ATCOECIS statistics

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Citations per year

Number of citations per year for the bioinformatics software tool ATCOECIS

Tool usage distribution map

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


Unique identifier OMICS_11677
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


  • Plants and Fungi
    • Arabidopsis thaliana


  • person_outline Klaas Vandepoele

Publication for ATCOECIS

ATCOECIS citations


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

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 […]


Auxin production in the endosperm drives seed coat development in Arabidopsis

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 […]


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

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 […]


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

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 […]


Transcriptional programming during cell wall maturation in the expanding Arabidopsis stem

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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