=2.5)
range <- (range[length(range)]+1):(range[length(range)]+nrow(tmpdf))
text(tmpdf$s.der3, tmpdf$s.der5 , labels=range, cex=1.2)
tmp <- rbind(tmp,tmpdf)
tmpdf <- sig[grep("^PS.",sig$set,ignore.case=TRUE),]
points(tmpdf$s.der3, tmpdf$s.der5 , pch=19,col="deepskyblue",cex=2.5)
range <- (range[length(range)]+1):(range[length(range)]+nrow(tmpdf))
text(tmpdf$s.der3, tmpdf$s.der5 , labels=range, cex=1.2)
tmp <- rbind(tmp,tmpdf)
rownames(tmp) <- 1:nrow(tmp)
tmp %>%
kbl(row.names=TRUE) %>%
kable_paper("hover", full_width = F)| set | setSize | pMANOVA | s.der3 | s.der5 | p.der3 | p.der5 | s.dist | SD | p.adjustMANOVA | |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | cell.wall.cellulose.synthesis | 12 | 0.0000256 | 0.6027185 | 0.7060311 | 0.0002996 | 0.0000228 | 0.9283047 | 0.0730531 | 0.0003669 |
| 2 | cell.wall.precursor.synthesis.GAE | 6 | 0.0045813 | 0.7038446 | 0.0592343 | 0.0028277 | 0.8016142 | 0.7063327 | 0.4558083 | 0.0224594 |
| 3 | cell.wall.pectin.esterases.acetyl.esterase | 11 | 0.0109122 | 0.3870906 | 0.4955246 | 0.0262107 | 0.0044283 | 0.6287955 | 0.0766745 | 0.0438672 |
| 4 | cell.wall.cell.wall.proteins.AGPs.AGP | 38 | 0.0000002 | 0.4899309 | 0.3932074 | 0.0000002 | 0.0000273 | 0.6282072 | 0.0683938 | 0.0000048 |
| 5 | cell.wall.hemicellulose.synthesis.glucuronoxylan | 9 | 0.0114997 | 0.5714928 | 0.2190112 | 0.0029872 | 0.2552381 | 0.6120212 | 0.2492421 | 0.0440488 |
| 6 | cell.wall.precursor.synthesis.UXS | 6 | 0.0144305 | 0.5420499 | -0.1063970 | 0.0214823 | 0.6517640 | 0.5523934 | 0.4585212 | 0.0493212 |
| 7 | cell.wall.degradation.pectate.lyases.and.polygalacturonases | 59 | 0.0012758 | 0.2338904 | 0.2393290 | 0.0018870 | 0.0014741 | 0.3346388 | 0.0038457 | 0.0082720 |
| 8 | cell.wall.modification | 53 | 0.0131420 | 0.1986915 | -0.0116570 | 0.0123409 | 0.8832958 | 0.1990332 | 0.1487388 | 0.0471705 |
| 9 | hormone.metabolism.gibberelin.signal.transduction | 8 | 0.0111369 | 0.4768097 | -0.1056928 | 0.0195202 | 0.6046971 | 0.4883835 | 0.4118915 | 0.0438923 |
| 10 | hormone.metabolism.ethylene.signal.transduction | 15 | 0.0000701 | 0.2932228 | -0.3681185 | 0.0492684 | 0.0135660 | 0.4706281 | 0.4676389 | 0.0007827 |
| 11 | signalling.light | 86 | 0.0004006 | 0.0022328 | 0.2170453 | 0.9714514 | 0.0005027 | 0.2170568 | 0.1518953 | 0.0032206 |
| 12 | not.assigned.unknown | 611 | 0.0134919 | -0.0379036 | -0.0693926 | 0.1098888 | 0.0034220 | 0.0790696 | 0.0222661 | 0.0475766 |
| 13 | PS.lightreaction.photosystem.II.LHC.II | 15 | 0.0000000 | -0.8070020 | 0.1551359 | 0.0000001 | 0.2982200 | 0.8217782 | 0.6803342 | 0.0000000 |
| 14 | PS.lightreaction.cyclic.electron.flow.chlororespiration | 9 | 0.0019458 | -0.6370720 | -0.5163707 | 0.0009335 | 0.0073046 | 0.8200606 | 0.0853487 | 0.0115032 |
| 15 | PS.lightreaction.photosystem.I.PSI.polypeptide.subunits | 16 | 0.0000000 | -0.8000301 | 0.0142978 | 0.0000000 | 0.9211274 | 0.8001579 | 0.5758168 | 0.0000001 |
| 16 | PS.lightreaction.NADH.DH | 9 | 0.0033271 | -0.6402509 | -0.4088024 | 0.0008799 | 0.0336930 | 0.7596319 | 0.1636588 | 0.0180740 |
| 17 | PS.lightreaction.photosystem.II.PSII.polypeptide.subunits | 32 | 0.0000000 | -0.6362288 | -0.3006835 | 0.0000000 | 0.0032406 | 0.7037029 | 0.2372664 | 0.0000002 |
| 18 | PS.calvin.cycle.rubisco.interacting | 6 | 0.0087133 | -0.4691388 | 0.2581588 | 0.0465827 | 0.2734875 | 0.5354784 | 0.5142770 | 0.0364871 |
Focus on ROS
DEL3 contrast
customsets <- c("redox.ascorbate.and.glutathione.ascorbate",
"misc.peroxidases",
"redox.dismutases.and.catalases",
"redox.glutaredoxins")
customsets <- genesets[which(names(genesets) %in% customsets)]
m <- mitch_import(x=as.data.frame(del3), DEtype="deseq2")## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 20884## Note: no. genes in output = 20884## Note: estimated proportion of input genes in output = 1del3m <- mitch_calc(x=m,genesets=customsets,priority="effect",minsetsize=5)## Note: Enrichments with large effect sizes may not be
