R Notebook
Last updated: 2019-04-10
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Knit directory: 10x-adipocyte-analysis/
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|---|---|---|---|---|
| Rmd | ea0009a | Pytrik Folkertsma | 2019-04-10 | TF analysis |
library(data.table)
library(readr)
library(dplyr)
Attaching package: 'dplyr'The following objects are masked from 'package:data.table':
between, first, lastThe following objects are masked from 'package:stats':
filter, lagThe following objects are masked from 'package:base':
intersect, setdiff, setequal, unionlibrary(knitr)
library(Seurat)Loading required package: ggplot2Loading required package: cowplot
Attaching package: 'cowplot'The following object is masked from 'package:ggplot2':
ggsaveLoading required package: Matrixseurobj <- readRDS('output/seurat_objects/180831/10x-180831')
gene_annotations <- fread('tables/tables_paper/all_tables/genes_biomart.txt', sep='\t', quote="", header=T)ids2symbols <- read.table('tables/tables_paper/all_tables/10x-180831-geneids-genesymbols.tsv', header=T)BEAM clusters
combined <- list()
for (i in 1:6){
beam_genelist <- read.table(paste('tables/tables_paper/all_tables/BEAM/heatmap_logFC0.3_ncluster6/genelist_cluster', i, '.tsv', sep=''), sep='\t', header=T)
beam_genelist['ensembl_gene_id'] <- ids2symbols$ensembl_gene_id[match(beam_genelist$gene_short_name, ids2symbols$gene_symbol)]
beam_genelist['cluster'] <- i
#add geneinfo
merged <- merge(beam_genelist, gene_annotations[,c('Gene stable ID', 'Gene type', 'GO term accession', 'GO term name')], by.y='Gene stable ID', by.x='ensembl_gene_id')
#filter for tf's and gene type != protein coding
filtered <- merged[c(which(c(merged$`GO term name`) %like% 'transcription factor'),
which(merged$`GO term definition` %like% 'transcription factor'),
which(merged$`Gene type` != 'protein_coding')),]
#filter out duplicate genes
filtered <- filtered[!duplicated(filtered$gene_short_name),]
combined[[i]] <- filtered
}
combined <- do.call("rbind", combined)kable(combined)| ensembl_gene_id | gene_short_name | pval | qval | avgLogFC_State2_State3 | cluster | Gene type | GO term accession | GO term name | |
|---|---|---|---|---|---|---|---|---|---|
| 1614 | ENSG00000108561 | C1QBP | 0 | 0 | 0.4210100 | 1 | protein_coding | GO:0008134 | transcription factor binding |
| 4113 | ENSG00000164924 | YWHAZ | 0 | 0 | 0.3358994 | 1 | protein_coding | GO:0008134 | transcription factor binding |
| 4589 | ENSG00000167085 | PHB | 0 | 0 | 0.3788402 | 1 | protein_coding | GO:0000981 | DNA-binding transcription factor activity, RNA polymerase II-specific |
| 238 | ENSG00000009950 | MLXIPL | 0 | 0 | 0.3673746 | 2 | protein_coding | GO:0000981 | DNA-binding transcription factor activity, RNA polymerase II-specific |
| 754 | ENSG00000025434 | NR1H3 | 0 | 0 | 0.3569965 | 2 | protein_coding | GO:0003700 | DNA-binding transcription factor activity |
| 1808 | ENSG00000072310 | SREBF1 | 0 | 0 | 0.4302819 | 2 | protein_coding | GO:0000981 | DNA-binding transcription factor activity, RNA polymerase II-specific |
| 4371 | ENSG00000121691 | CAT | 0 | 0 | 0.3321904 | 2 | protein_coding | GO:0032088 | negative regulation of NF-kappaB transcription factor activity |
| 5709 | ENSG00000132170 | PPARG | 0 | 0 | 0.3226131 | 2 | protein_coding | GO:0001103 | RNA polymerase II repressing transcription factor binding |
| 7406 | ENSG00000135218 | CD36 | 0 | 0 | 1.4585314 | 2 | protein_coding | GO:0051092 | positive regulation of NF-kappaB transcription factor activity |
