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. 2021 Jan 8;49(D1):D104-D111.
doi: 10.1093/nar/gkaa1057.

GTRD: an integrated view of transcription regulation

Semyon Kolmykov  1   2   3 , Ivan Yevshin  1   2 , Mikhail Kulyashov  1   2   4 , Ruslan Sharipov  1   2   4 , Yury Kondrakhin  1   2 , Vsevolod J Makeev  5   6   7   8 , Ivan V Kulakovskiy  5   8   9 , Alexander Kel  1   10   11 , Fedor Kolpakov  1   2
Affiliations

GTRD: an integrated view of transcription regulation

Semyon Kolmykov et al. Nucleic Acids Res. .

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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Figures

Figure 1.
Figure 1.
Current workflow for uniform annotation and analysis of experimental data in the GTRD. New data and tools added in the most recent version compared to the previous publication are highlighted in red. DEGs – differentially expressed genes.
Figure 2.
Figure 2.
Example of a summary report and an overview of data for a selected cell type.
Figure 3.
Figure 3.
Visualization of GTRD tracks in the UCSC genome browser.
Figure 4.
Figure 4.
GTRD – integrated view of transcription regulation.
See this image and copyright information in PMC

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