{"id":"https://openalex.org/W2212274337","doi":"https://doi.org/10.1109/bibm.2015.7359855","title":"Network signatures based on gene pair expression ratios improve classification and the analysis of muscle-invasive urothelial cancer","display_name":"Network signatures based on gene pair expression ratios improve classification and the analysis of muscle-invasive urothelial cancer","publication_year":2015,"publication_date":"2015-11-01","ids":{"openalex":"https://openalex.org/W2212274337","doi":"https://doi.org/10.1109/bibm.2015.7359855","mag":"2212274337"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2015.7359855","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2015.7359855","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5005661878","display_name":"Ricardo De Matos Simoes","orcid":"https://orcid.org/0000-0002-1700-5276"},"institutions":[{"id":"https://openalex.org/I126231945","display_name":"Queen's University Belfast","ror":"https://ror.org/00hswnk62","country_code":"GB","type":"education","lineage":["https://openalex.org/I126231945"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["GB","US"],"is_corresponding":true,"raw_author_name":"Ricardo de Matos Simoes","raw_affiliation_strings":["Center for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK","Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA"],"affiliations":[{"raw_affiliation_string":"Center for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK","institution_ids":["https://openalex.org/I126231945"]},{"raw_affiliation_string":"Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA","institution_ids":["https://openalex.org/I4210117453","https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012712111","display_name":"Constantine S. Mitsiades","orcid":"https://orcid.org/0000-0003-2321-8005"},"institutions":[{"id":"https://openalex.org/I126231945","display_name":"Queen's University Belfast","ror":"https://ror.org/00hswnk62","country_code":"GB","type":"education","lineage":["https://openalex.org/I126231945"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Constantine Mitsiades","raw_affiliation_strings":["Center for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK"],"affiliations":[{"raw_affiliation_string":"Center for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK","institution_ids":["https://openalex.org/I126231945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108433103","display_name":"Kate E. Williamson","orcid":null},"institutions":[{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kate E Williamson","raw_affiliation_strings":["Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA"],"affiliations":[{"raw_affiliation_string":"Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA","institution_ids":["https://openalex.org/I4210117453","https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057625030","display_name":"Frank Emmert\u2010Streib","orcid":"https://orcid.org/0000-0003-0745-5641"},"institutions":[{"id":"https://openalex.org/I4210133110","display_name":"Tampere University","ror":null,"country_code":"FI","type":null,"lineage":["https://openalex.org/I4210133110"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Frank Emmert-Streib","raw_affiliation_strings":["Tampere University of Technology, Tampere, Finland"],"affiliations":[{"raw_affiliation_string":"Tampere University of Technology, Tampere, Finland","institution_ids":["https://openalex.org/I4210133110"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5005661878"],"corresponding_institution_ids":["https://openalex.org/I126231945","https://openalex.org/I136199984","https://openalex.org/I4210117453"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.12849759,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"57","issue":null,"first_page":"1216","last_page":"1223"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11297","display_name":"Ferroptosis and cancer prognosis","score":0.9912999868392944,"subfield":{"id":"https://openalex.org/subfields/2740","display_name":"Pulmonary and Respiratory Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11297","display_name":"Ferroptosis and cancer prognosis","score":0.9912999868392944,"subfield":{"id":"https://openalex.org/subfields/2740","display_name":"Pulmonary and Respiratory Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12465","display_name":"Cancer, Lipids, and Metabolism","score":0.9873999953269958,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10458","display_name":"Bladder and Urothelial Cancer