GO::TermFinder protocols

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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

 (38)
2018
PMCID: 5755908
PMID: 29304067
DOI: 10.1371/journal.pone.0190685

[…] was determined using bedtools 2.25.0 []. splicing efficiency was then calculated as the ratio of transreads (mrna) to intron-end reads (pre-mrna). enriched go categories were searched for using go term finder 0.83 (http://www.yeastgenome.org/cgi-bin/go/gotermfinder.pl)., the roles of rpg paralogs in ribosome biogenesis and translation, both in unicellular eukaryotes and in metazoa, remain […]

2018
PMCID: 5764247
PMID: 29324867
DOI: 10.1371/journal.pone.0190096

[…] 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[]. genes usually […]

2018
PMCID: 5771622
PMID: 29342213
DOI: 10.1371/journal.pone.0191407

[…] we used the hclust package in r []. dendrograms were created using ward linkage from z-score normalized transcript levels., we performed gene set enrichment analysis using the open-source software go::termfinder (stanford university school of medicine, stanford, ca) []. this tool determined whether any gene ontology terms annotated two lists of genes (i.e., genes with higher expression […]

2018
PMCID: 5864082
PMID: 29529031
DOI: 10.1371/journal.pgen.1007253

[…] enrichment of sut/cut using exact binomial test. false discovery rate (fdr) was calculated using r. the biological functions of neighboring genes to ncrnas in each cluster were identified using go term finder in sgd., the pgal1 promoter was amplified from pav1901 [] using gal1.for and gal1.rev primers and cloned into the sali site in prs416 []. next the cyc1 terminator was amplified […]

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 component., identification of significantly degs was conducted according to , […]


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GO::TermFinder in publications

 (349)
PMCID: 5955888
PMID: 29769614
DOI: 10.1038/s41598-018-25717-w

[…] expressing either p110α with akt1 or kinase-dead akt1k179m were compared. table  show the 81 genes that were up-regulated over 1.7-fold and 39 genes down-regulated below 0.6-fold. genecodis and go term finder analyses on up-regulated genes highlighted three significantly enriched functional categories: “pentose phosphate shunt” (p-value = 9×10−15 by chi square test with bonferroni […]

PMCID: 5896889
PMID: 29649209
DOI: 10.1371/journal.pgen.1007130

[…] analyses were carried out for particular subsets of data that exhibited patterns of differential expression between white and green seedlings. to perform these analyses, we used gostat [] and go::termfinder [] implemented in the phytomine user interface (https://phytozome.jgi.doe.gov). for go term analyses, we used all annotated genes in the v2.0 im62 m. guttatus reference assembly […]

PMCID: 5874921
PMID: 29588408
DOI: 10.1128/mBio.02229-17

[…] expression analysis was performed using partek genomics suite software, v. 6.6, using a log2 data transformation. gene ontology (go) term analysis was performed through the candida genome database go term finder and the cytoscape v. 3 clue go plug-in (). network construction was performed with cytoscape v.3 freeware (). a statistical comparison among go term enrichment percentages […]

PMCID: 5864082
PMID: 29529031
DOI: 10.1371/journal.pgen.1007253

[…] enrichment of sut/cut using exact binomial test. false discovery rate (fdr) was calculated using r. the biological functions of neighboring genes to ncrnas in each cluster were identified using go term finder in sgd., the pgal1 promoter was amplified from pav1901 [] using gal1.for and gal1.rev primers and cloned into the sali site in prs416 []. next the cyc1 terminator was amplified […]

PMCID: 5845109
PMID: 29556248
DOI: 10.3389/fgene.2018.00058

[…] between conditions. gene expression datasets are available upon request., the functional annotations of differentially expressed genes were performed using david, go (gene ontology) elite, and go-termfinder (boyle et al., ). pathways were visualized using pathview/kegg and david bioinformatics resources 6.7/kegg pathway platforms (huang et al., ; huang da et al., ,)., western […]


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

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