期刊
NUCLEIC ACIDS RESEARCH
卷 45, 期 D1, 页码 D61-D67出版社
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkw951
关键词
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资金
- Targeted Program 'Research and development on priority directions of science and technology in Russia [14.604.21.0101, 2014-14-576-0109, RFMEFI60414X0101]
- Skolkovo Foundation [G73/15]
- BIOSOFT.RU, LLC
GTRD-Gene Transcription Regulation Database (http://gtrd.biouml.org)-is a database of transcription factor binding sites (TFBSs) identified by ChIP-seq experiments for human and mouse. Raw ChIP-seq 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.
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