ATCOECIS statistics

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Citations per year

Number of citations per year for the bioinformatics software tool ATCOECIS
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Tool usage distribution map

This map represents all the scientific publications referring to ATCOECIS per scientific context
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Associated diseases

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Popular tool citations

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ATCOECIS specifications

Information


Unique identifier OMICS_11677
Name ATCOECIS
Interface Web user interface
Restrictions to use None
Input data A GO category of interest or from a user-defined gene set
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Plants and Fungi
    • Arabidopsis thaliana

Maintainer


  • person_outline Klaas Vandepoele

Publication for ATCOECIS

ATCOECIS citations

 (5)
library_books

RNA Seq and Gene Network Analysis Uncover Activation of an ABA Dependent Signalosome During the Cork Oak Root Response to Drought

2016
Front Plant Sci
PMCID: 4707443
PMID: 26793200
DOI: 10.3389/fpls.2015.01195

[…] entified from Arabidopsis DEG orthologs using the AGRIS Arabidopsis TF database (AtTFDB; ), MapMan (transcripton pathway bin; ), and manual curation. Cis-element enrichment analysis was carried using AtCOECis () and Athena (), with default parameters. Gene networks were predicted in Cytoscape, using the Genemania App (; ) (Supplementary Methods ). Phylogenetic reconstruction was carried out by max […]

library_books

Auxin production in the endosperm drives seed coat development in Arabidopsis

2016
eLife
PMCID: 5135394
PMID: 27848912
DOI: 10.7554/eLife.20542.028

[…] e selected by overlapping the list of significantly upregulated genes in 2 DAP seeds and in vrn2 emf2 ovules. The list of commonly upregulated genes was then used to determine enriched GO-terms using AtCOECIS. Only significantly enriched biological processes were considered (p-value<0.05). REVIGO was used to remove redundant GO terms and summarize the list. For the transcriptome analysis of agl62 […]

library_books

Non reciprocal Interspecies Hybridization Barriers in the Capsella Genus Are Established in the Endosperm

2015
PLoS Genet
PMCID: 4472357
PMID: 26086217
DOI: 10.1371/journal.pgen.1005295

[…] aving a homologue in the other species were kept. The significance of the overlap between deregulated genes was estimated using a hypergeometric test. Enrichment of GO categories was determined using ATCOECIS []. Homologues of A. thaliana type I AGLs were identified in the C. rubella genome according to the Phytozome C. rubella v1.0 genome annotation. A. thaliana type I AGLs were determined as in […]

library_books

The Nuclear Immune Receptor RPS4 Is Required for RRS1SLH1 Dependent Constitutive Defense Activation in Arabidopsis thaliana

2014
PLoS Genet
PMCID: 4207616
PMID: 25340333
DOI: 10.1371/journal.pgen.1004655

[…] . In total, 719 genes were differentially expressed in an RRS1- and acetyltransferase activity-dependent manner in at least one of the time points surveyed (). Gene ontology enrichment analysis using ATCOECIS showed that most of the up-regulated genes are involved in defense, while most of the down-regulated genes are involved in photosynthesis and enriched in chloroplast-localized genes (). Inte […]

library_books

Transcriptional programming during cell wall maturation in the expanding Arabidopsis stem

2013
BMC Plant Biol
PMCID: 3635874
PMID: 23350960
DOI: 10.1186/1471-2229-13-14

[…] regulated genes, their annotations, gene ontology (GO) assignments and possible promoter motif enrichment were examined. GO term enrichment was determined relative to whole-genome averages using the ‘AtCoeCis’ web-tool [], which reports enrichment (fold-change), statistical significance (p-value), and the proportion of the genes in each short-list that have been assigned that specific GO term ('sc […]


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ATCOECIS institution(s)
Department of Plant Systems Biology, Flanders Institute for Biotechnology, Ghent, Belgium; Department of Plant Biotechnology and Genetics, Ghent University, Ghent, Belgium
ATCOECIS funding source(s)
The Interuniversity Attraction Poles Programme (IUAP VI/25 and VI/33), initiated by the Belgian State, Science Policy Office; postdoctoral fellows of the Research Foundation-Flanders

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