ATCOECIS pipeline

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

 (2)
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

[…] uniquely mapping reads were used for further analysis. differentially expressed genes were identified using the deseq package (anders and huber, 2010). analysis of go categories was performed using atcoecis (vandepoele et al., 2009) and revigo (rrid:scr_005825) (supek et al., 2011). to enrich for biologically relevant changes, probesets with signal log ratio (slr) > 0.6 were selected […]

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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