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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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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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).”
From Antifungal Drug Concentration Impacts the Spectrum of Adaptive Mutations in <i>Candida albicans</i> (2023) · cites this paper as Boyle et al. 2004
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“These include Gorilla [ 31], DAVID [ 32], WebGestalt [ 33], EnrichR [ 34], PANTHER Gene List Analysis [ 35], TermMapper [ 36], and g:profiler [ 37], which are frequently used to provide valuable interpretations into high-throughput omics.”
- 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
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-08-05
- Volume
- 20
- Issue
- 18
- Pages
- 3710-3715
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC3037731
- 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
- bronze
- doi.org
- 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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