Transcription factor binding site databases explained

Transcription factors are proteins that bind genomic regulatory sites. Identification of genomic regulatory elements is essential for understanding the dynamics of developmental, physiological and pathological processes. Recent advances in chromatin immunoprecipitation followed by sequencing (ChIP-seq) have provided powerful ways to identify genome-wide profiling of DNA-binding proteins and histone modifications.[1] [2] The application of ChIP-seq methods has reliably discovered transcription factor binding sites and histone modification sites.

Transcription factor binding site databases

Comprehensive List of transcription factor binding sites (TFBSs) databases based on ChIP-seq data as follows:

NameDescription typeLink References
ChIPBaseChIPBase a database for Transcription factor-binding sites, motifs (~1290 transcription factors) and decoding the transcriptional regulation of LncRNAs, miRNAs and protein-coding genes from ~10,200 curated peak datasets derived from ChIP-seq methods in 10 species database website [3]
ChEAtranscription factor regulation inferred from integrating genome-wide ChIP-X experiments. database website [4]
CIS-BPcollection of transcription factor binding sites models inferred by binding domains.database website [5]
CistromeMapa knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human. database website [6]
CTCFBSDBa database for CTCF binding sites and genome organization databasewebsite [7]
Factorbooka Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. database website [8]
hmChIPa database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data.database website [9]
HOCOMOCOa comprehensive collection of human and mouse transcription factor binding sites models.database website [10]
JASPARThe JASPAR CORE database contains a curated, non-redundant set of profiles, derived from published collections of experimentally defined transcription factor binding sites for eukaryotes.database website [11] [12]
MethMotifAn integrative cell-specific database of transcription factor binding motifs coupled with DNA methylation profiles.database website [13]
SwissRegulona database of genome-wide annotations of regulatory sites. database website [14]
TFLinkTFLink gateway provides comprehensive and highly accurate information on transcription factor - target gene interactions, nucleotide sequences and genomic locations of transcription factor binding sites for human and six model organisms.databasewebsite[15]
TRANSFACA long-standing curated database of regulatory sites, enhancers, binding site predictions, PSSMs and related analytical software. database website [16]

Notes and References

  1. Park PJ . ChIP-seq: advantages and challenges of a maturing technology . Nature Reviews. Genetics . 10 . 10 . 669–680 . October 2009 . 19736561 . 3191340 . 10.1038/nrg2641 .
  2. Farnham PJ . Insights from genomic profiling of transcription factors . Nature Reviews. Genetics . 10 . 9 . 605–616 . September 2009 . 19668247 . 2846386 . 10.1038/nrg2636 .
  3. Yang JH, Li JH, Jiang S, Zhou H, Qu LH . ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data . Nucleic Acids Research . 41 . Database issue . D177–D187 . January 2013 . 23161675 . 3531181 . 10.1093/nar/gks1060 .
  4. Lachmann A, Xu H, Krishnan J, Berger SI, Mazloom AR, Ma'ayan A . ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments . Bioinformatics . 26 . 19 . 2438–2444 . October 2010 . 20709693 . 2944209 . 10.1093/bioinformatics/btq466 .
  5. Weirauch MT, Yang A, Albu M, Cote AG, Montenegro-Montero A, Drewe P, Najafabadi HS, Lambert SA, Mann I, Cook K, Zheng H, Goity A, van Bakel H, Lozano JC, Galli M, Lewsey MG, Huang E, Mukherjee T, Chen X, Reece-Hoyes JS, Govindarajan S, Shaulsky G, Walhout AJ, Bouget FY, Ratsch G, Larrondo LF, Ecker JR, Hughes TR . 6 . Determination and inference of eukaryotic transcription factor sequence specificity . Cell . 158 . 6 . 1431–1443 . September 2014 . 25215497 . 4163041 . 10.1016/j.cell.2014.08.009 .
  6. Qin B, Zhou M, Ge Y, Taing L, Liu T, Wang Q, Wang S, Chen J, Shen L, Duan X, Hu S, Li W, Long H, Zhang Y, Liu XS . 6 . CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human . Bioinformatics . 28 . 10 . 1411–1412 . May 2012 . 22495751 . 3348563 . 10.1093/bioinformatics/bts157 .
  7. Ziebarth JD, Bhattacharya A, Cui Y . CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization . Nucleic Acids Research . 41 . Database issue . D188–D194 . January 2013 . 23193294 . 3531215 . 10.1093/nar/gks1165 .
  8. Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D, Birney E, Hung JH, Weng Z . 6 . Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium . Nucleic Acids Research . 41 . Database issue . D171–D176 . January 2013 . 23203885 . 3531197 . 10.1093/nar/gks1221 .
  9. Chen L, Wu G, Ji H . hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data . Bioinformatics . 27 . 10 . 1447–1448 . May 2011 . 21450710 . 3087956 . 10.1093/bioinformatics/btr156 .
  10. Kulakovskiy IV, Vorontsov IE, Yevshin IS, Soboleva AV, Kasianov AS, Ashoor H, Ba-Alawi W, Bajic VB, Medvedeva YA, Kolpakov FA, Makeev VJ . 6 . HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models . Nucleic Acids Research . 44 . D1 . D116–D125 . January 2016 . 26586801 . 4702883 . 10.1093/nar/gkv1249 .
  11. Sandelin A, Alkema W, Engström P, Wasserman WW, Lenhard B . JASPAR: an open-access database for eukaryotic transcription factor binding profiles . Nucleic Acids Research . 32 . Database issue . D91–D94 . January 2004 . 14681366 . 308747 . 10.1093/nar/gkh012 .
  12. Fornes O, Castro-Mondragon JA, Khan A, van der Lee R, Zhang X, Richmond PA, Modi BP, Correard S, Gheorghe M, Baranašić D, Santana-Garcia W, Tan G, Chèneby J, Ballester B, Parcy F, Sandelin A, Lenhard B, Wasserman WW, Mathelier A . 6 . JASPAR 2020: update of the open-access database of transcription factor binding profiles . Nucleic Acids Research . 48 . D1 . D87–D92 . January 2020 . 31701148 . 7145627 . 10.1093/nar/gkz1001 .
  13. Xuan Lin QX, Sian S, An O, Thieffry D, Jha S, Benoukraf T . MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles . Nucleic Acids Research . 47 . D1 . D145–D154 . January 2019 . 30380113 . 6323897 . 10.1093/nar/gky1005 . Touati Benoukraf .
  14. Pachkov M, Balwierz PJ, Arnold P, Ozonov E, van Nimwegen E . SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates . Nucleic Acids Research . 41 . Database issue . D214–D220 . January 2013 . 23180783 . 3531101 . 10.1093/nar/gks1145 .
  15. Liska O, Bohár B, Hidas A, Korcsmáros T, Papp B, Fazekas D, Ari E . TFLink: an integrated gateway to access transcription factor-target gene interactions for multiple species . Database . 2022 . September 2022 . 36124642 . 9480832 . 10.1093/database/baac083 .
  16. Kel A, Voss N, Jauregui R, Kel-Margoulis O, Wingender E . Beyond microarrays: find key transcription factors controlling signal transduction pathways . BMC Bioinformatics . 7 . Suppl 2 . S2–S13 . September 2006 . 17118134 . 1683568 . 10.1186/1471-2105-7-S2-S13 . free .

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