TY - JOUR
T1 - GTRD: An integrated view of transcription regulation
AU - Kolmykov, Semyon
AU - Yevshin, Ivan
AU - Kulyashov, Mikhail
AU - Sharipov, Ruslan
AU - Kondrakhin, Yury
AU - Makeev, Vsevolod J.
AU - Kulakovskiy, Ivan V.
AU - Kel, Alexander
AU - Kolpakov, Fedor
N1 - Funding Information:
Russian Science Foundation [19-14-00295 to S.K., I.Y., M.K, R.Sh., Y.K., F.K.]; ASB identification was supported by the Russian Science Foundation [20-74-10075 to I.V.K.]; V.J.M. was supported by the Ministry of Science and Higher Education of the Russian Federation [075-15-2019-1658]. Funding for open access charge: Russian Science Foundation [19-14-00295 to F.K.]. Conflict of interest statement. None declared.
Publisher Copyright:
© The Author(s) 2020.
Copyright:
Copyright 2021 Elsevier B.V., All rights reserved.
PY - 2021/1
Y1 - 2021/1
N2 - The Gene Transcription Regulation Database (GTRD; http://gtrd.biouml.org/) contains uniformly annotated and processed NGS data related to gene transcription regulation: ChIP-seq, ChIP-exo, DNase-seq, MNase-seq, ATAC-seq and RNA-seq. With the latest release, the database has reached a new level of data integration. All cell types (cell lines and tissues) presented in the GTRD were arranged into a dictionary and linked with different ontologies (BRENDA, Cell Ontology, Uberon, Cellosaurus and Experimental Factor Ontology) and with related experiments in specialized databases on transcription regulation (FANTOM5, ENCODE and GTEx). The updated version of the GTRD provides an integrated view of transcription regulation through a dedicated web interface with advanced browsing and search capabilities, an integrated genome browser, and table reports by cell types, transcription factors, and genes of interest.
AB - The Gene Transcription Regulation Database (GTRD; http://gtrd.biouml.org/) contains uniformly annotated and processed NGS data related to gene transcription regulation: ChIP-seq, ChIP-exo, DNase-seq, MNase-seq, ATAC-seq and RNA-seq. With the latest release, the database has reached a new level of data integration. All cell types (cell lines and tissues) presented in the GTRD were arranged into a dictionary and linked with different ontologies (BRENDA, Cell Ontology, Uberon, Cellosaurus and Experimental Factor Ontology) and with related experiments in specialized databases on transcription regulation (FANTOM5, ENCODE and GTEx). The updated version of the GTRD provides an integrated view of transcription regulation through a dedicated web interface with advanced browsing and search capabilities, an integrated genome browser, and table reports by cell types, transcription factors, and genes of interest.
KW - Animals
KW - Cell Line
KW - Databases, Genetic
KW - Drosophila melanogaster/genetics
KW - Gene Expression Regulation
KW - Gene Ontology
KW - Genome
KW - Humans
KW - Internet
KW - Mice
KW - Molecular Sequence Annotation
KW - Saccharomyces cerevisiae/genetics
KW - Software
KW - Transcription Factors/classification
KW - Transcription, Genetic
KW - OPEN CHROMATIN
UR - http://www.scopus.com/inward/record.url?scp=85099406329&partnerID=8YFLogxK
U2 - 10.1093/nar/gkaa1057
DO - 10.1093/nar/gkaa1057
M3 - Review article
C2 - 33231677
AN - SCOPUS:85099406329
VL - 49
SP - D104-D111
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - D1
ER -