Faculty Collaboration Database

MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses. Genetics 2022 Apr 04;220(4)

Date

04/06/2022

Pubmed ID

35380657

Pubmed Central ID

PMC8982048

DOI

10.1093/genetics/iyac005

Scopus ID

2-s2.0-85128160560 (requires institutional sign-in at Scopus site)   7 Citations

Abstract

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some enrichment tools are not updated frequently with recent information from databases, thus giving users inaccurate, outdated or uninformative data.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.

Author List

Vedi M, Nalabolu HS, Lin CW, Hoffman MJ, Smith JR, Brodie K, De Pons JL, Demos WM, Gibson AC, Hayman GT, Hill ML, Kaldunski ML, Lamers L, Laulederkind SJF, Thorat K, Thota J, Tutaj M, Tutaj MA, Wang SJ, Zacher S, Dwinell MR, Kwitek AE

Authors

Melinda R. Dwinell PhD Professor in the Physiology department at Medical College of Wisconsin
G. Thomas Hayman PhD Research Scientist II in the Physiology department at Medical College of Wisconsin
Anne E. Kwitek PhD Professor in the Physiology department at Medical College of Wisconsin
Stanley J. Laulederkind Research Scientist II in the Physiology department at Medical College of Wisconsin
Chien-Wei Lin PhD Associate Professor in the Data Science Institute department at Medical College of Wisconsin
Monika Tutaj Research Scientist II in the Physiology department at Medical College of Wisconsin
Mahima Vedi Research Scientist I in the Physiology department at Medical College of Wisconsin
Shur-Jen Wang Research Scientist II in the Physiology department at Medical College of Wisconsin

MESH terms used to index this publication - Major topics in bold

Animals
Databases, Genetic
Gene Ontology
Genome
Internet
Mice
Rats
Software