| 11046 | ENSG00000166823 | MESP1 | 0 | 0 | 0.4067898 | 2 | protein_coding | GO:0003700 | DNA-binding transcription factor activity |
| 11896 | ENSG00000174804 | FZD4 | 0 | 0 | 0.3027719 | 2 | protein_coding | GO:0051091 | positive regulation of DNA-binding transcription factor activity |
| 12856 | ENSG00000187514 | PTMA | 0 | 0 | 0.6008086 | 2 | protein_coding | GO:0033613 | activating transcription factor binding |
| 14113 | ENSG00000245848 | CEBPA | 0 | 0 | 0.3466449 | 2 | protein_coding | GO:0000981 | DNA-binding transcription factor activity, RNA polymerase II-specific |
| 13969 | ENSG00000229153 | EPHA1-AS1 | 0 | 0 | 0.3000552 | 2 | antisense | ||
| 264 | ENSG00000019549 | SNAI2 | 0 | 0 | -0.5313284 | 3 | protein_coding | GO:0000981 | DNA-binding transcription factor activity, RNA polymerase II-specific |
| 1320 | ENSG00000120738 | EGR1 | 0 | 0 | -0.4104048 | 3 | protein_coding | GO:0000981 | DNA-binding transcription factor activity, RNA polymerase II-specific |
| 1409 | ENSG00000120885 | CLU | 0 | 0 | -0.7825588 | 3 | protein_coding | GO:0051092 | positive regulation of NF-kappaB transcription factor activity |
| 2373 | ENSG00000148516 | ZEB1 | 0 | 0 | -0.4307388 | 3 | protein_coding | GO:0000981 | DNA-binding transcription factor activity, RNA polymerase II-specific |
| 2683 | ENSG00000152518 | ZFP36L2 | 0 | 0 | -0.3991944 | 3 | protein_coding | GO:0003700 | DNA-binding transcription factor activity |
| 2993 | ENSG00000162407 | PPAP2B | 0 | 0 | -0.5215079 | 3 | protein_coding | GO:0051091 | positive regulation of DNA-binding transcription factor activity |
| 3109 | ENSG00000164920 | OSR2 | 0 | 0 | -0.5893658 | 3 | protein_coding | GO:0000981 | DNA-binding transcription factor activity, RNA polymerase II-specific |
| 3745 | ENSG00000170345 | FOS | 0 | 0 | -0.6405352 | 3 | protein_coding | GO:0051090 | regulation of DNA-binding transcription factor activity |
| 3982 | ENSG00000174059 | CD34 | 0 | 0 | -0.4275094 | 3 | protein_coding | GO:0008134 | transcription factor binding |
| 4254 | ENSG00000185650 | ZFP36L1 | 0 | 0 | -0.5867891 | 3 | protein_coding | GO:0003700 | DNA-binding transcription factor activity |
| 4537 | ENSG00000267519 | MIR24-2 | 0 | 0 | -0.3113038 | 3 | antisense | ||
| 2073 | ENSG00000124212 | PTGIS | 0 | 0 | -0.3420740 | 4 | protein_coding | GO:0032088 | negative regulation of NF-kappaB transcription factor activity |
| 2661 | ENSG00000138061 | CYP1B1 | 0 | 0 | -0.6809188 | 4 | protein_coding | GO:0032088 | negative regulation of NF-kappaB transcription factor activity |
| 3478 | ENSG00000150347 | ARID5B | 0 | 0 | -0.4524769 | 4 | protein_coding | GO:0000981 | DNA-binding transcription factor activity, RNA polymerase II-specific |
| 3580 | ENSG00000153048 | CARHSP1 | 0 | 0 | -0.3443580 | 4 | protein_coding | GO:0000981 | DNA-binding transcription factor activity, RNA polymerase II-specific |
| 5930 | ENSG00000205542 | TMSB4X | 0 | 0 | -0.3553073 | 4 | protein_coding | GO:0032088 | negative regulation of NF-kappaB transcription factor activity |
| 4861 | ENSG00000172965 | MIR4435-1HG | 0 | 0 | -0.4703532 | 4 | lincRNA | ||
| 5050 | ENSG00000177410 | ZFAS1 | 0 | 0 | -0.3843600 | 4 | antisense | ||
| 6029 | ENSG00000222041 | LINC00152 | 0 | 0 | -0.5044662 | 4 | lincRNA | ||
| 6067 | ENSG00000232527 | RP11-14N7.2 | 0 | 0 | -0.3392808 | 4 | lincRNA | ||
| 411 | ENSG00000116132 | PRRX1 | 0 | 0 | -0.5139881 | 5 | protein_coding | GO:0000981 | DNA-binding transcription factor activity, RNA polymerase II-specific |
| 1868 | ENSG00000162733 | DDR2 | 0 | 0 | -0.4279312 | 5 | protein_coding | GO:0051091 | positive regulation of DNA-binding transcription factor activity |
| 2060 | ENSG00000171223 | JUNB | 0 | 0 | -0.7652085 | 5 | protein_coding | GO:0000981 | DNA-binding transcription factor activity, RNA polymerase II-specific |
| 2452 | ENSG00000196628 | TCF4 | 0 | 0 | -0.4466219 | 5 | protein_coding | GO:0005667 | transcription factor complex |
| 3593 | ENSG00000206538 | VGLL3 | 0 | 0 | -0.4709351 | 5 | protein_coding | GO:0000981 | DNA-binding transcription factor activity, RNA polymerase II-specific |
| 1562 | ENSG00000163170 | BOLA3 | 0 | 0 | 0.3568609 | 6 | protein_coding | GO:0000981 | DNA-binding transcription factor activity, RNA polymerase II-specific |
| 1608 | ENSG00000167815 | PRDX2 | 0 | 0 | 0.5220889 | 6 | protein_coding | GO:0032088 | negative regulation of NF-kappaB transcription factor activity |
#write.table(combined, file='../tables/tables_paper/all_tables/BEAM/heatmap_logFC0.3_ncluster6/genelist_TFs.tsv', sep='\t', quote=F, row.names=F)
#write.table(combined, file='../tables/tables_paper/supplementary_tables/BEAM_logFC0.3_nclusters6/genelist_TFs.tsv', sep='\t', quote=F, row.names=F)FeaturePlot(seurobj, features.plot=as.vector(combined$gene_short_name), nCol=2, cols.use=c('gray', 'blue'), no.legend=F)
sessionInfo()R version 3.5.3 (2019-03-11)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Storage
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.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] Seurat_2.3.4 Matrix_1.2-17 cowplot_0.9.4 ggplot2_3.1.0
[5] knitr_1.22 dplyr_0.8.0.1 readr_1.3.1 data.table_1.12.0
loaded via a namespace (and not attached):
[1] Rtsne_0.15 colorspace_1.4-1 class_7.3-15
[4] modeltools_0.2-22 ggridges_0.5.1 mclust_5.4.3
[7] rprojroot_1.3-2 htmlTable_1.13.1 base64enc_0.1-3
[10] fs_1.2.7 rstudioapi_0.10 proxy_0.4-23
[13] npsurv_0.4-0 flexmix_2.3-15 bit64_0.9-7
[16] mvtnorm_1.0-10 codetools_0.2-16 splines_3.5.3
[19] R.methodsS3_1.7.1 lsei_1.2-0 robustbase_0.93-4
[22] jsonlite_1.6 Formula_1.2-3 workflowr_1.2.0
[25] ica_1.0-2 cluster_2.0.7-1 kernlab_0.9-27
[28] png_0.1-7 R.oo_1.22.0 compiler_3.5.3
[31] httr_1.4.0 backports_1.1.3 assertthat_0.2.1
[34] lazyeval_0.2.2 lars_1.2 acepack_1.4.1
[37] htmltools_0.3.6 tools_3.5.3 igraph_1.2.4
[40] gtable_0.3.0 glue_1.3.1 reshape2_1.4.3
[43] RANN_2.6.1 Rcpp_1.0.1 trimcluster_0.1-2.1
[46] gdata_2.18.0 ape_5.3 nlme_3.1-137
[49] iterators_1.0.10 fpc_2.1-11.1 gbRd_0.4-11
[52] lmtest_0.9-36 xfun_0.5 stringr_1.4.0
[55] irlba_2.3.3 gtools_3.8.1 DEoptimR_1.0-8
[58] zoo_1.8-5 MASS_7.3-51.1 scales_1.0.0
[61] hms_0.4.2 doSNOW_1.0.16 parallel_3.5.3
[64] RColorBrewer_1.1-2 yaml_2.2.0 reticulate_1.11.1
[67] pbapply_1.4-0 gridExtra_2.3 segmented_0.5-3.0
[70] rpart_4.1-13 latticeExtra_0.6-28 stringi_1.4.3
[73] highr_0.8 foreach_1.4.4 checkmate_1.9.1
[76] caTools_1.17.1.2 bibtex_0.4.2 Rdpack_0.10-1
[79] SDMTools_1.1-221 rlang_0.3.2 pkgconfig_2.0.2
[82] dtw_1.20-1 prabclus_2.2-7 bitops_1.0-6
[85] evaluate_0.13 lattice_0.20-38 ROCR_1.0-7
[88] purrr_0.3.2 labeling_0.3 htmlwidgets_1.3
[91] bit_1.1-14 tidyselect_0.2.5 plyr_1.8.4
[94] magrittr_1.5 R6_2.4.0 snow_0.4-3
[97] gplots_3.0.1.1 Hmisc_4.2-0 pillar_1.3.1
[100] whisker_0.3-2 foreign_0.8-71 withr_2.1.2
[103] mixtools_1.1.0 fitdistrplus_1.0-14 survival_2.43-3
[106] nnet_7.3-12 tsne_0.1-3 tibble_2.1.1
[109] crayon_1.3.4 hdf5r_1.1.1 KernSmooth_2.23-15
[112] rmarkdown_1.12 grid_3.5.3 git2r_0.25.2
[115] metap_1.1 digest_0.6.18 diptest_0.75-7
[118] tidyr_0.8.3 R.utils_2.8.0 stats4_3.5.3
[121] munsell_0.5.0