GTRD: an integrated view of transcription regulation

Semyon Kolmykov(Institute of Cytology and Genetics), Ivan Yevshin(Federal Research Center for Information and Computational Technologies), Mikhail A. Kulyashov(Novosibirsk State University), Ruslan Sharipov(Novosibirsk State University), Yury V. Kondrakhin(Federal Research Center for Information and Computational Technologies), Vsevolod J. Makeev(Engelhardt Institute of Molecular Biology), Ivan V. Kulakovskiy(Engelhardt Institute of Molecular Biology), Alexander Kel(Institute of Chemical Biology and Fundamental Medicine), Fedor Kolpakov(Federal Research Center for Information and Computational Technologies)
Nucleic Acids Research
November 3, 2020
10.1093/nar/gkaa1057
Cited by 297Open Access
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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.

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