Инд. авторы:	Yevshin I.S., Sharipov R.N., Valeev T., Kel A., Kolpakov F.
Заглавие:	GTRD: A database of transcription factor binding sites identified by ChIP-seq experiments
Библ. ссылка:	Yevshin I.S., Sharipov R.N., Valeev T., Kel A., Kolpakov F. GTRD: A database of transcription factor binding sites identified by ChIP-seq experiments // Nucleic Acids Research. - 2017. - Vol.45. - Iss. D1. - P.D61-D67. - ISSN 0305-1048. - EISSN 1362-4962.
Внешние системы:	DOI: 10.1093/nar/gkw951; РИНЦ: 29483744; SCOPUS: 2-s2.0-85016108719; WoS: 000396575500010;
Реферат:	eng: GTRD - Gene Transcription Regulation Database (http://gtrd.biouml.org) - is a database of transcription factor binding sites (TFBSs) identified by ChIPseq experiments for human and mouse. Raw ChIPseq data were obtained from ENCODE and SRA and uniformly processed: (i) reads were aligned using Bowtie2; (ii) ChIP-seq peaks were called using peak callers MACS, SISSRs, GEM and PICS; (iii) peaks for the same factor and peak callers, but different experiment conditions (cell line, treatment, etc.), were merged into clusters; (iv) such clusters for different peak callers were merged into metaclusters that were considered as non-redundant sets of TFBSs. In addition to information on location in genome, the sets contain structured information about cell lines and experimental conditions extracted from descriptions of corresponding ChIP-seq experiments. A web interface to access GTRD was developed using the BioUML platform. It provides: (i) browsing and displaying information; (ii) advanced search possibilities, e.g. search of TFBSs near the specified gene or search of all genes potentially regulated by a specified transcription factor; (iii) integrated genome browser that provides visualization of the GTRD data: read alignments, peaks, clusters, metaclusters and information about gene structures from the Ensembl database and binding sites predicted using position weight matrices from the HOCOMOCO database. © The Author(s) 2016.
Издано:	2017
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