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GeneCAT specifications

Information


Unique identifier OMICS_11669
Name GeneCAT
Alternative name Gene Co-expression Analysis Toolbox
Interface Web user interface
Restrictions to use None
Programming languages Python
Computer skills Basic
Stability No
Maintained No

Taxon


  • Plants and Fungi
    • Arabidopsis thaliana
    • Hordeum vulgare

Maintainer


This tool is not available anymore.

Publication for Gene Co-expression Analysis Toolbox

GeneCAT citations

 (9)
library_books

Glycosylation of a Fasciclin Like Arabinogalactan Protein (SOS5) Mediates Root Growth and Seed Mucilage Adherence via a Cell Wall Receptor Like Kinase (FEI1/FEI2) Pathway in Arabidopsis

2016
PLoS One
PMCID: 4701510
PMID: 26731606
DOI: 10.1371/journal.pone.0145092

[…] ved expression patterns were similar to that observed for SOS5, CESA5, FEI1, FEI2, GALT2 and GALT5 using microarray analysis of seed coat development []. Furthermore, co-expression analysis using the GeneCAT tool (http://genecat.mpg.de) indicated expression of FEI1 and FEI2 is tightly correlated with the expression of AGP-specific glycosyltransferases as well as numerous candidate AGPs () []. Coll […]

library_books

Two Hydroxyproline Galactosyltransferases, GALT5 and GALT2, Function in Arabinogalactan Protein Glycosylation, Growth and Development in Arabidopsis

2015
PLoS One
PMCID: 4431829
PMID: 25974423
DOI: 10.1371/journal.pone.0125624

[…] ed in root and stem, whereas GALT5 was highly expressed in stem, root and leaf. These findings are consistent with data from publicly available expression databases (). Transcriptomics analysis using GeneCAT (http://genecat.mpg.de) [], Genevestigator (http://www.genevestigator.com/gv/) [] and the Arabidopsis eFP browser (http://bar.utoronto.ca/efp/cgi-bin/efpWeb.cgi) [] indicate both genes are wid […]

library_books

Lignin, mitochondrial family, and photorespiratory transporter classification as case studies in using co expression, co response, and protein locations to aid in identifying transport functions

2014
Front Plant Sci
PMCID: 3955873
PMID: 24672529
DOI: 10.3389/fpls.2014.00075

[…] mmalian (; ; ; ; ; ; ), and plant research (; ; ). For plant research several web-based tools including ATTED-II (; ), AraNet (), Expression Angler of the Bio-Array resource [BAR; (], KappaViewer (), GeneCAT (), Genevestigator (), and VirtualPlant () simplify this task yet further. One of the strongest demonstrations of the power of this technique in plants comes from its early utility in the iden […]

library_books

Analysis of the role of Arabidopsis class I TCP genes AtTCP7, AtTCP8, AtTCP22, and AtTCP23 in leaf development

2013
Front Plant Sci
PMCID: 3797442
PMID: 24137171
DOI: 10.3389/fpls.2013.00406

[…] detected in inflorescences and mature leaves (Figure ). Expression data from Genevestigator (Hruz et al., ), the Arabidopsis eFP browser at BAR (Winter et al., ), AtGenExpress (Schmid et al., ), and GeneCAT (Mutwil et al., ) supports our RT-PCR analysis for AtTCP8, AtTCP14, AtTCP15, AtTCP21, and AtTCP23, while for AtTCP7 and AtTCP22 there is no expression data yet available in these resources. Is […]

library_books

Brittle Culm1, a COBRA Like Protein, Functions in Cellulose Assembly through Binding Cellulose Microfibrils

2013
PLoS Genet
PMCID: 3749933
PMID: 23990797
DOI: 10.1371/journal.pgen.1003704

[…] ClustalW2 (www.ebi.ac.uk/Tools/msa/clustalw2). Sequence logo of the BC1's CBM was generated with Weblogo3 (http://weblogo.berkeley.edu/). Coexpression network of BC1 was analyzed with GenCAT (http://genecat.mpg.de) and the expression profiles of BC1 and SCW CESAs were generated based on the data obtained from RiceGE (http://signal.salk.edu/cgi-bin/RiceGE). […]

call_split

The Arabidopsis LRR RLK, PXC1, is a regulator of secondary wall formation correlated with the TDIF PXY/TDR WOX4 signaling pathway

2013
BMC Plant Biol
PMCID: 3716795
PMID: 23815750
DOI: 10.1186/1471-2229-13-94
call_split See protocol

[…] ted AtLRR-RLK genes using the Arabidopsis Affymetrix GeneChip® average data available on the GENEVESTIGATOR analysis tool site (http://www.genevestigator.ethz.ch) []. The Gene Co-expression Analysis (GeneCAT) Toolbox at http://genecat.mpg.de/cgi-bin/Ainitiator.py[] was used to generate the Expression Tree which clustered genes by the similarity of their expression profiles and visualized those sim […]

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GeneCAT institution(s)
Department of Molecular Biology, University of Copenhagen, Copenhagen, Denmark; Max-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
GeneCAT funding source(s)
The Max-Planck Society

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