MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses

• Main Authors: Brodie, K. (Author), De Pons, J.L (Author), Demos, W.M (Author), Dwinell, M.R (Author), Gibson, A.C (Author), Hayman, G.T (Author), Hill, M.L (Author), Hoffman, M.J (Author), Kaldunski, M.L (Author), Kwitek, A.E (Author), Lamers, L. (Author), Laulederkind, S.J.F (Author), Lin, C.-W (Author), Nalabolu, H.S (Author), Smith, J.R (Author), Thorat, K. (Author), Thota, J. (Author), Tutaj, M. (Author), Tutaj, M.A (Author), Vedi, M. (Author), Wang, S.-J (Author), Zacher, S. (Author)
• Format: Article
• Language: English
• Published: NLM (Medline) 2022
• Subjects: animal; Animals; Databases, Genetic; gene ontology; Gene Ontology; gene set enrichment; genetic database; genetics; genome; Genome; Internet; Mice; model organism database; mouse; multiple ontology; multiple species analysis; ontology; rat; Rats; software; Software; web tool
• Online Access: View Fulltext in Publisher

 Biological interpretation of a large amount of gene or protein data is complex. Ontology analysis tools are imperative in finding functional similarities through overrepresentation or enrichment of terms associated with the input gene or protein lists. However, most tools are limited by their ability to do ontology-specific and species-limited analyses. Furthermore, some enrichment tools are not updated frequently with recent information from databases, thus giving users inaccurate, outdated or uninformative data. Here, we present MOET or the Multi-Ontology Enrichment Tool (v.1 released in April 2019 and v.2 released in May 2021), an ontology analysis tool leveraging data that the Rat Genome Database (RGD) integrated from in-house expert curation and external databases including the National Center for Biotechnology Information (NCBI), Mouse Genome Informatics (MGI), The Kyoto Encyclopedia of Genes and Genomes (KEGG), The Gene Ontology Resource, UniProt-GOA, and others. Given a gene or protein list, MOET analysis identifies significantly overrepresented ontology terms using a hypergeometric test and provides nominal and Bonferroni corrected P-values and odds ratios for the overrepresented terms. The results are shown as a downloadable list of terms with and without Bonferroni correction, and a graph of the P-values and number of annotated genes for each term in the list. MOET can be accessed freely from https://rgd.mcw.edu/rgdweb/enrichment/start.html. © The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America.