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GOAtools specifications

Information


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

 (18)
2018
PMCID: 5815590
PMID: 29451882
DOI: 10.1371/journal.pone.0192610

[…] change ≥1 (log2fc ≥1). degs were subsequently mapped to the database for pathway enrichment analysis []., in addition, the go and kegg enrichment analysis of degs were approved using the software goatools (https://github.com/tanghaibao/goatools) [, ] and kobas (http://kobas.cbi.pku.edu.cn/home.do) [] with the p-value< 0.05., the transcription factors in the transcriptome of c. officinalis […]

2017
PMCID: 5381539
PMID: 28204478
DOI: 10.1093/gbe/evx030

[…] domains in amino acid sequences were predicted using interpro scan version 5.17-56.0 (), which was also used to retrieve gene ontology (go) () terms. go terms were mapped to “go-slim” terms using goatools version 0.5.9 (available at https://libraries.io/github/tanghair/goatools)., putative effector prediction was carried out using the following pipeline: 1) signalp version 4.1 () was used […]

2017
PMCID: 5428373
PMID: 28250432
DOI: 10.1038/s41598-017-00078-y

[…] metabolic pathways. a bonferroni-corrected p value of ≤0.05 was used for comparison with the whole-transcriptome background. kegg pathway and go functional enrichment analyses were performed with goatools (https://github.com/tanghaibao/goatools) and kobas (http://kobas.cbi.pku.edu.cn/home.do). the significantly enriched pathways among organs were analyzed according to wang et al. ., total rna […]

2017
PMCID: 5484670
PMID: 28652609
DOI: 10.1038/s41598-017-04606-8

[…] (https://bioconductor.org/packages/release/bioc/html/edger.html). to study the functions of the differentially expressed genes, go functional enrichment and kegg pathway analysis were carried out by goatools (https://github.com/tanghaibao/goatools) and kobas (http://kobas.cbi.pku.edu.cn/home.do) respectively. gene expression changes higher than 2-fold with p-values less than 0.05 were regarded […]

2017
PMCID: 5487381
PMID: 28702378
DOI: 10.3389/fcimb.2017.00287

[…] non-redundant (nr), swiss-prot, kyoto encyclopedia of genes and genome (kegg), and cluster of orthologous groups (cog) protein databases. go functional enrichment analyses were carried out using goatools and kobas (xie et al., ). degs were significantly enriched in go terms and metabolic pathways at bonferroni-corrected p-values of < 0.05., to validate of the reliability of transcriptome […]


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GOAtools in publications

 (67)
PMCID: 5954278
PMID: 29764394
DOI: 10.1186/s12864-018-4458-7

[…] of zebrafish coding-gene was downloaded from gene ontology consortium (only biological process annotations were considered). while, go annotation of zebrafish lncrna was predicted using the goatools (version 0.6.4) [], which determines the go annotation of one gene in our network according to the go annotations of its immediate neighbor genes (p-value < 0.05)., the kegg annotation […]

PMCID: 5894186
PMID: 29636006
DOI: 10.1186/s12864-018-4616-y

[…] (go:0007165), metabolic process (go:0008152) and transmembrane transport (go:0055085).fig. 5, to investigate enrichment and purification (under-representation) of strs in go terms, we used goatools., [] (fig. , additional file : figure s2). we corrected for multiple testing. for some terms, both cod and haddock are enriched, whereas this is not the case in the other species. […]

PMCID: 5863848
PMID: 29566653
DOI: 10.1186/s12870-018-1257-x

[…] []. the p-values of degs were corrected by benjamini–hochberg fdr (false discovery rate) correction []. the over-representation of go terms and kegg pathways of degs were identified using the goatools (https://github.com/tanghaibao/goatools) and r go package [] respectively. the p-value of the enriched analyses was corrected by the fdr method., to verify the expression levels of tobacco […]

PMCID: 5861657
PMID: 29558886
DOI: 10.1186/s12864-018-4596-y

[…] to classify the degs. pathway analysis was performed using the kyoto encyclopedia of genes and genomes (kegg) database []. the enrichment analyses of go terms and kegg pathways were performed using goatools [] and kobas [] based on fisher’s exact test, respectively. multiple corrections including bonferroni, holm, sidak, and false discovery rate were used for correcting the p-value as described […]

PMCID: 5869528
PMID: 29562634
DOI: 10.3390/v10030135

[…] rate (fdr) was selected as the key index for screening degs. in this study, the fdr was <0.01, and the fold-change was ≥3., gene ontology (go) is a functional annotation of the degs. using the goatools software (https://github.com/tanghaibao/goatool) for feature enrichment, significant enrichment was observed when the fdr was <0.05. cog classification of degs from various groups […]


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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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