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Old 02-14-2013, 09:43 PM   #1
yjhua2110
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Default Comprehensive List of transcription factor binding site databases based on ChIP-Seq

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 ~10,200 curated peak datasets derived from ChIP-seq methods 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.

Last edited by yjhua2110; 10-15-2016 at 05:47 PM.
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Old 04-29-2013, 06:48 PM   #2
DanWebster
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Thank you for posting this very useful collection!
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Old 11-12-2013, 09:01 PM   #3
rnaNGS
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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
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Old 01-26-2014, 10:11 PM   #4
emp
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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...
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Old 10-15-2016, 05:51 PM   #5
yjhua2110
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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).
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