TY - JOUR

T1 - GTRD

T2 - A database of transcription factor binding sites identified by ChIP-seq experiments

AU - Yevshin, Ivan

AU - Sharipov, Ruslan

AU - Valeev, Tagir

AU - Kel, Alexander

AU - Kolpakov, Fedor

N1 - © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

PY - 2017/1/4

Y1 - 2017/1/4

N2 - 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.

AB - 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.

KW - Animals

KW - Binding Sites

KW - Cell Line

KW - Databases, Genetic

KW - Humans

KW - Immunoprecipitation

KW - Mice

KW - Regulatory Elements, Transcriptional

KW - Sequence Analysis, DNA

KW - Transcription Factors/metabolism

KW - PROTEIN-DNA INTERACTIONS

KW - RESOLUTION

KW - GENOME

KW - ARCHIVE

KW - RECEPTOR GENE

UR - http://www.scopus.com/inward/record.url?scp=85016108719&partnerID=8YFLogxK

U2 - 10.1093/nar/gkw951

DO - 10.1093/nar/gkw951

M3 - Article

C2 - 27924024

AN - SCOPUS:85016108719

VL - 45

SP - D61-D67

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - D1

ER -