title: GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments.
abstract: 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.
authors.affiliation: BIOSOFT.RU, LLC, Novosibirsk 630058, Russian Federation.|Institute of Computational Technologies SB RAS, Novosibirsk 630090, Russian Federation.
authors.forename: Ivan
authors.initials: I
authors.lastname: Yevshin
authors.affiliation: BIOSOFT.RU, LLC, Novosibirsk 630058, Russian Federation.|Institute of Computational Technologies SB RAS, Novosibirsk 630090, Russian Federation.|Novosibirsk State University, Novosibirsk 630090, Russian Federation.
authors.forename: Ruslan
authors.identifier: 0000-0003-2182-5493
authors.initials: R
authors.lastname: Sharipov
authors.affiliation: BIOSOFT.RU, LLC, Novosibirsk 630058, Russian Federation.|A.P. Ershov Institute of Informatics Systems SB RAS, Novosibirsk 630090, Russian Federation.
authors.forename: Tagir
authors.initials: T
authors.lastname: Valeev
authors.affiliation: BIOSOFT.RU, LLC, Novosibirsk 630058, Russian Federation.|Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russian Federation.
authors.forename: Alexander
authors.initials: A
authors.lastname: Kel
authors.affiliation: BIOSOFT.RU, LLC, Novosibirsk 630058, Russian Federation fedor@biouml.org.|Institute of Computational Technologies SB RAS, Novosibirsk 630090, Russian Federation.
authors.forename: Fedor
authors.initials: F
authors.lastname: Kolpakov
mesh_terms: D000818:Animals; D001665:Binding Sites; D002460:Cell Line; D030541:Databases, Genetic; D006801:Humans; D047468:Immunoprecipitation; D051379:Mice; D050436:Regulatory Elements, Transcriptional; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors