GTRD: An integrated view of transcription regulation

Semyon Kolmykov, Ivan Yevshin, Mikhail Kulyashov, Ruslan Sharipov, Yury Kondrakhin, Vsevolod J. Makeev, Ivan V. Kulakovskiy, Alexander Kel, Fedor Kolpakov

Research output: Contribution to journalReview articlepeer-review

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.

Original languageEnglish
Pages (from-to)D104-D111
Number of pages8
JournalNucleic Acids Research
Volume49
Issue numberD1
DOIs
Publication statusPublished - Jan 2021

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

Fingerprint Dive into the research topics of 'GTRD: An integrated view of transcription regulation'. Together they form a unique fingerprint.

Cite this