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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | cd4dc12 | khembach | 2021-03-31 | compare DE genes to HEK cell TDP CLIP-seq targets |
library(dplyr)
library(cowplot)
library(ggplot2)
library(stringr)tbl_fil2 <- readRDS(file.path("output", "tbl_TDP-08-01-muscat.rds"))
## TDP-43 CLIP-seq of HEK cells target list
gdf <- read.table("/home/kathi/Manu_TDP_CLIP/analysis/clipper_analysis/gene_cluster_count_merge_peaks.txt",
header = TRUE)
## we only keep the genes that are bound by WT
targets <- gdf %>% dplyr::filter(nclus_WT > 0)
dim(targets)[1] 4923 18We compare the DE genes per cluster with the list of WT TDP-43 target genes.
tbl_fil2 <- lapply(tbl_fil2, function(x) {
x$gene_id <- str_split(x$gene, pattern = "\\.", simplify = TRUE)[,1]
x$target_hek <- x$gene_id %in% targets$gene_id
x
})
## how many of the DE genes are also TDP-43 targets in HEK cells?
lapply(tbl_fil2, function(x) table(x$target_hek))$`0`
FALSE
1
$`1`
FALSE TRUE
1 1
$`5`
FALSE
6
$`7`
FALSE
7
$`8`
FALSE
4
$`10`
FALSE TRUE
48 12
$`11`
FALSE
3
$`12`
FALSE TRUE
55 16
$`13`
FALSE TRUE
166 81
$`14`
FALSE TRUE
23 5 ## what are the DE target genes and what's the percentage of all DE genes?
res <- lapply(tbl_fil2, function(x) {
list("percentage" = round(sum(x$target_hek)/nrow(x)*100, 2),
"targets" = x$gene[x$target_hek])
})
res$`0`
$`0`$percentage
[1] 0
$`0`$targets
character(0)
$`1`
$`1`$percentage
[1] 50
$`1`$targets
[1] "ENSG00000197747.S100A10"
$`5`
$`5`$percentage
[1] 0
$`5`$targets
character(0)
$`7`
$`7`$percentage
[1] 0
$`7`$targets
character(0)
$`8`
$`8`$percentage
[1] 0
$`8`$targets
character(0)
$`10`
$`10`$percentage
[1] 20
$`10`$targets
[1] "ENSG00000065911.MTHFD2" "ENSG00000054598.FOXC1" "ENSG00000106105.GARS"
[4] "ENSG00000105281.SLC1A5" "ENSG00000265972.TXNIP" "ENSG00000113739.STC2"
[7] "ENSG00000138829.FBN2" "ENSG00000163430.FSTL1" "ENSG00000113161.HMGCR"
[10] "ENSG00000070669.ASNS" "ENSG00000147889.CDKN2A" "ENSG00000196305.IARS"
$`11`
$`11`$percentage
[1] 0
$`11`$targets
character(0)
$`12`
$`12`$percentage
[1] 22.54
$`12`$targets
[1] "ENSG00000197747.S100A10" "ENSG00000160752.FDPS"
[3] "ENSG00000099194.SCD" "ENSG00000175183.CSRP2"
[5] "ENSG00000120075.HOXB5" "ENSG00000104549.SQLE"
[7] "ENSG00000112972.HMGCS1" "ENSG00000079459.FDFT1"
[9] "ENSG00000188229.TUBB4B" "ENSG00000120437.ACAT2"
[11] "ENSG00000141682.PMAIP1" "ENSG00000184486.POU3F2"
[13] "ENSG00000110492.MDK" "ENSG00000134824.FADS2"
[15] "ENSG00000114861.FOXP1" "ENSG00000113161.HMGCR"
$`13`
$`13`$percentage
[1] 32.79
$`13`$targets
[1] "ENSG00000068305.MEF2A" "ENSG00000168209.DDIT4"
[3] "ENSG00000187240.DYNC2H1" "ENSG00000165891.E2F7"
[5] "ENSG00000176890.TYMS" "ENSG00000102172.SMS"
[7] "ENSG00000137720.C11orf1" "ENSG00000129521.EGLN3"
[9] "ENSG00000145335.SNCA" "ENSG00000047579.DTNBP1"
[11] "ENSG00000116584.ARHGEF2" "ENSG00000114861.FOXP1"
[13] "ENSG00000276644.DACH1" "ENSG00000167740.CYB5D2"
[15] "ENSG00000169738.DCXR" "ENSG00000214078.CPNE1"
[17] "ENSG00000114120.SLC25A36" "ENSG00000176171.BNIP3"
