markers coef pvalue dataset
1 CDIPT 1.2840052 4.101476e-05 GSE10358
2 PRMT5 0.9325224 1.613859e-03 GSE10358
3 PPIL2 -1.2599542 1.099318e-04 GSE10358
4 NCKAP1L 0.8657959 6.304739e-03 GSE10358
5 SLC39A7 -0.7662949 7.919072e-03 GSE10358
6 WDR1 -0.7841336 6.485637e-03 GSE10358
vennTable = read.table(file = "out/FS_Venn.txt", row.names = 1, header = TRUE, sep = "\t")
source("/sibcb2/bioinformatics/Script/IDconverter.R")
load("/sibcb2/bioinformatics/KnowledgeBase/IDbase/GeneID2Symbol/geneInforTable.RData")
load("/sibcb2/bioinformatics/KnowledgeBase/IDbase/HomoloGene/homologeneTable.RData")
x = HM_IDAnnotation(gsub(" Mm", "", rownames(vennTable)), geneInforTable, homologeneTable)
mergedT = data.frame(vennTable, humanSymbol = x[, "Homolog_Human"])
idx = mergedT$humanSymbol != ""
sT = mergedT[idx, ]
head(sT)
ma_vitro hm_vitro ma_vivo hm_vivo group humanSymbol
Rraga Mm 1 1 1 1 shared RRAGA
Pabpc1 Mm 1 1 1 1 shared PABPC1
Wdr43 Mm 1 1 1 1 shared WDR43
Cdipt Mm 1 1 1 1 shared CDIPT
Vwa9 Mm 1 1 1 1 shared VWA9
Bop1 Mm 1 1 1 1 shared BOP1
subT = filter(sigTable, coef > 0)
s1 = summary(factor(subT$markers), maxsum = 1000)
subT = filter(sigTable, coef < 0)
s2 = summary(factor(subT$markers), maxsum = 1000)
acNum = reNum = rep(0, nrow(sT))
names(acNum) = names(reNum) = sT$humanSymbol
acNum[names(s1)] = s1
reNum[names(s2)] = s2
res = data.frame(sT, acNum, reNum) %>% arrange(desc(acNum))
# write.table(res, file = "out/FS_Survival_Summary.txt", row.names = FALSE, col.names = TRUE, sep = "\t")
head(res)
ma_vitro hm_vitro ma_vivo hm_vivo group humanSymbol
Fermt3 Mm 0 0 1 1 vivo_only FERMT3
Ppcdc Mm 1 1 1 1 shared PPCDC
Mef2c Mm 1 0 1 0 shared MEF2C
Aco2 Mm 1 1 1 1 shared ACO2
Tubg2 Mm 1 1 1 0 shared TUBG2
Fkbp1a Mm 1 1 0 0 vitro_only FKBP1A
acNum reNum
Fermt3 Mm 4 0
Ppcdc Mm 3 0
Mef2c Mm 3 0
Aco2 Mm 3 0
Tubg2 Mm 3 0
Fkbp1a Mm 3 0
vis = filter(res, acNum >= 1, group == "vivo_only")
visM = as.matrix(vis[, 1:4])
rownames(visM) = paste(vis$humanSymbol, sep = "")
pheatmap(visM,
main = "",
border_color = "grey60", color = c("#f5f5f5","#f5f5f5","#dd1c77"),
legend_breaks = c(-1,0,1),
legend_labels = c("NC", "NC", "Depleted"),
fontsize_row = 6,
show_rownames = TRUE, show_colnames = TRUE,
cluster_rows = FALSE, cluster_cols = FALSE)
x = table(res$group, res$acNum > 0)
x
FALSE TRUE
ND 163 61
shared 396 260
vitro_only 27 9
vivo_only 49 21
FALSE TRUE
ND 0.7276786 0.2723214
shared 0.6036585 0.3963415
vitro_only 0.7500000 0.2500000
vivo_only 0.7000000 0.3000000
y = table(res$group, res$reNum > 0)
y
FALSE TRUE
ND 193 31
shared 567 89
vitro_only 30 6
vivo_only 54 16
FALSE TRUE
ND 0.8616071 0.1383929
shared 0.8643293 0.1356707
vitro_only 0.8333333 0.1666667
vivo_only 0.7714286 0.2285714