{"id":"https://openalex.org/W2097266635","doi":"https://doi.org/10.1093/bioinformatics/bth373","title":"Constrained clusters of gene expression profiles with pathological features","display_name":"Constrained clusters of gene expression profiles with pathological features","publication_year":2004,"publication_date":"2004-06-24","ids":{"openalex":"https://openalex.org/W2097266635","doi":"https://doi.org/10.1093/bioinformatics/bth373","mag":"2097266635","pmid":"https://pubmed.ncbi.nlm.nih.gov/15217814"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bth373","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth373","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022912020","display_name":"Jun Sese","orcid":"https://orcid.org/0000-0003-3495-4382"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]},{"id":"https://openalex.org/I4210128160","display_name":"Division of Undergraduate Education","ror":"https://ror.org/02kd4km72","country_code":"US","type":"government","lineage":["https://openalex.org/I1311060795","https://openalex.org/I4210101031","https://openalex.org/I4210128160"]}],"countries":["JP","US"],"is_corresponding":true,"raw_author_name":"Jun Sese","raw_affiliation_strings":["Undergraduate Program for Bioinformatics and Systems Biology, Graduate School of Frontier Sciences, University of Tokyo, Bunkyo, Tokyo, Japan. sesejun@gi.k.u-tokyo.ac.jp","Undergraduate Program for Bioinformatics and Systems Biology#TAB#"],"affiliations":[{"raw_affiliation_string":"Undergraduate Program for Bioinformatics and Systems Biology, Graduate School of Frontier Sciences, University of Tokyo, Bunkyo, Tokyo, Japan. sesejun@gi.k.u-tokyo.ac.jp","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"Undergraduate Program for Bioinformatics and Systems Biology#TAB#","institution_ids":["https://openalex.org/I4210128160"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043504350","display_name":"Yukinori Kurokawa","orcid":"https://orcid.org/0000-0002-2883-0132"},"institutions":[{"id":"https://openalex.org/I75917431","display_name":"Nara Institute of Science and Technology","ror":"https://ror.org/05bhada84","country_code":"JP","type":"education","lineage":["https://openalex.org/I75917431"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yukinori Kurokawa","raw_affiliation_strings":["Department of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan#TAB#","institution_ids":["https://openalex.org/I75917431"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108403721","display_name":"Morito Monden","orcid":null},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"Osaka University","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Morito Monden","raw_affiliation_strings":["Department of Surgery and Clinical Oncology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Surgery and Clinical Oncology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan","institution_ids":["https://openalex.org/I98285908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059682485","display_name":"Kikuya Kato","orcid":"https://orcid.org/0000-0003-1863-6253"},"institutions":[{"id":"https://openalex.org/I75917431","display_name":"Nara Institute of Science and Technology","ror":"https://ror.org/05bhada84","country_code":"JP","type":"education","lineage":["https://openalex.org/I75917431"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kikuya Kato","raw_affiliation_strings":["Department of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan#TAB#","institution_ids":["https://openalex.org/I75917431"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049124202","display_name":"Shinichi Morishita","orcid":"https://orcid.org/0000-0002-6201-8885"},"institutions":[{"id":"https://openalex.org/I4210128160","display_name":"Division of Undergraduate Education","ror":"https://ror.org/02kd4km72","country_code":"US","type":"government","lineage":["https://openalex.org/I1311060795","https://openalex.org/I4210101031","https://openalex.org/I4210128160"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shinichi Morishita","raw_affiliation_strings":["Undergraduate Program for Bioinformatics and Systems Biology#TAB#"],"affiliations":[{"raw_affiliation_string":"Undergraduate Program for Bioinformatics and Systems Biology#TAB#","institution_ids":["https://openalex.org/I4210128160"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5022912020"],"corresponding_institution_ids":["https://openalex.org/I4210128160","https://openalex.org/I74801974"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.05,"has_fulltext":false,"cited_by_count":39,"citation_normalized_percentile":{"value":0.86058307,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"20","issue":"17","first_page":"3137","last_page":"3145"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10538","display_name":"Data Mining Algorithms and