## statistically significant.del3m$enrichment_result %>%
kbl() %>%
kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 3 | redox.dismutases.and.catalases | 11 | 0.1478761 | 0.2519784 | 0.2167740 |
| 4 | misc.peroxidases | 61 | 0.0409257 | -0.1513404 | 0.1637026 |
| 2 | redox.glutaredoxins | 33 | 0.1625805 | -0.1404642 | 0.2167740 |
| 1 | redox.ascorbate.and.glutathione.ascorbate | 16 | 0.6396966 | -0.0675975 | 0.6396966 |
mitch_barplot(del3m)
vioplot(del3m$detailed_sets,horizontal=TRUE,las=1) ; grid()
mitch_bubbleplot(del3m,30)
#unlink("del3m_redox.html")
#capture.output(
# mitch_report(del3m, outfile="del3m_redox.html"),
# file = "/dev/null", append = FALSE,
# type = c("output", "message"), split = FALSE)DEL5
m <- mitch_import(x=as.data.frame(del5), DEtype="deseq2")## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 20839## Note: no. genes in output = 20839## Note: estimated proportion of input genes in output = 1del5m <- mitch_calc(x=m,genesets=customsets,priority="effect",minsetsize=5)## Note: Enrichments with large effect sizes may not be
## statistically significant.del5m$enrichment_result %>%
kbl() %>%
kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 3 | redox.dismutases.and.catalases | 11 | 0.0299923 | 0.3778829 | 0.1034886 |
| 1 | redox.ascorbate.and.glutathione.ascorbate | 16 | 0.0517443 | 0.2808853 | 0.1034886 |
| 2 | redox.glutaredoxins | 38 | 0.8883664 | 0.0131598 | 0.9355988 |
| 4 | misc.peroxidases | 60 | 0.9355988 | -0.0060317 | 0.9355988 |
mitch_barplot(del5m)
vioplot(del5m$detailed_sets,horizontal=TRUE,las=1) ; grid()
mitch_bubbleplot(del5m,30)
#unlink("del5m_redox.html")
#capture.output(
# mitch_report(del5m, outfile="del5m_redox.html"),
# file = "/dev/null", append = FALSE,
# type = c("output", "message"), split = FALSE)DER3
m <- mitch_import(x=as.data.frame(der3), DEtype="deseq2")## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21102## Note: no. genes in output = 21102## Note: estimated proportion of input genes in output = 1der3m <- mitch_calc(x=m,genesets=customsets,priority="effect",minsetsize=5)## Note: Enrichments with large effect sizes may not be
## statistically significant.der3m$enrichment_result %>%
kbl() %>%
kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 4 | misc.peroxidases | 63 | 0.0015049 | 0.2311874 | 0.0060194 |
| 2 | redox.glutaredoxins | 29 | 0.0422461 | 0.2179075 | 0.0844921 |
| 1 | redox.ascorbate.and.glutathione.ascorbate | 17 | 0.6761372 | -0.0585222 | 0.7781246 |
| 3 | redox.dismutases.and.catalases | 11 | 0.7781246 | -0.0490644 | 0.7781246 |
mitch_barplot(der3m)
vioplot(der3m$detailed_sets,horizontal=TRUE,las=1) ; grid()
mitch_bubbleplot(der3m,30)
unlink("der3m_redox.html")
capture.output(
mitch_report(der3m, outfile="der3m_redox.html"),
file = "/dev/null", append = FALSE,
type = c("output", "message"), split = FALSE)## Dataset saved as " /tmp/RtmpshgKK6/der3m_redox.rds ".##
##
## processing file: mitch.Rmd## Contour plot does not apply to unidimensional analysis.## output file: /mnt/bfx10/projects/tohidul_bfx10/296_DU_MTI/dge/mitch.knit.md##
## Output created: /tmp/RtmpshgKK6/mitch_report.html
DER5
#m <- mitch_import(x=as.data.frame(der5), DEtype="deseq2")
#der5m <- mitch_calc(x=m,genesets=customsets,priority="effect",minsetsize=5)
#der5m$enrichment_result %>%
# kbl() %>%
# kable_paper("hover", full_width = F)
#mitch_barplot(der5m)
#vioplot(der5m$detailed_sets,horizontal=TRUE,las=1) ; grid()
#mitch_bubbleplot(der5m,30)
#unlink("der5m_redox.html")
#capture.output(
# mitch_report(der5m, outfile="der5m_redox.html"),
# file = "/dev/null", append = FALSE,
# type = c("output", "message"), split = FALSE)Session information
So you know what version of R and packages was used.
