Cited by 2,067Bioinformatics and Genomic NetworksBiomedical Text Mining and OntologiesGenomics and Phylogenetic Studies

GO::TermFinder–open source software for accessing gene ontology information and finding significantly enriched gene ontology terms associated with a list of genes

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Boyle, Elizabeth I., Weng, Shuai, Gollub, Jeremy, Jin, Heng, Botstein, David, Cherry, J. Michael, Sherlock, Gavin·2004·Bioinformatics

Abstract

SUMMARY: GO::TermFinder comprises a set of object-oriented Perl modules for accessing Gene Ontology (GO) information and evaluating and visualizing the collective annotation of a list of genes to GO terms. It can be used to draw conclusions from microarray and other biological data, calculating the statistical significance of each annotation. GO::TermFinder can be used on any system on which Perl can be run, either as a command line application, in single or batch mode, or as a web-based CGI script. AVAILABILITY: The full source code and documentation for GO::TermFinder are freely available from http://search.cpan.org/dist/GO-TermFinder/.

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Crossref · 10.1093/bioinformatics/bth456

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  • GO Term Finder analysis of genes with SNVs from drug-treated (1, 8, 64 μg/ml FLC) strains with progenitors SC5314 or P75063 identified only one significantly enriched GO term: long-chain fatty acid metabolic process (P < 0.05, hypergeometric distribution with Bonferroni correction).

    “The only significant cluster detected is for the GO term long-chain fatty acid metabolic process (P < 0.05, hypergeometric distribution with Bonferroni Correction).”

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Authors
Boyle, E. I., Weng, S., Gollub, J., Jin, H., Botstein, D., Cherry, J. M., & Sherlock, G.
Affiliations
Stanford Medicine (US)
Corresponding author
Boyle, Elizabeth I.
Venue
Bioinformatics
Published
2004-08-05
Volume
20
Issue
18
Pages
3710-3715
ISSN
  • 1367-4803 (ISSN-L)
  • 1367-4811
OpenAlex
W2166574880
Cited by
2,067
References
13
Citations by year
2026: 54 · 2025: 84 · 2024: 102 · 2023: 119 · 2022: 151 · 2021: 135 · 2020: 123 · 2019: 117 · 2018: 85 · 2017: 92 · 2016: 97 · 2015: 105 · 2014: 109 · 2013: 114 · 2012: 103
FWCI
18.16
Type
journal article
Language
en
Open access
Locations
  • Bioinformatics (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • National Institutes of Health
  • National Human Genome Research Institute (R01HG002732)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
Gene Ontology, Perl module, genome annotation, microarray data analysis, open source software
MeSH terms
Abstracting and Indexing, Database Management Systems, Natural Language Processing, Programming Languages, Software, User-Computer Interface, Information Storage and Retrieval, Vocabulary, Controlled, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Databases, Protein

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