Applications","score":0.992900013923645,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9811000227928162,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.8294069766998291},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5148712396621704},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5084428191184998},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.46719834208488464},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.45649850368499756},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4381019175052643},{"id":"https://openalex.org/keywords/constraint","display_name":"Constraint (computer-aided design)","score":0.4206044673919678},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4188610315322876},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.36191868782043457},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3322179317474365},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.31277352571487427},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.26938921213150024},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.12710770964622498}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.8294069766998291},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5148712396621704},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5084428191184998},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46719834208488464},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.45649850368499756},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4381019175052643},{"id":"https://openalex.org/C2776036281","wikidata":"https://www.wikidata.org/wiki/Q48769818","display_name":"Constraint (computer-aided design)","level":2,"score":0.4206044673919678},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4188610315322876},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36191868782043457},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3322179317474365},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.31277352571487427},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.26938921213150024},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.12710770964622498},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003936","descriptor_name":"Diagnosis, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003936","descriptor_name":"Diagnosis, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003936","descriptor_name":"Diagnosis, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bth373","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth373","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:15217814","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15217814","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.97.7568","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.97.7568","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/cgi/reprint/bth373v2.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6800000071525574,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W54893182","https://openalex.org/W1491953564","https://openalex.org/W1493217831","https://openalex.org/W1499399028","https://openalex.org/W1527883571","https://openalex.org/W2009418433","https://openalex.org/W2019330983","https://openalex.org/W2029817244","https://openalex.org/W2053043119","https://openalex.org/W2074228092","https://openalex.org/W2109363337","https://openalex.org/W2125055259","https://openalex.org/W2135187880","https://openalex.org/W2141115288","https://openalex.org/W2147246240","https://openalex.org/W2988864014","https://openalex.org/W3085162807"],"related_works":["https://openalex.org/W2804364458","https://openalex.org/W4298130764","https://openalex.org/W2132641928","https://openalex.org/W2090259340","https://openalex.org/W4310225030","https://openalex.org/W2083665254","https://openalex.org/W2393816671","https://openalex.org/W1534720161","https://openalex.org/W2804957450","https://openalex.org/W2942177010"],"abstract_inverted_index":{"We":[0],"present":[1],"the":[2,12,17,30,94],"novel":[3],"technique":[4],"of":[5,20,53],"'itemset":[6],"constrained":[7],"clustering'":[8],"(IC-Clustering),":[9],"which":[10,25,56,72],"computes":[11],"optimal":[13],"cluster":[14,49],"that":[15,32,35,58],"maximizes":[16],"interclass":[18],"variance":[19],"gene":[21,69],"expression":[22,70],"between":[23],"groups,":[24],"are":[26,42],"divided":[27],"according":[28],"to":[29,62],"restriction":[31],"only":[33],"divisions":[34],"can":[36],"be":[37,74],"expressed":[38],"using":[39],"common":[40],"features":[41,55],"allowed.":[43],"This":[44],"constraint":[45],"automatically":[46],"labels":[47],"each":[48],"with":[50,76],"a":[51],"set":[52],"pathological":[54,78],"characterize":[57],"cluster.":[59],"When":[60],"applied":[61],"liver":[63,90],"cancer":[64],"datasets,":[65],"IC-Clustering":[66],"revealed":[67],"informative":[68],"clusters,":[71],"could":[73],"annotated":[75],"various":[77],"features,":[79],"such":[80],"as":[81],"'tumor'":[82],"and":[83,88],"'man',":[84],"or":[85],"'except":[86],"tumor'":[87],"'normal":[89],"function'.":[91],"In":[92],"contrast,":[93],"k-means":[95],"method":[96],"overlooked":[97],"these":[98],"clusters.":[99]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":3}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}