Research output: Contribution to journal › Article › peer-review
GTRD : A database of transcription factor binding sites identified by ChIP-seq experiments. / Yevshin, Ivan; Sharipov, Ruslan; Valeev, Tagir et al.
In: Nucleic Acids Research, Vol. 45, No. D1, 04.01.2017, p. D61-D67.Research output: Contribution to journal › Article › peer-review
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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 -
ID: 12693619