List of regulator genes for a number of model organisms — regulators_per

Those particular genes are known to be transcriptionnal actors, and are needed to infer gene regulatory networks in DIANE.

regulators_per_organism

Format

A named list with the following elements:

Arabidopsis thaliana: Character vector of the known transcriptional regulators in Arabidopsis thaliana
Homo sapiens: Character vector of the known transcription factors in Human
Mus musculus: Character vector of the known transcription factors in Mouse
Drosophilia melanogaster: Character vector of the known transcription factors in Drosophilia melanogaster
Caenorhabditis elegans: Character vector of the known transcription factors in C elegans
Escherichia coli: Character vector of the known transcription factors and sigma elements in E coli K12

Source

For Arabidopsis thaliana: http://plntfdb.bio.uni-potsdam.de/v3.0/index.php?sp_id=ATH
For Human: http://humantfs.ccbr.utoronto.ca/download.php
Mus musculus: http://bioinfo.life.hust.edu.cn/AnimalTFDB/#!/download
Drosophilia melanogaster: https://flybase.org/reports/FBgg0000745.html
C elegans: http://www.wormbook.org/chapters/www_transcriptionalregulation.2/transregulate.html#sec5-1
E coli: http://regulondb.ccg.unam.mx/menu/download/datasets/index.jsp

Examples

{
 print(head(regulators_per_organism[["Arabidopsis thaliana"]]))
 print(head(regulators_per_organism[["Homo sapiens"]]))
 print(head(regulators_per_organism[["Mus musculus"]]))
 print(head(regulators_per_organism[["Drosophilia melanogaster"]]))
 print(head(regulators_per_organism[["Caenorhabditis elegans"]]))
 print(head(regulators_per_organism[["Escherichia coli"]]))
}
#> [1] "AT1G04880" "AT1G20910" "AT1G55650" "AT1G76110" "AT1G76510" "AT2G17410"
#> [1] "ENSG00000004848" "ENSG00000005073" "ENSG00000005102" "ENSG00000005513"
#> [5] "ENSG00000005801" "ENSG00000005889"
#> [1] "ENSMUSG00000037029" "ENSMUSG00000032035" "ENSMUSG00000021485"
#> [4] "ENSMUSG00000097200" "ENSMUSG00000098022" "ENSMUSG00000027985"
#> [1] "FBgn0002522" "FBgn0051481" "FBgn0004054" "FBgn0004053" "FBgn0000166"
#> [6] "FBgn0000439"
#> [1] "WBGene00019424" "WBGene00009202" "WBGene00009203" "WBGene00013383"
#> [5] "WBGene00000476" "WBGene00002717"
#> [1] "accB" "acrR" "ada"  "adiY" "agaR" "aidB"