sessionInfo()## R version 4.1.2 (2021-11-01)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] parallel stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] pkgload_1.2.1 GGally_2.1.2
## [3] beeswarm_0.4.0 gtools_3.9.2
## [5] tibble_3.1.3 dplyr_1.0.7
## [7] echarts4r_0.4.1 ggplot2_3.3.5
## [9] vioplot_0.3.6 zoo_1.8-9
## [11] sm_2.2-5.6 UpSetR_1.4.0
## [13] eulerr_6.1.0 kableExtra_1.3.4
## [15] mitch_1.4.0 DESeq2_1.32.0
## [17] SummarizedExperiment_1.22.0 Biobase_2.52.0
## [19] MatrixGenerics_1.4.0 matrixStats_0.59.0
## [21] GenomicRanges_1.44.0 GenomeInfoDb_1.28.1
## [23] IRanges_2.26.0 S4Vectors_0.30.0
## [25] BiocGenerics_0.38.0 gplots_3.1.1
## [27] reshape2_1.4.4
##
## loaded via a namespace (and not attached):
## [1] colorspace_2.0-2 ellipsis_0.3.2 rprojroot_2.0.2
## [4] XVector_0.32.0 rstudioapi_0.13 farver_2.1.0
## [7] bit64_4.0.5 AnnotationDbi_1.54.1 fansi_0.5.0
## [10] xml2_1.3.2 splines_4.1.2 cachem_1.0.5
## [13] geneplotter_1.70.0 knitr_1.33 polyclip_1.10-0
## [16] jsonlite_1.7.2 annotate_1.70.0 png_0.1-7
## [19] shiny_1.6.0 compiler_4.1.2 httr_1.4.2
## [22] assertthat_0.2.1 Matrix_1.4-0 fastmap_1.1.0
## [25] later_1.2.0 prettyunits_1.1.1 htmltools_0.5.1.1
## [28] tools_4.1.2 gtable_0.3.0 glue_1.4.2
## [31] GenomeInfoDbData_1.2.6 Rcpp_1.0.7 jquerylib_0.1.4
## [34] vctrs_0.3.8 Biostrings_2.60.1 svglite_2.0.0
## [37] polylabelr_0.2.0 xfun_0.24 stringr_1.4.0
## [40] rvest_1.0.0 mime_0.11 lifecycle_1.0.0
## [43] XML_3.99-0.6 zlibbioc_1.38.0 MASS_7.3-55
## [46] scales_1.1.1 hms_1.1.0 promises_1.2.0.1
## [49] RColorBrewer_1.1-2 yaml_2.2.1 memoise_2.0.0
## [52] gridExtra_2.3 sass_0.4.0 reshape_0.8.8
## [55] stringi_1.7.3 RSQLite_2.2.7 highr_0.9
## [58] genefilter_1.74.0 desc_1.3.0 caTools_1.18.2
## [61] BiocParallel_1.26.1 rlang_0.4.11 pkgconfig_2.0.3
## [64] systemfonts_1.0.2 bitops_1.0-7 evaluate_0.14
## [67] lattice_0.20-45 purrr_0.3.4 labeling_0.4.2
## [70] htmlwidgets_1.5.3 bit_4.0.4 tidyselect_1.1.1
## [73] plyr_1.8.6 magrittr_2.0.1 R6_2.5.0
## [76] generics_0.1.0 DelayedArray_0.18.0 DBI_1.1.1
## [79] withr_2.4.2 pillar_1.6.1 survival_3.2-13
## [82] KEGGREST_1.32.0 RCurl_1.98-1.3 crayon_1.4.1
## [85] KernSmooth_2.23-20 utf8_1.2.2 rmarkdown_2.9
## [88] progress_1.2.2 locfit_1.5-9.4 grid_4.1.2
## [91] blob_1.2.2 digest_0.6.27 webshot_0.5.2
## [94] xtable_1.8-4 httpuv_1.6.1 munsell_0.5.0
## [97] viridisLite_0.4.0 bslib_0.2.5.1 tcltk_4.1.2References
Bray NL, Pimentel H, Melsted P, Pachter L. Near-optimal probabilistic RNA-seq quantification [published correction appears in Nat Biotechnol. 2016 Aug 9;34(8):888]. Nat Biotechnol. 2016;34(5):525-527. doi:10.1038/nbt.3519
Jiang H, Lei R, Ding SW, Zhu S. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics. 2014;15:182. Published 2014 Jun 12. doi:10.1186/1471-2105-15-182
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. doi:10.1186/s13059-014-0550-8
Kaspi A, Ziemann M. mitch: multi-contrast pathway enrichment for multi-omics and single-cell profiling data. BMC Genomics. 2020;21(1):447. Published 2020 Jun 29. doi:10.1186/s12864-020-06856-9