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

(1) ChIPBase: a database for transcription factor binding maps and decoding the transcriptional regulation of protein-coding genes, lncRNAs and miRNAs from ChIP-Seq data. release date: 2013 January.
http://deepbase.sysu.edu.cn/chipbase/index.php

(2) ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. release date: 2010 Oct.
http://amp.pharm.mssm.edu/lib/chea.jsp

(3) CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human. release date: 2012 April.
http://cistrome.dfci.harvard.edu/pc/

(4) CTCFBSDB: a database for CTCF binding sites and genome organization. release date: 2013 January.
http://insulatordb.uthsc.edu

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

(6) hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data. release date: 2011 March.
http://jilab.biostat.jhsph.edu/database/cgi-bin/hmChIP.pl

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

(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.
http://jaspar.genereg.net

(9) SwissRegulon: a database of genome-wide annotations of regulatory sites. release date: 2013 January.
http://swissregulon.unibas.ch/fcgi/sr/swissregulon
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From:

http://www.protocol-online.org/forums/topic/31029-comprehensive-list-of-transcription-factor-binding-site-databases-based-on-chip-seq/

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