{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,18]],"date-time":"2025-10-18T10:42:33Z","timestamp":1760784153220},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,11,15]]},"abstract":"<jats:p>Motivation: Gene enrichment is a requisite for the interpretation of biological complexity related to specific molecular pathways and biological processes. Furthermore, when interpreting NGS data and human variations, including those related to pathologies, gene enrichment allows the inclusion of other genes that in the human interactome space may also play important key roles in the emergency of the phenotype. Here, we describe NET-GE, a web server for associating biological processes and pathways to sets of human proteins involved in the same phenotype<\/jats:p>\n               <jats:p>Results: NET-GE is based on protein\u2013protein interaction networks, following the notion that for a set of proteins, the context of their specific interactions can better define their function and the processes they can be related to in the biological complexity of the cell. Our method is suited to extract statistically validated enriched terms from Gene Ontology, KEGG and REACTOME annotation databases. Furthermore, NET-GE is effective even when the number of input proteins is small.<\/jats:p>\n               <jats:p>Availability and Implementation: NET-GE web server is publicly available and accessible at http:\/\/net-ge.biocomp.unibo.it\/enrich.<\/jats:p>\n               <jats:p>Contact: \u00a0gigi@biocomp.unibo.it<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw508","type":"journal-article","created":{"date-parts":[[2016,8,3]],"date-time":"2016-08-03T02:08:47Z","timestamp":1470190127000},"page":"3489-3491","source":"Crossref","is-referenced-by-count":15,"title":["NET-GE: a web-server for NETwork-based human gene enrichment"],"prefix":"10.1093","volume":"32","author":[{"given":"Samuele","family":"Bovo","sequence":"first","affiliation":[{"name":"1Biocomputing Group, CIG, Interdepartmental Center \u00abLuigi Galvani\u00bb for Integrated Studies of Bioinformatics, Biophysics and Biocomplexity, University of Bologna, Bologna, Italy"}]},{"given":"Pietro","family":"Di Lena","sequence":"additional","affiliation":[{"name":"2DISI, University of Bologna, Bologna, Italy"}]},{"given":"Pier Luigi","family":"Martelli","sequence":"additional","affiliation":[{"name":"1Biocomputing Group, CIG, Interdepartmental Center \u00abLuigi Galvani\u00bb for Integrated Studies of Bioinformatics, Biophysics and Biocomplexity, University of Bologna, Bologna, Italy"}]},{"given":"Piero","family":"Fariselli","sequence":"additional","affiliation":[{"name":"3BCA, University of Padova, Padova, Italy"}]},{"given":"Rita","family":"Casadio","sequence":"additional","affiliation":[{"name":"1Biocomputing Group, CIG, Interdepartmental Center \u00abLuigi Galvani\u00bb for Integrated Studies of Bioinformatics, Biophysics and Biocomplexity, University of Bologna, Bologna, Italy"},{"name":"4Interdepartmental Center \u00abGiorgio Prodi\u00bb for Cancer Research, University of Bologna, Bologna, Italy"}]}],"member":"286","published-online":{"date-parts":[[2016,8,2]]},"reference":[{"key":"2023020113525249200_btw508-B1","doi-asserted-by":"crossref","first-page":"S6.","DOI":"10.1186\/1471-2164-16-S8-S6","article-title":"NET-GE: a novel NETwork-based gene enrichment for detecting biological processes associated to Mendelian diseases","volume":"16","author":"Di Lena","year":"2015","journal-title":"BMC Genomics"},{"key":"2023020113525249200_btw508-B2","doi-asserted-by":"crossref","first-page":"D481","DOI":"10.1093\/nar\/gkv1351","article-title":"The reactome pathway knowledgebase","volume":"44","author":"Fabregat","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023020113525249200_btw508-B3","doi-asserted-by":"crossref","first-page":"D447","DOI":"10.1093\/nar\/gku1003","article-title":"STRING v10: protein\u2013protein interaction networks, integrated over the tree of life","volume":"44","author":"Szklarczyk","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023020113525249200_btw508-B4","doi-asserted-by":"crossref","first-page":"D1049","DOI":"10.1093\/nar\/gku1179","article-title":"Gene Ontology Consortium: going forward","volume":"43","author":"Gene Ontology Consortium","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023020113525249200_btw508-B5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/nar\/gkn923","article-title":"Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists","volume":"37","author":"Huang","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2023020113525249200_btw508-B6","doi-asserted-by":"crossref","first-page":"D457","DOI":"10.1093\/nar\/gkv1070","article-title":"KEGG as a reference resource for gene and protein annotation","volume":"44","author":"Kanehisa","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023020113525249200_btw508-B7","doi-asserted-by":"crossref","first-page":"981","DOI":"10.1002\/pmic.201400296","article-title":"Bioinformatics approaches for the functional interpretation of protein lists: from ontology term enrichment to network analysis","volume":"15","author":"Laukens","year":"2015","journal-title":"Proteomics"},{"key":"2023020113525249200_btw508-B8","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1002\/ajmg.b.32328","article-title":"Gene set analysis: A step-by-step guide","volume":"168","author":"Mooney","year":"2015","journal-title":"Am. 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