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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.

SUBMITTER: Kolmykov S

PROVIDER: S-EPMC7778956 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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GTRD: an integrated view of transcription regulation.

Kolmykov Semyon S Yevshin Ivan I Kulyashov Mikhail M Sharipov Ruslan R Kondrakhin Yury Y Makeev Vsevolod J VJ Kulakovskiy Ivan V IV Kel Alexander A Kolpakov Fedor F

Nucleic acids research 20210101 D1

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 Exper ...[more]

PMID: 33231677

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