GRG-X statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

GRG-X specifications

Information


Unique identifier OMICS_15024
Name GRG-X
Alternative name AtRegNet
Interface Web user interface
Restrictions to use None
Input data A network.
Input format GRAPHML, XGMML,SIF
Output format PNG,SVG,PDF,XGMML,GRAPHML,SIF
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Plants and Fungi
    • Arabidopsis thaliana
    • Oryza sativa
    • Zea mays

Maintainer


  • person_outline Wen-Chi Chang

Additional information


http://agris-knowledgebase.org/grgx/help.html

Publication for GRG-X

GRG-X citations

 (4)
library_books

Genome wide identification of transcription factors and transcription factor binding sites in oleaginous microalgae Nannochloropsis

2014
Sci Rep
PMCID: 5154493
PMID: 24965723
DOI: 10.1038/srep05454

[…] vely correlated and 1,071 negatively correlated (, ).We next compared our network with those connections between the TFs and their target genes in the Arabidopsis thaliana regulatory network database AtRegNet (Methods). As the result, 76 connections in the IMET1 network were supported by AtRegNet, with 11 of them supported by the “confirmed” connections in AtRegNet ().There are on average 68 gene […]

library_books

Network component analysis provides quantitative insights on an Arabidopsis transcription factor gene regulatory network

2013
BMC Syst Biol
PMCID: 3843564
PMID: 24228871
DOI: 10.1186/1752-0509-7-126

[…] ut the regulatory aspects of a system given the basic structural information about the underlying network. In the case of plants, there is lesser information available about TF-gene interactions. The AtRegNet database from AGRIS, which is the most comprehensive resource for such information, contains 768 confirmed TF-gene interactions for 46 TFs in A. thaliana, which is estimated to contain more t […]

library_books

Genome scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes

2013
BMC Genomics
PMCID: 3829657
PMID: 24148294
DOI: 10.1186/1471-2164-14-722

[…] iterature. There were 59 TFs reported as associated to cold responses in GO (Gene Ontology) database and TAIR (The Arabidopsis Information Resources). Unfortunately, none of them were included in the AtRegNet server which contained experimentally validated regulatory interactions for only 69 out of nearly 1922 known Arabidopsis TFs.Nimblgen12-plex Arabidopsis microarray chip included 3822 transpos […]

library_books

Temporal transcriptional response to ethylene gas drives growth hormone cross regulation in Arabidopsis

2013
eLife
PMCID: 3679525
PMID: 23795294
DOI: 10.7554/eLife.00675.022

[…] e TFs that can explain them. This allows us to assign a time of activation to static TF-gene interactions data. To obtain the static interaction data we extracted 11,355 TF-gene interactions from the AtRegNet AGRIS database (). In addition, for this work we have extended DREM so that it can utilize temporal EIN3 binding profiles as well as allowing us to identify functional binding events (those w […]

Citations

Looking to check out a full list of citations?

GRG-X institution(s)
Human Cancer Genetics Program, Comprehensive Cancer Center, Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH, USA; Department of Plant Cellular and Molecular Biology, The Ohio State University, Columbus, OH, USA, Plant Biotechnology Center, The Ohio State University, Columbus, OH, USA
GRG-X funding source(s)
Supported by the National Science Foundation (grant no. MCB–0418891).

GRG-X reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review GRG-X