GOAtools protocols

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GOAtools computational protocol

GOAtools specifications

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Unique identifier OMICS_17943
Name GOAtools
Alternative name Gene Ontology Association tools
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data GO Association files, NCBI's gene2go GO association file.
Input format GAF
Operating system Unix/Linux
Programming languages Python
License BSD 2-clause “Simplified” License
Computer skills Advanced
Version 0.6.10
Stability Stable
Source code URL https://codeload.github.com/tanghaibao/goatools/tar.gz/v0.6.10
Maintained Yes

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Maintainer


  • person_outline Haibao Tang <>

Publication for Gene Ontology Association tools

GOAtools IN pipelines

 (6)
2017
PMCID: 5698048
PMID: 28371176
DOI: 10.1111/pbi.12737

[…] degs. a twofold difference in expression levels was set as the threshold for the determination of the significant changes. go functional enrichment and kegg pathway analysis were carried out with goatools (https://github.com/tanghaibao/goatools) and kobas (http://kobas.cbi.pku.edu.cn/home. do). all rna‐seq data were available in data s2 online., all experiments were repeated three times […]

2017
PMCID: 5698048
PMID: 28371176
DOI: 10.1111/pbi.12737

[…] levels was set as the threshold for the determination of the significant changes. go functional enrichment and kegg pathway analysis were carried out with goatools (https://github.com/tanghaibao/goatools) and kobas (http://kobas.cbi.pku.edu.cn/home. do). all rna‐seq data were available in data s2 online., all experiments were repeated three times independently, and all results […]

2016
PMCID: 5042791
PMID: 27509884
DOI: 10.3892/mmr.2016.5607

[…] expressed were further analyzed, as described in the results section. differentially expressed genes were classified according to their gene ontology (go; http://www.geneontology.org/), using goatools (https://github.com/tanghaibao/goatools). cellular pathway association was analyzed according to the kyoto encyclopedia of genes and genomes (kegg) database (http://www.genome.jp/kegg/) […]

2016
PMCID: 5042791
PMID: 27509884
DOI: 10.3892/mmr.2016.5607

[…] as described in the results section. differentially expressed genes were classified according to their gene ontology (go; http://www.geneontology.org/), using goatools (https://github.com/tanghaibao/goatools). cellular pathway association was analyzed according to the kyoto encyclopedia of genes and genomes (kegg) database (http://www.genome.jp/kegg/) using the kegg orthology based annotation […]

2016
PMCID: 5148802
PMID: 27920259
DOI: 10.1530/REP-16-0484

[…] using the cuffdiff module of the cufflinks package. the sequences were further annotated using the go and kegg databases. we categorized gene function with an emphasis on biochemical pathways. goatools was used for go enrichment analysis. kobas was used for kegg pathway enrichment analysis (xie et al. 2011) (example is shown in supplementary fig. 5). figure 2 , rna was extracted […]

GOAtools institution(s)
School of Biomedical Engineering, Science, and Health Systems, Drexel University, Philadelphia, PA, USA; Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China; Department of Human Genetics, University of Utah, Salt Lake City, UT, USA; Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany; Department of Genetics, Evolution and Environment, University College London, London, UK; Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; UC Berkeley - UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, CA, USA; Independent Researcher, Philadelphia, PA, USA; Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA; School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA, USA
GOAtools funding source(s)
Supported by the Fujian provincial government for a Fujian “100 Talent Plan” award.

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