GO::TermFinder protocols

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description
GO::TermFinder computational protocol

GO::TermFinder specifications

Information


Unique identifier OMICS_10339
Name GO::TermFinder
Alternative names GO-Term Finder, 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
Alternative names GO-Term Finder, 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 <>

Publication for GO::TermFinder

GO::TermFinder IN pipelines

 (9)
2017
PMCID: 5470080
PMID: 28659961
DOI: 10.3389/fpls.2017.01022

[…] 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 […]

2017
PMCID: 5567665
PMID: 28787458
DOI: 10.1371/journal.pgen.1006949

[…] fragments that uniquely aligned to all genes, and “l” is the number of bases of gene a. go functional enrichment analysis was carried out according to go terminology determined using the online cgd go term finder tool (http://www.candidagenome.org/cgi-bin/go/gotermfinder)., the chromatin immunoprecipitation (chip) protocol was adapted from nobile et al. (2012) [54]. c. albicans cells were grown […]

2017
PMCID: 5700172
PMID: 29167521
DOI: 10.1038/s41598-017-16357-7

[…] was performed by mapping genes to go terms (http://www.geneontology.org), and go enrichment analysis of differentially expressed genes (degs) was conducted by hypergeometric test based on ‘go::termfinder’ (http://www.yeastgenome.org/help/analyze/go-term-finder). the calculated p-value was processed by using bonferroni correction and the corrected p-value ≤ 0.05 was used as threshold. […]

2017
PMCID: 5700172
PMID: 29167521
DOI: 10.1038/s41598-017-16357-7

[…] and go enrichment analysis of differentially expressed genes (degs) was conducted by hypergeometric test based on ‘go::termfinder’ (http://www.yeastgenome.org/help/analyze/go-term-finder). the calculated p-value was processed by using bonferroni correction and the corrected p-value ≤ 0.05 was used as threshold. kegg pathway annotation and enrichment analysis […]

2016
PMCID: 4895440
PMID: 27272719
DOI: 10.1038/srep27463

[…] 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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