[19] "ENSG00000155846.PPARGC1B" "ENSG00000186020.ZNF529"
[21] "ENSG00000164292.RHOBTB3" "ENSG00000105849.TWISTNB"
[23] "ENSG00000188229.TUBB4B" "ENSG00000167085.PHB"
[25] "ENSG00000130522.JUND" "ENSG00000075391.RASAL2"
[27] "ENSG00000198712.MT-CO2" "ENSG00000197958.RPL12"
[29] "ENSG00000243927.MRPS6" "ENSG00000124766.SOX4"
[31] "ENSG00000170004.CHD3" "ENSG00000108511.HOXB6"
[33] "ENSG00000160014.CALM3" "ENSG00000120889.TNFRSF10B"
[35] "ENSG00000108587.GOSR1" "ENSG00000163602.RYBP"
[37] "ENSG00000126953.TIMM8A" "ENSG00000115963.RND3"
[39] "ENSG00000126267.COX6B1" "ENSG00000101079.NDRG3"
[41] "ENSG00000198743.SLC5A3" "ENSG00000198899.MT-ATP6"
[43] "ENSG00000159164.SV2A" "ENSG00000134308.YWHAQ"
[45] "ENSG00000104763.ASAH1" "ENSG00000176105.YES1"
[47] "ENSG00000116729.WLS" "ENSG00000102024.PLS3"
[49] "ENSG00000130770.ATP5IF1" "ENSG00000151729.SLC25A4"
[51] "ENSG00000117614.SYF2" "ENSG00000136758.YME1L1"
[53] "ENSG00000196498.NCOR2" "ENSG00000183684.ALYREF"
[55] "ENSG00000171130.ATP6V0E2" "ENSG00000156650.KAT6B"
[57] "ENSG00000177885.GRB2" "ENSG00000101361.NOP56"
[59] "ENSG00000100836.PABPN1" "ENSG00000166170.BAG5"
[61] "ENSG00000198727.MT-CYB" "ENSG00000114503.NCBP2"
[63] "ENSG00000125304.TM9SF2" "ENSG00000067225.PKM"
[65] "ENSG00000198938.MT-CO3" "ENSG00000150779.TIMM8B"
[67] "ENSG00000182541.LIMK2" "ENSG00000186260.MRTFB"
[69] "ENSG00000149313.AASDHPPT" "ENSG00000111716.LDHB"
[71] "ENSG00000185658.BRWD1" "ENSG00000196405.EVL"
[73] "ENSG00000197746.PSAP" "ENSG00000113739.STC2"
[75] "ENSG00000089157.RPLP0" "ENSG00000123106.CCDC91"
[77] "ENSG00000033178.UBA6" "ENSG00000167081.PBX3"
[79] "ENSG00000198886.MT-ND4" "ENSG00000122705.CLTA"
[81] "ENSG00000170689.HOXB9"
$`14`
$`14`$percentage
[1] 17.86
$`14`$targets
[1] "ENSG00000197747.S100A10" "ENSG00000182481.KPNA2"
[3] "ENSG00000124766.SOX4" "ENSG00000134057.CCNB1"
[5] "ENSG00000101224.CDC25B" We save the tables to file.
for( i in names(tbl_fil2)){
write.table(tbl_fil2[[i]],
file.path("output",
paste0("tbl_TDP-08-02-targets_hek_cluster_", i, ".txt")),
sep = "\t", row.names = FALSE, quote = FALSE)
}saveRDS(tbl_fil2, file.path("output", "tbl_TDP-08-02-targets_hek.rds"))
sessionInfo()R version 4.0.0 (2020-04-24)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.7 LTS
Matrix products: default
BLAS: /usr/local/R/R-4.0.0/lib/libRblas.so
LAPACK: /usr/local/R/R-4.0.0/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] stringr_1.4.0 ggplot2_3.3.2 cowplot_1.0.0 dplyr_1.0.2
[5] workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 pillar_1.4.6 compiler_4.0.0 later_1.1.0.1
[5] git2r_0.27.1 tools_4.0.0 digest_0.6.25 evaluate_0.14
[9] lifecycle_0.2.0 tibble_3.0.3 gtable_0.3.0 pkgconfig_2.0.3
[13] rlang_0.4.7 yaml_2.2.1 xfun_0.15 withr_2.2.0
[17] knitr_1.29 generics_0.0.2 fs_1.4.2 vctrs_0.3.4
[21] rprojroot_1.3-2 grid_4.0.0 tidyselect_1.1.0 glue_1.4.2
[25] R6_2.4.1 rmarkdown_2.3 purrr_0.3.4 magrittr_1.5
[29] whisker_0.4 codetools_0.2-16 backports_1.1.9 scales_1.1.1
[33] promises_1.1.1 ellipsis_0.3.1 htmltools_0.5.0 colorspace_1.4-1
[37] httpuv_1.5.4 stringi_1.4.6 munsell_0.5.0 crayon_1.3.4