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Published, Version of Record (VoR)CC BY V4.0, Open
Journal article
GOATOOLS: A Python library for Gene Ontology analyses
Scientific reports, v 8(1), pp 10872-17
18 Jul 2018
PMID: 30022098
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
The biological interpretation of gene lists with interesting shared properties, such as up- or down-regulation in a particular experiment, is typically accomplished using gene ontology enrichment analysis tools. Given a list of genes, a gene ontology (GO) enrichment analysis may return hundreds of statistically significant GO results in a "flat" list, which can be challenging to summarize. It can also be difficult to keep pace with rapidly expanding biological knowledge, which often results in daily changes to any of the over 47,000 gene ontologies that describe biological knowledge. GOATOOLS, a Python-based library, makes it more efficient to stay current with the latest ontologies and annotations, perform gene ontology enrichment analyses to determine over- and under-represented terms, and organize results for greater clarity and easier interpretation using a novel GOATOOLS GO grouping method. We performed functional analyses on both stochastic simulation data and real data from a published RNA-seq study to compare the enrichment results from GOATOOLS to two other popular tools: DAVID and GOstats. GOATOOLS is freely available through GitHub: https://github.com/tanghaibao/goatools .
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Details
- Title
- GOATOOLS: A Python library for Gene Ontology analyses
- Creators
- D V Klopfenstein - Drexel UniversityLiangsheng Zhang - Fujian Agriculture and Forestry UniversityBrent S Pedersen - University of UtahFidel Ramírez - Max Planck Institute of Immunobiology and EpigeneticsAlex Warwick Vesztrocy - Department of Genetics, Evolution and Environment, University College London, London, UKAurélien Naldi - University of LausanneChristopher J Mungall - Lawrence Berkeley National LaboratoryJeffrey M Yunes - University of California, San FranciscoOlga Botvinnik - University of California, San DiegoMark Weigel - ArcherWill Dampier - Drexel UniversityChristophe Dessimoz - University College LondonPatrick Flick - Georgia Institute of TechnologyHaibao Tang - Fujian Agriculture and Forestry UniversityLawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Publication Details
- Scientific reports, v 8(1), pp 10872-17
- Publisher
- Springer Nature
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Microbiology and Immunology
- Web of Science ID
- WOS:000439026000033
- Scopus ID
- 2-s2.0-85050369398
- Other Identifier
- 991019176640604721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Multidisciplinary Sciences