Treatments","score":0.9728999733924866,"subfield":{"id":"https://openalex.org/subfields/2746","display_name":"Surgery"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/bladder-cancer","display_name":"Bladder cancer","score":0.6315872073173523},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6142477989196777},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.5907536149024963},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5648818016052246},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.5484389662742615},{"id":"https://openalex.org/keywords/gene-co-expression-network","display_name":"Gene co-expression network","score":0.5227980017662048},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5217210054397583},{"id":"https://openalex.org/keywords/gene-signature","display_name":"Gene signature","score":0.47711923718452454},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.44397518038749695},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.42667102813720703},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3407045304775238},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.30148857831954956},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.25761914253234863},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1437380015850067},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.08971050381660461}],"concepts":[{"id":"https://openalex.org/C2780352672","wikidata":"https://www.wikidata.org/wiki/Q504775","display_name":"Bladder cancer","level":3,"score":0.6315872073173523},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6142477989196777},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5907536149024963},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5648818016052246},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.5484389662742615},{"id":"https://openalex.org/C2778022302","wikidata":"https://www.wikidata.org/wiki/Q18207329","display_name":"Gene co-expression network","level":5,"score":0.5227980017662048},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5217210054397583},{"id":"https://openalex.org/C2779733811","wikidata":"https://www.wikidata.org/wiki/Q5531562","display_name":"Gene signature","level":4,"score":0.47711923718452454},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.44397518038749695},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.42667102813720703},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3407045304775238},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.30148857831954956},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.25761914253234863},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1437380015850067},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.08971050381660461}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/bibm.2015.7359855","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2015.7359855","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},{"id":"pmh:oai:pure.qub.ac.uk/portal:publications/79bbcc5e-f53d-4a80-b9a9-ddd424862fb8","is_oa":false,"landing_page_url":"https://pure.qub.ac.uk/en/publications/79bbcc5e-f53d-4a80-b9a9-ddd424862fb8","pdf_url":null,"source":{"id":"https://openalex.org/S4306402319","display_name":"Research Portal (Queen's University Belfast)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I126231945","host_organization_name":"Queen's University Belfast","host_organization_lineage":["https://openalex.org/I126231945"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"De Matos Simoes , R , Mitsiades , C , Williamson , K &amp; Emmert-Streib , F 2015 , Network signatures based on gene pair expression ratios improve classification and the analysis of muscle-invasive urothelial cancer . in Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 . , 7359855 , Institute of Electrical and Electronics Engineers Inc. , pp. 1216-1223 , IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 , Washington , United States , 09/11/2015 . https://doi.org/10.1109/BIBM.2015.7359855","raw_type":"contributionToPeriodical"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6600000262260437,"display_name":"Reduced inequalities","id":"https://metadata.un.org/sdg/10"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320314204","display_name":"Invest Northern Ireland","ror":"https://ror.org/00qnrsq87"},{"id":"https://openalex.org/F4320330412","display_name":"Scheme for Promotion of Academic and Research