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GTRD: An integrated view of transcription regulation. / Kolmykov, Semyon; Yevshin, Ivan; Kulyashov, Mikhail et al.

In: Nucleic Acids Research, Vol. 49, No. D1, 01.2021, p. D104-D111.

Research output: Contribution to journal › Review article › peer-review

Harvard

Kolmykov, S, Yevshin, I, Kulyashov, M, Sharipov, R, Kondrakhin, Y, Makeev, VJ, Kulakovskiy, IV, Kel, A & Kolpakov, F 2021, 'GTRD: An integrated view of transcription regulation', Nucleic Acids Research, vol. 49, no. D1, pp. D104-D111. https://doi.org/10.1093/nar/gkaa1057

APA

Kolmykov, S., Yevshin, I., Kulyashov, M., Sharipov, R., Kondrakhin, Y., Makeev, V. J., Kulakovskiy, I. V., Kel, A., & Kolpakov, F. (2021). GTRD: An integrated view of transcription regulation. Nucleic Acids Research, 49(D1), D104-D111. https://doi.org/10.1093/nar/gkaa1057

Vancouver

Kolmykov S, Yevshin I, Kulyashov M, Sharipov R, Kondrakhin Y, Makeev VJ et al. GTRD: An integrated view of transcription regulation. Nucleic Acids Research. 2021 Jan;49(D1):D104-D111. doi: 10.1093/nar/gkaa1057

Author

Kolmykov, Semyon ; Yevshin, Ivan ; Kulyashov, Mikhail et al. / GTRD: An integrated view of transcription regulation. In: Nucleic Acids Research. 2021 ; Vol. 49, No. D1. pp. D104-D111.

BibTeX

@article{3763e3ed3a8b413f8c442fb5255c4f1e,
title = "GTRD: An integrated view of transcription regulation",
abstract = "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.",
keywords = "Animals, Cell Line, Databases, Genetic, Drosophila melanogaster/genetics, Gene Expression Regulation, Gene Ontology, Genome, Humans, Internet, Mice, Molecular Sequence Annotation, Saccharomyces cerevisiae/genetics, Software, Transcription Factors/classification, Transcription, Genetic, OPEN CHROMATIN",
author = "Semyon Kolmykov and Ivan Yevshin and Mikhail Kulyashov and Ruslan Sharipov and Yury Kondrakhin and Makeev, {Vsevolod J.} and Kulakovskiy, {Ivan V.} and Alexander Kel and Fedor Kolpakov",
note = "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: {\textcopyright} The Author(s) 2020. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.",
year = "2021",
month = jan,
doi = "10.1093/nar/gkaa1057",
language = "English",
volume = "49",
pages = "D104--D111",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "D1",

}

RIS

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

UR - https://www.mendeley.com/catalogue/84436de6-bb4b-3832-b105-4f6e5dd35221/

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 -

ID: 27487928