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MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses
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 abilit...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8982048/ https://www.ncbi.nlm.nih.gov/pubmed/35380657 http://dx.doi.org/10.1093/genetics/iyac005 |
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author | Vedi, Mahima Nalabolu, Harika S Lin, Chien-Wei Hoffman, Matthew J Smith, Jennifer R Brodie, Kent De Pons, Jeffrey L Demos, Wendy M Gibson, Adam C Hayman, G Thomas Hill, Morgan L Kaldunski, Mary L Lamers, Logan Laulederkind, Stanley J F Thorat, Ketaki Thota, Jyothi Tutaj, Monika Tutaj, Marek A Wang, Shur-Jen Zacher, Stacy Dwinell, Melinda R Kwitek, Anne E |
author_facet | Vedi, Mahima Nalabolu, Harika S Lin, Chien-Wei Hoffman, Matthew J Smith, Jennifer R Brodie, Kent De Pons, Jeffrey L Demos, Wendy M Gibson, Adam C Hayman, G Thomas Hill, Morgan L Kaldunski, Mary L Lamers, Logan Laulederkind, Stanley J F Thorat, Ketaki Thota, Jyothi Tutaj, Monika Tutaj, Marek A Wang, Shur-Jen Zacher, Stacy Dwinell, Melinda R Kwitek, Anne E |
author_sort | Vedi, Mahima |
collection | PubMed |
description | 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some enrichment tools are not updated frequently with recent information from databases, thus giving users inaccurate, outdated or uninformative data.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. |
format | Online Article Text |
id | pubmed-8982048 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-89820482022-04-05 MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses Vedi, Mahima Nalabolu, Harika S Lin, Chien-Wei Hoffman, Matthew J Smith, Jennifer R Brodie, Kent De Pons, Jeffrey L Demos, Wendy M Gibson, Adam C Hayman, G Thomas Hill, Morgan L Kaldunski, Mary L Lamers, Logan Laulederkind, Stanley J F Thorat, Ketaki Thota, Jyothi Tutaj, Monika Tutaj, Marek A Wang, Shur-Jen Zacher, Stacy Dwinell, Melinda R Kwitek, Anne E Genetics Knowledgebase and Database Resources 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. Oxford University Press 2022-01-28 /pmc/articles/PMC8982048/ /pubmed/35380657 http://dx.doi.org/10.1093/genetics/iyac005 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Knowledgebase and Database Resources Vedi, Mahima Nalabolu, Harika S Lin, Chien-Wei Hoffman, Matthew J Smith, Jennifer R Brodie, Kent De Pons, Jeffrey L Demos, Wendy M Gibson, Adam C Hayman, G Thomas Hill, Morgan L Kaldunski, Mary L Lamers, Logan Laulederkind, Stanley J F Thorat, Ketaki Thota, Jyothi Tutaj, Monika Tutaj, Marek A Wang, Shur-Jen Zacher, Stacy Dwinell, Melinda R Kwitek, Anne E MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses |
title | MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses |
title_full | MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses |
title_fullStr | MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses |
title_full_unstemmed | MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses |
title_short | MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses |
title_sort | moet: a web-based gene set enrichment tool at the rat genome database for multiontology and multispecies analyses |
topic | Knowledgebase and Database Resources |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8982048/ https://www.ncbi.nlm.nih.gov/pubmed/35380657 http://dx.doi.org/10.1093/genetics/iyac005 |
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