Collaboration","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":43,"referenced_works":["https://openalex.org/W1831050183","https://openalex.org/W1980477405","https://openalex.org/W1982428412","https://openalex.org/W2003516452","https://openalex.org/W2011546561","https://openalex.org/W2036953628","https://openalex.org/W2050559302","https://openalex.org/W2053808261","https://openalex.org/W2061805562","https://openalex.org/W2064553234","https://openalex.org/W2077997913","https://openalex.org/W2084331800","https://openalex.org/W2094346650","https://openalex.org/W2097360283","https://openalex.org/W2099951161","https://openalex.org/W2100706001","https://openalex.org/W2100714130","https://openalex.org/W2102140136","https://openalex.org/W2105924489","https://openalex.org/W2106248311","https://openalex.org/W2109972881","https://openalex.org/W2110065044","https://openalex.org/W2110520112","https://openalex.org/W2114299743","https://openalex.org/W2116063398","https://openalex.org/W2119589567","https://openalex.org/W2122825543","https://openalex.org/W2124614719","https://openalex.org/W2128209214","https://openalex.org/W2128689695","https://openalex.org/W2128873464","https://openalex.org/W2134672568","https://openalex.org/W2134976939","https://openalex.org/W2135959680","https://openalex.org/W2145424370","https://openalex.org/W2150420891","https://openalex.org/W2154947819","https://openalex.org/W2155723007","https://openalex.org/W2156295630","https://openalex.org/W2157132621","https://openalex.org/W4211054902","https://openalex.org/W4294541781","https://openalex.org/W7073956601"],"related_works":["https://openalex.org/W2898558914","https://openalex.org/W4237262135","https://openalex.org/W2042571415","https://openalex.org/W2061000157","https://openalex.org/W2055417018","https://openalex.org/W2096022647","https://openalex.org/W1988798370","https://openalex.org/W3196601718","https://openalex.org/W2755552661","https://openalex.org/W3112275362"],"abstract_inverted_index":{"Urothelial":[0],"cancer":[1,54,141,193,229],"(UC)":[2],"is":[3,74,103],"highly":[4],"recurrent":[5],"and":[6,48,109,134,161,166,198,214],"can":[7,41],"progress":[8],"from":[9,150,185],"non-invasive":[10],"(NMIUC)":[11],"to":[12,44,105,173,227,232],"a":[13,30,69,86,114,130,189,202],"more":[14],"aggressive":[15],"muscle-invasive":[16],"(MIUC)":[17],"subtype":[18],"that":[19,35,81,145,182,236],"invades":[20],"the":[21,26,49,59,91,137,146,162,169,212],"muscle":[22],"tissue":[23],"layer":[24],"of":[25,32,38,52,62,68,139,153,192,216],"bladder.":[27],"We":[28,112,143,200],"present":[29],"proof":[31],"principle":[33],"study":[34],"network-based":[36,101,147,233],"features":[37],"gene":[39,55,71,77,148,175,208,230],"pairs":[40],"be":[42],"used":[43],"improve":[45],"classifier":[46],"performance":[47,171],"functional":[50,131],"analysis":[51,133,210],"urothelial":[53],"expression":[56,72,79,209,234,242],"data.":[57],"In":[58,90],"first":[60],"step":[61,93],"our":[63,224],"procedure":[64,99],"each":[65],"individual":[66],"sample":[67],"UC":[70],"dataset":[73],"inflated":[75],"by":[76,129],"pair":[78],"ratios":[80],"are":[82,237],"defined":[83],"based":[84,176,180],"on":[85],"given":[87],"network":[88,125,179],"structure.":[89],"second":[92],"an":[94],"elastic":[95],"net":[96],"feature":[97],"selection":[98],"for":[100,136,206,211],"signatures":[102,126,149,181,235],"applied":[104],"discriminate":[106],"between":[107],"NMIUC":[108],"MIUC":[110],"samples.":[111],"performed":[113],"repeated":[115],"random":[116],"subsampling":[117],"cross":[118],"validation":[119],"in":[120,220,240],"three":[121],"independent":[122],"datasets.":[123],"The":[124,178],"were":[127,183],"characterized":[128],"enrichment":[132,138,191],"studied":[135],"known":[140],"genes.":[142],"observed":[144,239],"meta":[151],"collections":[152],"protein-protein":[154],"interaction":[155],"(PPI)":[156],"databases":[157,164,187],"such":[158],"as":[159],"CPDB":[160],"PPI":[163,186],"HPRD":[165],"BioGrid":[167],"improved":[168],"classification":[170],"compared":[172],"single":[174],"signatures.":[177,243],"derived":[184],"showed":[188],"prominent":[190],"genes":[194],"(e.g.,":[195],"TP53,":[196],"TRIM27":[197],"HNRNPA2B1).":[199],"provide":[201],"novel":[203,217],"integrative":[204],"approach":[205],"large-scale":[207],"identification":[213],"development":[215],"diagnostical":[218],"targets":[219],"bladder":[221],"cancer.":[222],"Further,":[223],"method":[225],"allowed":[226],"link":[228],"associations":[231],"not":[238],"gene-based":[241]},"counts_by_year":[{"year":2023,"cited_by_count":1}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
