GTRD: an integrated view of transcription regulation-Reference-Cited by-同舟云学术

GTRD: an integrated view of transcription regulation

Published:2020-11-24 Issue:D1 Volume:49 Page:D104-D111
ISSN:0305-1048
Container-title:Nucleic Acids Research
language:en
Short-container-title:

Author:

Kolmykov Semyon¹²³,Yevshin Ivan¹²,Kulyashov Mikhail¹²⁴,Sharipov Ruslan¹²⁴^ORCID,Kondrakhin Yury¹²,Makeev Vsevolod J⁵⁶⁷⁸,Kulakovskiy Ivan V⁵⁸⁹,Kel Alexander¹¹⁰¹¹,Kolpakov Fedor¹²

Affiliation:

1. BIOSOFT.RU, LLC, Novosibirsk 630090, Russian Federation

2. Federal Research Center for Information and Computational Technologies, Novosibirsk 630090, Russian Federation

3. Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russian Federation

4. Novosibirsk State University, Novosibirsk 630090, Russian Federation

5. Vavilov Institute of General Genetics RAS, Moscow 119991, Russian Federation

6. Moscow Institute of Physics and Technology (State University), Dolgoprudny 141700, Russian Federation

7. NRC «Kurchatov Institute» - GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow 123182, Russian Federation

8. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russian Federation

9. Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russian Federation

10. geneXplain GmbH, 38302 Wolfenbüttel, Germany

11. Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russian Federation

Abstract

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.

Funder

Russian Science Foundation

Ministry of Science and Higher Education of the Russian Federation

Publisher

Oxford University Press (OUP)

Subject

Genetics

Link

http://academic.oup.com/nar/article-pdf/49/D1/D104/35364856/gkaa1057.pdf

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