{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T07:36:40Z","timestamp":1775029000514,"version":"3.50.1"},"reference-count":51,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2019,5,9]],"date-time":"2019-05-09T00:00:00Z","timestamp":1557360000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["U54-HL127624"],"award-info":[{"award-number":["U54-HL127624"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["U24-CA224260"],"award-info":[{"award-number":["U24-CA224260"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["U54-OD020353"],"award-info":[{"award-number":["U54-OD020353"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["T32-GM062754"],"award-info":[{"award-number":["T32-GM062754"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["OT3-OD025467"],"award-info":[{"award-number":["OT3-OD025467"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>High-throughput experiments produce increasingly large datasets that are difficult to analyze and integrate. While most data integration approaches focus on aligning metadata, data integration can be achieved by abstracting experimental results into gene sets. Such gene sets can be made available for reuse through gene set enrichment analysis tools such as Enrichr. Enrichr currently only supports gene sets compiled from human and mouse, limiting accessibility for investigators that study other model organisms. modEnrichr is an expansion of Enrichr for four model organisms: fish, fly, worm and yeast. The gene set libraries within FishEnrichr, FlyEnrichr, WormEnrichr and YeastEnrichr are created from the Gene Ontology, mRNA expression profiles, GeneRIF, pathway databases, protein domain databases and other organism-specific resources. Additionally, libraries were created by predicting gene function from RNA-seq co-expression data processed uniformly from the gene expression omnibus for each organism. The modEnrichr suite of tools provides the ability to convert gene lists across species using an ortholog conversion tool that automatically detects the species. For complex analyses, modEnrichr provides API access that enables submitting batch queries. In summary, modEnrichr leverages existing model organism databases and other resources to facilitate comprehensive hypothesis generation through data integration.<\/jats:p>","DOI":"10.1093\/nar\/gkz347","type":"journal-article","created":{"date-parts":[[2019,4,25]],"date-time":"2019-04-25T15:20:13Z","timestamp":1556205613000},"page":"W183-W190","source":"Crossref","is-referenced-by-count":96,"title":["modEnrichr: a suite of gene set enrichment analysis tools for model organisms"],"prefix":"10.1093","volume":"47","author":[{"given":"Maxim V","family":"Kuleshov","sequence":"first","affiliation":[{"name":"Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA"}]},{"given":"Jennifer E L","family":"Diaz","sequence":"additional","affiliation":[{"name":"Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1020, New York, NY 10029, USA"}]},{"given":"Zachary N","family":"Flamholz","sequence":"additional","affiliation":[{"name":"Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA"}]},{"given":"Alexandra B","family":"Keenan","sequence":"additional","affiliation":[{"name":"Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA"}]},{"given":"Alexander","family":"Lachmann","sequence":"additional","affiliation":[{"name":"Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA"}]},{"given":"Megan L","family":"Wojciechowicz","sequence":"additional","affiliation":[{"name":"Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA"}]},{"given":"Ross L","family":"Cagan","sequence":"additional","affiliation":[{"name":"Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1020, New York, NY 10029, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6904-1017","authenticated-orcid":false,"given":"Avi","family":"Ma\u2019ayan","sequence":"additional","affiliation":[{"name":"Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA"}]}],"member":"286","published-online":{"date-parts":[[2019,5,9]]},"reference":[{"key":"2019062808130719000_B1","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2019062808130719000_B2","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources","volume":"4","author":"Huang","year":"2008","journal-title":"Nat. Protoc."},{"key":"2019062808130719000_B3","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1038\/ng0506-500","article-title":"GenePattern 2.0","volume":"38","author":"Reich","year":"2006","journal-title":"Nat. Genet."},{"key":"2019062808130719000_B4","doi-asserted-by":"crossref","first-page":"W741","DOI":"10.1093\/nar\/gki475","article-title":"WebGestalt: an integrated system for exploring gene sets in various biological contexts","volume":"33","author":"Zhang","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2019062808130719000_B5","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1093\/bioinformatics\/btn615","article-title":"AmiGO: online access to ontology and annotation data","volume":"25","author":"Carbon","year":"2008","journal-title":"Bioinformatics"},{"key":"2019062808130719000_B6","doi-asserted-by":"crossref","first-page":"W472","DOI":"10.1093\/nar\/gkl172","article-title":"BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments","volume":"34","author":"Al-Shahrour","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2019062808130719000_B7","doi-asserted-by":"crossref","first-page":"420747","DOI":"10.1155\/2008\/420747","article-title":"Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes","volume":"2008","author":"Hruz","year":"2008","journal-title":"Adv.Bioinformatics"},{"key":"2019062808130719000_B8","doi-asserted-by":"crossref","first-page":"W358","DOI":"10.1093\/nar\/gkn276","article-title":"GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis","volume":"36","author":"Zheng","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2019062808130719000_B9","doi-asserted-by":"crossref","first-page":"1551","DOI":"10.1038\/nprot.2013.092","article-title":"Large-scale gene function analysis with the PANTHER classification system","volume":"8","author":"Mi","year":"2013","journal-title":"Nat. Protoc."},{"key":"2019062808130719000_B10","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1186\/1471-2105-14-128","article-title":"Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool","volume":"14","author":"Chen","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2019062808130719000_B11","doi-asserted-by":"crossref","first-page":"W90","DOI":"10.1093\/nar\/gkw377","article-title":"Enrichr: a comprehensive gene set enrichment analysis web server 2016 update","volume":"44","author":"Kuleshov","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2019062808130719000_B12","doi-asserted-by":"crossref","first-page":"W83","DOI":"10.1093\/nar\/gkw199","article-title":"g:Profiler-a web server for functional interpretation of gene lists (2016 update)","volume":"44","author":"Reimand","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2019062808130719000_B13","doi-asserted-by":"crossref","first-page":"W316","DOI":"10.1093\/nar\/gkr483","article-title":"KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases","volume":"39","author":"Xie","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2019062808130719000_B14","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1186\/1471-2164-13-526","article-title":"LRpath analysis reveals common pathways dysregulated via DNA methylation across cancer types","volume":"13","author":"Kim","year":"2012","journal-title":"BMC Genomics"},{"key":"2019062808130719000_B15","doi-asserted-by":"crossref","first-page":"D882","DOI":"10.1093\/nar\/gkv1257","article-title":"Lynx: a knowledge base and an analytical workbench for integrative medicine","volume":"44","author":"Sulakhe","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2019062808130719000_B16","doi-asserted-by":"crossref","first-page":"3505","DOI":"10.1093\/bioinformatics\/btx426","article-title":"modPhE:a model organism phenotype enrichment analysis of eukaryotic gene sets","volume":"33","author":"Weng","year":"2017","journal-title":"Bioinformatics"},{"key":"2019062808130719000_B17","doi-asserted-by":"crossref","first-page":"D607","DOI":"10.1093\/nar\/gky1131","article-title":"STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets","volume":"47","author":"Szklarczyk","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2019062808130719000_B18","doi-asserted-by":"crossref","first-page":"W305","DOI":"10.1093\/nar\/gkp427","article-title":"ToppGene Suite for gene list enrichment analysis and candidate gene prioritization","volume":"37","author":"Chen","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2019062808130719000_B19","doi-asserted-by":"crossref","first-page":"D869","DOI":"10.1093\/nar\/gkx998","article-title":"WormBase 2017: molting into a new stage","volume":"46","author":"Lee","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2019062808130719000_B20","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: Kyoto Encyclopedia of Genes and Genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2019062808130719000_B21","doi-asserted-by":"crossref","first-page":"e184","DOI":"10.1371\/journal.pbio.0060184","article-title":"WikiPathways: pathway editing for the people","volume":"6","author":"Pico","year":"2008","journal-title":"PLoS Biol."},{"key":"2019062808130719000_B22","doi-asserted-by":"crossref","first-page":"D351","DOI":"10.1093\/nar\/gky1100","article-title":"InterPro in 2019: improving coverage, classification and access to protein sequence annotations","volume":"47","author":"Mitchell","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2019062808130719000_B23","doi-asserted-by":"crossref","first-page":"D427","DOI":"10.1093\/nar\/gky995","article-title":"The Pfam protein families database in 2019","volume":"47","author":"El-Gebali","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2019062808130719000_B24","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene Ontology: tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet."},{"key":"2019062808130719000_B25","first-page":"460","article-title":"Gene indexing: characterization and analysis of NLM's GeneRIFs","volume-title":"AMIA Annual Symposium Proceedings","author":"Mitchell","year":"2003"},{"key":"2019062808130719000_B26","doi-asserted-by":"crossref","DOI":"10.1101\/115022","article-title":"Tagger: BeCalm API for rapid named entity recognition","author":"Jensen","year":"2017"},{"key":"2019062808130719000_B27","doi-asserted-by":"crossref","first-page":"830","DOI":"10.1093\/bioinformatics\/btk048","article-title":"Hierarchical multi-label prediction of gene function","volume":"22","author":"Barutcuoglu","year":"2006","journal-title":"Bioinformatics"},{"key":"2019062808130719000_B28","doi-asserted-by":"crossref","first-page":"8348","DOI":"10.1073\/pnas.0832373100","article-title":"A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae)","volume":"100","author":"Troyanskaya","year":"2003","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2019062808130719000_B29","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1038\/47048","article-title":"A combined algorithm for genome-wide prediction of protein function","volume":"402","author":"Marcotte","year":"1999","journal-title":"Nature"},{"key":"2019062808130719000_B30","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1038\/msb4100129","article-title":"Network-based prediction of protein function","volume":"3","author":"Sharan","year":"2007","journal-title":"Mol. Syst. Biol."