{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T13:31:49Z","timestamp":1760707909263},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The R package HCGene (Hierarchical Classification of Genes) implements methods to process and analyze the Gene Ontology and the FunCat taxonomy in order to support the functional classification of genes. HCGene allows the extraction of subgraphs and subtrees related to specific biological problems, the labeling of genes and gene products with multiple and hierarchical functional classes, and the association of different types of bio-molecular data to genes for learning to predict their functions.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/homes.dsi.unimi.it\/~valenti\/SW\/hcgene\/download\/hcgene_1.0.tar.gz<\/jats:p>\n               <jats:p>Contact: \u00a0valentini@dsi.unimi.it<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at http:\/\/homes.dsi.unimi.it\/~valenti\/SW\/hcgene<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn015","type":"journal-article","created":{"date-parts":[[2008,1,20]],"date-time":"2008-01-20T01:13:55Z","timestamp":1200791635000},"page":"729-731","source":"Crossref","is-referenced-by-count":10,"title":["HCGene: a software tool to support the hierarchical classification of genes"],"prefix":"10.1093","volume":"24","author":[{"given":"Giorgio","family":"Valentini","sequence":"first","affiliation":[{"name":"DSI; Dip. di Scienze dell'Informazione, Universit\u00e0 degli Studi di Milano, Via Comelico 39, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicol\u00f2","family":"Cesa-Bianchi","sequence":"additional","affiliation":[{"name":"DSI; Dip. di Scienze dell'Informazione, Universit\u00e0 degli Studi di Milano, Via Comelico 39, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,1,18]]},"reference":[{"key":"2023020210121558100_B1","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":"2023020210121558100_B2","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1073\/pnas.97.1.262","article-title":"Knowledge-base analysis of microarray gene expression data by using support vector machines","volume":"97","author":"Brown","year":"2000","journal-title":"PNAS"},{"key":"2023020210121558100_B3","article-title":"The Gene Ontology Annotation (GOA) database","volume-title":"Silico Genomics and Proteomics.","author":"Camon","year":"2006"},{"key":"2023020210121558100_B4","article-title":"Functional interpretation of microarray experiments","volume":"3","author":"Dopazo","year":"2006","journal-title":"OMICS"},{"key":"2023020210121558100_B5","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: open software development for computational biology and bioinformatics","volume":"5","author":"Gentleman","year":"2004","journal-title":"Genome Biol"},{"key":"2023020210121558100_B6","doi-asserted-by":"crossref","first-page":"D258","DOI":"10.1093\/nar\/gkh036","article-title":"The Gene Ontology (GO) database and informatics resource","volume":"32","author":"Harris","year":"2004","journal-title":"Nucleic Acid Res"},{"key":"2023020210121558100_B7","doi-asserted-by":"crossref","first-page":"2753","DOI":"10.1093\/bioinformatics\/btl475","article-title":"Support vector machine learning from heterogeneous data: an empirical analysis using protein sequence and structure","volume":"22","author":"Lewis","year":"2006","journal-title":"Bioinformatics"},{"key":"2023020210121558100_B8","doi-asserted-by":"crossref","first-page":"2256","DOI":"10.1093\/bioinformatics\/btm322","article-title":"Annotation-based distance measures for patient subgroup discovery in clinical microarray studies","volume":"17","author":"Lottaz","year":"2007","journal-title":"Bioinformatics"},{"key":"2023020210121558100_B9","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1089\/10665270252935539","article-title":"Learning gene functional classification from multiple data","author":"Pavlidis","year":"2002","journal-title":"J. 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