GOATOOLS: A Python library for Gene Ontology analyses

Scientific Reports
D V KlopfensteinHaibao Tang

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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Citations

Oct 26, 2018·Nucleic Acids Research·Xian ZengYu Zong Chen
Dec 12, 2018·Genome Biology and Evolution·Jamie McGowanDavid A Fitzpatrick
Feb 5, 2019·Microbial Genomics·Charley G P McCarthy, David A Fitzpatrick
Feb 5, 2019·ELife·Tomáš ZavřelJan Červený
Jul 13, 2019·Genes·Charley G P McCarthy, David A Fitzpatrick
Sep 29, 2019·Database : the Journal of Biological Databases and Curation·Lingfeng MaoLongjiang Fan
Oct 28, 2019·Science·Milo S JohnsonMichael M Desai
Nov 16, 2019·PLoS Neglected Tropical Diseases·Awtum M BrashearLiwang Cui
Jul 11, 2019·Molecular Biology and Evolution·Dafni Anastasiadi, Francesc Piferrer
Dec 31, 2019·Molecular Systems Biology·Marco GalardiniPedro Beltrao
Oct 29, 2019·Cancer Biomarkers : Section a of Disease Markers·Zhen ZhaoRongrong Chen
Oct 12, 2019·NPJ Systems Biology and Applications·Bede P BusbyPaul H Atkinson
May 6, 2019·Scientific Reports·Jan LudwiczakStanislaw Dunin-Horkawicz
Jul 23, 2020·PLoS Computational Biology·David MoiChristophe Dessimoz
Dec 22, 2019·International Journal of Molecular Sciences·Saura R SilvaAlessandro M Varani
Nov 20, 2018·F1000Research·Linhua WangGaurav Pandey
Dec 12, 2018·BMC Bioinformatics·Mikhail PomaznoyBjoern Peters

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Software Mentioned

GOEAs
GOEA
Bioconductor
Python
GOATOOLS GOEA
Ensembl
ReviGO ( Reduce and Visualize Gene Ontology )
R
DAVID
DAVID Knowledgebase

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