Comprehensive List of transcription factor binding site databases based on ChIP-Seq

[yjhua2110]

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

(1) ChIPBase: a database for Transcription Factor Binding Sites, Motifs and Profiles from ~10200 ChIP-seq and ~20000 RNA-seq tumor and normal samples, and It also decoding the transcriptional regulation of protein-coding genes, lncRNAs and miRNAs in 10 species. release date: 2016 October.

(2) ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. release date: 2010 Oct.

(3) CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human. release date: 2012 April.

(4) CTCFBSDB: a database for CTCF binding sites and genome organization. release date: 2013 January.

(5) Factorbook: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. release date: 2013 January.

(6) hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data. release date: 2011 March.

(7) HOCOMOCO: a comprehensive collection of human transcription factor binding sites models. release date: 2013 January.

(8) JASPAR 2010: The JASPAR CORE database contains a curated, non-redundant set of profiles, derived from published collections of experimentally defined transcription factor binding sites for eukaryotes. release date: 2010 January.

(9) SwissRegulon: a database of genome-wide annotations of regulatory sites. release date: 2013 January.

[DanWebster]

Thank you for posting this very useful collection!

[rnaNGS]

two new databases
(1) TFBSshape (http://rohslab.cmb.usc.edu/TFBSshape/): a motif database for DNA shape features of transcription factor binding sites.
(2) BloodChIP (http://www.med.unsw.edu.au/CRCWeb.nsf/page/BloodChIP): a database of comparative genome-wide transcription factor binding profiles in human blood cells

[emp]

Respected yjhua2110,

Can u pls provide me help for one of my problem.

I have find the Transcription Binding sites for Oryza sativa. For the same I have few 1000 ID's of the genes.

If possible kindly suggest some database which can accept gene IDs and give the transcription factors for the same.
Thnkq in advance...

[yjhua2110]

ChIPBase (http://rna.sysu.edu.cn/chipbase/) has been updated to discover transcription factor binding motifs, profiles and targets (lncRNAs, miRNAs, proteins, snoRNAs, tRNAs, pseudogenes...) from ~10,200 curated peak datasets derived from ChIP-seq methods in 10 species(Human, Mouse, Fruitfly, Worm, A. Thaliana, Yeast, Rat, Zebrafish, X. tropicalis, Chicken).

[yjhua2110]

Respected yjhua2110,

Can u pls provide me help for one of my problem.

I have find the Transcription Binding sites for Oryza sativa. For the same I have few 1000 ID's of the genes.

If possible kindly suggest some database which can accept gene IDs and give the transcription factors for the same.
Thnkq in advance...

You can try Ensembl Plants database: https://plants.ensembl.org/index.html

[rnaNGS]

TransmiR is a transcription factor-microRNA regulation database.
TransmiR v2.0 has been published in the Nucleic Acids Research Database Issue.