GO::TermFinder specifications

Information


Unique identifier OMICS_10339
Name GO::TermFinder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A list of genes, one per line or a file containing lists of gene
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 0.86
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Gavin Sherlock <>

Information


Unique identifier OMICS_10339
Name GO::TermFinder
Interface Web user interface
Restrictions to use None
Input data A list of genes, one per line or a file containing lists of gene
Programming languages Perl
Computer skills Basic
Version 0.86
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Gavin Sherlock <>

GO::TermFinder article

GO::TermFinder citations

 (5)
2018
PMCID: 5764247

[…] system based on molecular functions, cellular components, and biological processes. in this study, the degs were annotated by go using the (http://www.geneontology.org/) database and the 'go term finder' (http://www.yeastgenome.org/help/analyze/go-term-finder). after obtaining the go annotations for the degs, the go functional classification was executed with wego[25]. genes usually […]

2017
PMCID: 5470080

[…] the best match per blast search was used to annotate the transcript tags. the contigs with no matches were classified as “predicted” or “uncharacterized” annotation. go analysis was performed using go term finder to describe the biology of a gene product, such as molecular function, biological process, and cellular component1., identification of significantly degs was conducted according […]

2016
PMCID: 5174095

[…] go terms in the database3, calculating the gene numbers for every term, and subsequently using the hypergeometric test to identify significantly enriched go terms in the input list of degs, based on go::termfinder4., to further analyze the degs, the strategy of weighted gene co-expression network (wgcna) was used to identify the key genes. co-expression focused on dynamic changes in the gene […]

2016
PMCID: 5097433

[…] a refseq database of proteins from ncbi (version from october 2013). go terms were determined using the interproscan pipeline (http://www.ebi.ac.uk/interpro/; [21]) and the online tool generic go term finder [22]. go term enrichment was done using revigo [23]., from the set of genes (additional file 1: table s1) that were conserved in dd, dl, pp and df and were over 3-fold upregulated […]

2016
PMCID: 4895440

[…] false discovery rate at 1%69. for identification of go terms overrepresented in each of the differentially expressed gene lists, enrichment analysis was conducted with the candida genome database go term finder tool70., primers for reverse transcription were designed using primer-blast (www.ncbi.nlm.nih.gov/tools/primer-blast) (supplementary table s2). dnase treatment, reverse transcription […]

GO::TermFinder institution(s)
Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA

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