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Database Commons - GTRD

GTRD

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Short name GTRD
Full name Gene Transcription Regulation Database
Description a database of transcription factor binding sites (TFBSs) identified by ChIP-seq experiments for human and mouse. Raw ChIP-seq data were obtained from ENCODE and SRA and uniformly processed. A web interface to access GTRD was developed using the BioUML platform
URL http://gtrd.biouml.org/
Year founded 2016
Last update & version 2016-08-26    v 16.07
Availability Free to all users
University/Institution hosted Institute of Computational Technologies Siberian Branch of the Russian Academy of Sciences (SB RAS)
Address
City Novosibirsk
Province/State Novosibirskaya Oblast
Country/Region Russian Federation
Contact name Fedor Kolpakov
Contact email fedor@biouml.org
Data type(s)
Major organism(s)
Keyword(s)
  • transcription factor binding site
Publication(s)
  • GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments. [PMID: 27924024]

    Ivan Yevshin, Ruslan Sharipov, Tagir Valeev, Alexander Kel, Fedor Kolpakov
    Nucleic acids research 2017:45(D1)
    0 Citations (Google Scholar as of 2017-02-08)

    Abstract: GTRD-Gene Transcription Regulation Database (http://gtrd.biouml.org)-is a database of transcription factor binding sites (TFBSs) identified by ChIP-seq experiments for human and mouse. Raw ChIP-seq data were obtained from ENCODE and SRA and uniformly processed: (i) reads were aligned using Bowtie2; (ii) ChIP-seq peaks were called using peak callers MACS, SISSRs, GEM and PICS; (iii) peaks for the same factor and peak callers, but different experiment conditions (cell line, treatment, etc.), were merged into clusters; (iv) such clusters for different peak callers were merged into metaclusters that were considered as non-redundant sets of TFBSs. In addition to information on location in genome, the sets contain structured information about cell lines and experimental conditions extracted from descriptions of corresponding ChIP-seq experiments. A web interface to access GTRD was developed using the BioUML platform. It provides: (i) browsing and displaying information; (ii) advanced search possibilities, e.g. search of TFBSs near the specified gene or search of all genes potentially regulated by a specified transcription factor; (iii) integrated genome browser that provides visualization of the GTRD data: read alignments, peaks, clusters, metaclusters and information about gene structures from the Ensembl database and binding sites predicted using position weight matrices from the HOCOMOCO database. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Accessibility

Rate of accessibility:
HTTP status codeDate requested
200 OK2018-11-16
200 OK2018-11-13
200 OK2018-11-09
200 OK2018-11-06
200 OK2018-11-02
200 OK2018-10-30
200 OK2018-10-26
200 OK2018-10-23
200 OK2018-10-19
200 OK2018-10-16
200 OK2018-10-12
200 OK2018-10-09
200 OK2018-10-05
200 OK2018-10-02
200 OK2018-09-28
200 OK2018-09-25
200 OK2018-09-21
200 OK2018-09-18
200 OK2018-09-14
200 OK2018-09-11
200 OK2018-09-07
-1 Failed2018-09-04
200 OK2018-08-31
200 OK2018-08-28
200 OK2018-08-24
200 OK2018-08-21
200 OK2018-08-17
200 OK2018-08-14
200 OK2018-08-10
200 OK2018-08-07
200 OK2018-08-03
200 OK2018-07-31
200 OK2018-07-27
200 OK2018-07-24
200 OK2018-07-20
200 OK2018-07-17
200 OK2018-07-13
200 OK2018-07-10
200 OK2018-07-06
200 OK2018-07-03
200 OK2018-06-29
200 OK2018-06-26
200 OK2018-06-22
200 OK2018-06-19
200 OK2018-06-15
200 OK2018-06-12
200 OK2018-06-08
200 OK2018-06-05
200 OK2018-06-01
200 OK2018-05-29
200 OK2018-05-25
200 OK2018-05-22
200 OK2018-05-18
200 OK2018-05-15
200 OK2018-05-11
200 OK2018-05-08
200 OK2018-05-04
200 OK2018-05-01
200 OK2018-04-27
200 OK2018-04-24
200 OK2018-04-20
200 OK2018-04-17
200 OK2018-04-13
200 OK2018-04-10
200 OK2018-04-06
200 OK2018-04-03
200 OK2018-02-27
200 OK2018-02-23
200 OK2018-02-20
200 OK2018-02-16
200 OK2018-02-13
200 OK2018-02-09
200 OK2018-02-06
200 OK2018-02-02
200 OK2018-01-30
200 OK2018-01-26
200 OK2018-01-23
200 OK2018-01-19
200 OK2018-01-16
200 OK2018-01-12
200 OK2018-01-09
200 OK2018-01-05
200 OK2018-01-02
200 OK2017-12-29
200 OK2017-12-26
200 OK2017-12-22
200 OK2017-12-19
200 OK2017-12-15
200 OK2017-12-12
200 OK2017-12-08
200 OK2017-12-05
200 OK2017-12-01
200 OK2017-11-28
200 OK2017-11-24
200 OK2017-11-21
200 OK2017-11-17
200 OK2017-11-14
200 OK2017-11-10
200 OK2017-11-07
200 OK2017-11-03
200 OK2017-10-31
200 OK2017-10-27
200 OK2017-10-24
200 OK2017-10-20
200 OK2017-10-17
200 OK2017-10-13
200 OK2017-10-10
200 OK2017-10-06
200 OK2017-10-03
200 OK2017-09-29
200 OK2017-09-26
200 OK2017-09-22
200 OK2017-09-19
200 OK2017-09-15
200 OK2017-09-12
200 OK2017-09-08
200 OK2017-09-05
200 OK2017-09-01
200 OK2017-08-29
200 OK2017-08-25
200 OK2017-08-22
200 OK2017-08-18
200 OK2017-08-15
200 OK2017-08-11
200 OK2017-08-08
200 OK2017-08-04
200 OK2017-08-01
200 OK2017-07-28
200 OK2017-07-25
200 OK2017-07-21
200 OK2017-07-18
200 OK2017-07-14
200 OK2017-07-04
200 OK2017-06-30
200 OK2017-06-27
200 OK2017-06-23
200 OK2017-06-20
200 OK2017-06-16
200 OK2017-06-13
200 OK2017-06-09
200 OK2017-06-06
200 OK2017-06-02
200 OK2017-05-30
200 OK2017-05-26
200 OK2017-05-23
200 OK2017-05-19
200 OK2017-05-16
200 OK2017-05-12
200 OK2017-05-09
200 OK2017-05-05
200 OK2017-05-02
200 OK2017-04-28
200 OK2017-04-25
200 OK2017-04-21
200 OK2017-04-18
200 OK2017-04-14
200 OK2017-04-11
200 OK2017-04-07
200 OK2017-04-04
200 OK2017-03-31
200 OK2017-03-28
200 OK2017-03-24
200 OK2017-03-21
200 OK2017-03-17
200 OK2017-03-14
200 OK2017-03-10
200 OK2017-03-07
200 OK2017-03-03
200 OK2017-02-28
200 OK2017-02-24
200 OK2017-02-21
200 OK2017-02-17
200 OK2017-02-14
200 OK2017-02-10

Tags

DNA Interaction and Network
Homo sapiens Mus musculus
transcription factor binding site

Record metadata

  • Created on: 2017-02-08
  • Curated by:
    • Shixiang Sun [2017-02-08]
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