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

IF 3.3 3区生物学

Genetics Pub Date : 2022-01-28 DOI:10.1093/genetics/iyac005

M. Vedi, H. S. Nalabolu, Chien-Wei Lin, M. Hoffman, Jennifer R. Smith, K. Brodie, J. D. De Pons, W. Demos, A. Gibson, G. Hayman, M. L. Hill, M. Kaldunski, L. Lamers, S. Laulederkind, K. Thorat, J. Thota, M. Tutaj, M. Tutaj, Shur-Jen Wang, S. Zacher, M. Dwinell, A. Kwitek

{"title":"MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses","authors":"M. Vedi, H. S. Nalabolu, Chien-Wei Lin, M. Hoffman, Jennifer R. Smith, K. Brodie, J. D. De Pons, W. Demos, A. Gibson, G. Hayman, M. L. Hill, M. Kaldunski, L. Lamers, S. Laulederkind, K. Thorat, J. Thota, M. Tutaj, M. Tutaj, Shur-Jen Wang, S. Zacher, M. Dwinell, A. Kwitek","doi":"10.1093/genetics/iyac005","DOIUrl":null,"url":null,"abstract":"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some enrichment tools are not updated frequently with recent information from databases, thus giving users inaccurate, outdated or uninformative data.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.","PeriodicalId":12706,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3000,"publicationDate":"2022-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"4","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genetics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/genetics/iyac005","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}

引用次数: 4

Abstract

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.

查看原文本刊更多论文

MOET：大鼠基因组数据库中用于多本体和多物种分析的基于网络的基因集富集工具

摘要大量基因或蛋白质数据的生物学解释是复杂的。本体分析工具在通过过度表达或丰富与输入基因或蛋白质列表相关的术语来寻找功能相似性方面是必不可少的。然而，大多数工具都受到其进行本体特定和物种有限分析的能力的限制。此外，一些丰富工具没有经常更新数据库中的最新信息，因此给用户提供了不准确、过时或无信息的数据。在这里，我们介绍了MOET或多本体丰富工具（2019年4月发布的v.1和2021年5月发布的v.2），这是一种利用大鼠基因组数据库（RGD）从内部专家管理和外部数据库（包括国家生物技术信息中心（NCBI）、小鼠基因组信息学（MGI），京都基因和基因组百科全书（KEGG）、基因本体论资源、UniProt GOA等。给定基因或蛋白质列表，MOET分析使用超几何检验来识别显著过度表达的本体术语，并为过度表达的术语提供标称和Bonferroni校正的P值和比值比。结果显示为带有和不带有Bonferroni校正的术语的可下载列表，以及列表中每个术语的P值和注释基因数量的图表。MOET可以从https://rgd.mcw.edu/rgdweb/enrichment/start.html.

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Genetics 生物-遗传学

CiteScore

6.20

自引率

6.10%

发文量

177

期刊介绍： GENETICS is published by the Genetics Society of America, a scholarly society that seeks to deepen our understanding of the living world by advancing our understanding of genetics. Since 1916, GENETICS has published high-quality, original research presenting novel findings bearing on genetics and genomics. The journal publishes empirical studies of organisms ranging from microbes to humans, as well as theoretical work. While it has an illustrious history, GENETICS has changed along with the communities it serves: it is not your mentor''s journal. The editors make decisions quickly – in around 30 days – without sacrificing the excellence and scholarship for which the journal has long been known. GENETICS is a peer reviewed, peer-edited journal, with an international reach and increasing visibility and impact. All editorial decisions are made through collaboration of at least two editors who are practicing scientists. GENETICS is constantly innovating: expanded types of content include Reviews, Commentary (current issues of interest to geneticists), Perspectives (historical), Primers (to introduce primary literature into the classroom), Toolbox Reviews, plus YeastBook, FlyBook, and WormBook (coming spring 2016). For particularly time-sensitive results, we publish Communications. As part of our mission to serve our communities, we''ve published thematic collections, including Genomic Selection, Multiparental Populations, Mouse Collaborative Cross, and the Genetics of Sex.