},{"key":"2019062808130719000_B31","doi-asserted-by":"crossref","first-page":"baw100","DOI":"10.1093\/database\/baw100","article-title":"The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins","volume":"2016","author":"Rouillard","year":"2016","journal-title":"Database"},{"key":"2019062808130719000_B32","doi-asserted-by":"crossref","first-page":"1366","DOI":"10.1038\/s41467-018-03751-6","article-title":"Massive mining of publicly available RNA-seq data from human and mouse","volume":"9","author":"Lachmann","year":"2018","journal-title":"Nat. Commun."},{"key":"2019062808130719000_B33","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","article-title":"Biopython: freely available Python tools for computational molecular biology and bioinformatics","volume":"25","author":"Cock","year":"2009","journal-title":"Bioinformatics"},{"key":"2019062808130719000_B34","doi-asserted-by":"crossref","first-page":"bat004","DOI":"10.1093\/database\/bat004","article-title":"The YeastGenome app: the Saccharomyces Genome Database at your fingertips","volume":"2013","author":"Wong","year":"2013","journal-title":"Database"},{"key":"2019062808130719000_B35","doi-asserted-by":"crossref","first-page":"D854","DOI":"10.1093\/nar\/gks938","article-title":"ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics","volume":"41","author":"Howe","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2019062808130719000_B36","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1186\/1471-2164-10-22","article-title":"BioMart\u2014biological queries made easy","volume":"10","author":"Smedley","year":"2009","journal-title":"BMC Genomics"},{"key":"2019062808130719000_B37","doi-asserted-by":"crossref","first-page":"D19","DOI":"10.1093\/nar\/gkq1019","article-title":"The sequence read archive","volume":"39","author":"Leinonen","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2019062808130719000_B38","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1038\/nbt.3519","article-title":"Near-optimal probabilistic RNA-seq quantification","volume":"34","author":"Bray","year":"2016","journal-title":"Nat. Biotechnol."},{"key":"2019062808130719000_B39","first-page":"2","article-title":"Docker: lightweight linux containers for consistent development and deployment","volume":"2014","author":"Merkel","year":"2014","journal-title":"Linux J."},{"key":"2019062808130719000_B40","volume-title":"Mesos in Action","author":"Ignazio","year":"2016"},{"key":"2019062808130719000_B41","doi-asserted-by":"crossref","first-page":"1952","DOI":"10.1002\/cpe.3708","article-title":"Integrating apache airavata with docker, marathon, and mesos","volume":"28","author":"Saha","year":"2016","journal-title":"Concurr. Comput."},{"key":"2019062808130719000_B42","doi-asserted-by":"crossref","first-page":"D807","DOI":"10.1093\/nar\/gky1053","article-title":"OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs","volume":"47","author":"Kriventseva","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2019062808130719000_B43","doi-asserted-by":"crossref","first-page":"160018","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR Guiding Principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci. Data"},{"key":"2019062808130719000_B44","first-page":"14","article-title":"Swagger restful api documentation specification 1.2. Techn Ber Technical report","author":"Team","year":"2014","journal-title":"Wordnik"},{"key":"2019062808130719000_B45","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1007\/978-3-319-58451-5_11","article-title":"smartAPI: towards a more intelligent network of Web APIs","volume-title":"European Semantic Web Conference","author":"Zaveri","year":"2017"},{"key":"2019062808130719000_B46","doi-asserted-by":"crossref","first-page":"13500","DOI":"10.1093\/nar\/gku1228","article-title":"Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes","volume":"42","author":"Pujato","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2019062808130719000_B47","doi-asserted-by":"crossref","first-page":"D535","DOI":"10.1093\/nar\/gkj109","article-title":"BioGRID: a general repository for interaction datasets","volume":"34","author":"Stark","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2019062808130719000_B48","doi-asserted-by":"crossref","first-page":"D1021","DOI":"10.1093\/nar\/gks1170","article-title":"GenomeRNAi: a database for cell-based and in vivo RNAi phenotypes, 2013 update","volume":"41","author":"Schmidt","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2019062808130719000_B49","doi-asserted-by":"crossref","first-page":"D736","DOI":"10.1093\/nar\/gkq1092","article-title":"DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila","volume":"39","author":"Murali","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2019062808130719000_B50","doi-asserted-by":"crossref","first-page":"D759","DOI":"10.1093\/nar\/gky1003","article-title":"FlyBase 2.0: the next generation","volume":"47","author":"Thurmond","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2019062808130719000_B51","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1093\/nar\/26.1.73","article-title":"SGD: Saccharomyces genome database","volume":"26","author":"Cherry","year":"1998","journal-title":"Nucleic Acids Res."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/advance-article-pdf\/doi\/10.1093\/nar\/gkz347\/28572603\/gkz347.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/47\/W1\/W183\/28880318\/gkz347.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,9,22]],"date-time":"2019-09-22T23:46:07Z","timestamp":1569195967000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/47\/W1\/W183\/5487261"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,5,9]]},"references-count":51,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2019,5,9]]},"published-print":{"date-parts":[[2019,7,2]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkz347","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,7,2]]},"published":{"date-parts":[[2019,5,9]]}}}