ATCOECIS protocols

View ATCOECIS computational protocol

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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 in pipelines

 (3)
2016
PMCID: 5135394
PMID: 27848912
DOI: 10.7554/eLife.20542.028

[…] 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 […]

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

[…] (). only uniquely mapping reads were used for further analysis. differentially expressed genes were identified using the deseq package (). analysis of go categories was performed using atcoecis () and revigo (rrid:scr_005825) (). to enrich for biologically relevant changes, probesets with signal log ratio (slr) > 0.6 were selected for the transcriptome analysis of vrn2/- emf2/+ […]

2013
PMCID: 3893512
PMID: 24168327
DOI: 10.1186/1471-2229-13-170

[…] expressed genes were conducted using the following web-based tools; the classification superviewer (the bar; http://bar.utoronto.ca/ntools/cgi-bin/ntools_classification_superviewer.cgi), atcoecis (http://bioinformatics.psb.ugent.be/atcoecis), and athena (http://www.bioinformatics2.wsu.edu/cgi-bin/athena/cgi/analysis_select.pl). to compare expression levels of the wild-type […]


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ATCOECIS in publications

 (11)
PMCID: 4707443
PMID: 26793200
DOI: 10.3389/fpls.2015.01195

[…] 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 […]

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

[…] 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 […]

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

[…] 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 […]

PMCID: 4589659
PMID: 26344545
DOI: 10.7554/eLife.10074.020

[…] run with 100 permutations and gene selection was corrected for multiple comparison errors using a pfp (percentage of false prediction) < 0.05. gene ontology (go) categories were identified using atcoecis ()., to determine the imprinting status of selected genes, rna was extracted from crosses col x col, ler x ler, ler x col and ler x osd1 at 4 dap. primers used for allele specific expression […]

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 (). […]


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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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