{"id":"https://openalex.org/W2952732051","doi":"https://doi.org/10.1093/bioinformatics/bty698","title":"DCARS: differential correlation across ranked samples","display_name":"DCARS: differential correlation across ranked samples","publication_year":2018,"publication_date":"2018-08-07","ids":{"openalex":"https://openalex.org/W2952732051","doi":"https://doi.org/10.1093/bioinformatics/bty698","mag":"2952732051","pmid":"https://pubmed.ncbi.nlm.nih.gov/30102408"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty698","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty698","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/A5087355766","display_name":"Shila Ghazanfar","orcid":"https://orcid.org/0000-0001-7861-6997"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Shila Ghazanfar","raw_affiliation_strings":["School of Mathematics and Statistics, University of Sydney, Sydney, NSW, Australia","The Judith and David Coffey Life Lab, Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia"],"raw_orcid":"https://orcid.org/0000-0001-7861-6997","affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, University of Sydney, Sydney, NSW, Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"The Judith and David Coffey Life Lab, Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia","institution_ids":["https://openalex.org/I129604602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033872539","display_name":"Dario Strbenac","orcid":"https://orcid.org/0000-0001-9234-3243"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Dario Strbenac","raw_affiliation_strings":["School of Mathematics and Statistics, University of Sydney, Sydney, NSW, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, University of Sydney, Sydney, NSW, Australia","institution_ids":["https://openalex.org/I129604602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050677327","display_name":"John T. Ormerod","orcid":"https://orcid.org/0000-0002-4650-7507"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]},{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I4210123005","display_name":"ARC Centre of Excellence for Mathematical and Statistical Frontiers","ror":"https://ror.org/02vcqg248","country_code":"AU","type":"facility","lineage":["https://openalex.org/I1337719021","https://openalex.org/I165779595","https://openalex.org/I2801453606","https://openalex.org/I4210123005","https://openalex.org/I4210132349"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"John T Ormerod","raw_affiliation_strings":["ARC Centre of Excellence for Mathematical and Statistical Frontiers (ACEMS), Richard Berry Building, The University of Melbourne, Melbourne, Parkville, VIC, Australia","School of Mathematics and Statistics, University of Sydney, Sydney, NSW, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ARC Centre of Excellence for Mathematical and Statistical Frontiers (ACEMS), Richard Berry Building, The University of Melbourne, Melbourne, Parkville, VIC, Australia","institution_ids":["https://openalex.org/I165779595","https://openalex.org/I4210123005"]},{"raw_affiliation_string":"School of Mathematics and Statistics, University of Sydney, Sydney, NSW, Australia","institution_ids":["https://openalex.org/I129604602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028524705","display_name":"Jean Yang","orcid":"https://orcid.org/0000-0002-5271-2603"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Jean Y H Yang","raw_affiliation_strings":["School of Mathematics and Statistics, University of Sydney, Sydney, NSW, Australia","The Judith and David Coffey Life Lab, Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, University of Sydney, Sydney, NSW, Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"The Judith and David Coffey Life Lab, Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia","institution_ids":["https://openalex.org/I129604602"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042620584","display_name":"Ellis Patrick","orcid":"https://orcid.org/0000-0002-5253-4747"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]},{"id":"https://openalex.org/I4210145422","display_name":"Westmead Institute for Medical Research","ror":"https://ror.org/04zj3ra44","country_code":"AU","type":"facility","lineage":["https://openalex.org/I4210145422"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Ellis Patrick","raw_affiliation_strings":["School of Mathematics and Statistics, University of Sydney, Sydney, NSW, Australia","Westmead Institute for Medical Research, University of Sydney, Westmead, NSW, Australia"],"raw_orcid":"https://orcid.org/0000-0002-5253-4747","affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, University of Sydney, Sydney, NSW, Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"Westmead Institute for Medical Research, University of Sydney, Westmead, NSW, Australia","institution_ids":["https://openalex.org/I129604602","https://openalex.org/I4210145422"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5087355766"],"corresponding_institution_ids":["https://openalex.org/I129604602"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.4136,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.60425699,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"35","issue":"5","first_page":"823","last_page":"829"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9922999739646912,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.9629999995231628,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/correlation","display_name":"Correlation","score":0.709720253944397},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.6818351745605469},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5084623098373413},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4770837724208832},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.465268611907959},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.42223498225212097},{"id":"https://openalex.org/keywords/differential","display_name":"Differential (mechanical device)","score":0.41384217143058777},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4024888873100281},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3663089871406555},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.21072790026664734},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.19582244753837585},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.13715609908103943}],"concepts":[{"id":"https://openalex.org/C117220453","wikidata":"https://www.wikidata.org/wiki/Q5172842","display_name":"Correlation","level":2,"score":0.709720253944397},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.6818351745605469},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5084623098373413},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4770837724208832},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.465268611907959},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.42223498225212097},{"id":"https://openalex.org/C93226319","wikidata":"https://www.wikidata.org/wiki/Q193137","display_name":"Differential (mechanical device)","level":2,"score":0.41384217143058777},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4024888873100281},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3663089871406555},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21072790026664734},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.19582244753837585},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.13715609908103943},{"id":"https://openalex.org/C146978453","wikidata":"https://www.wikidata.org/wiki/Q3798668","display_name":"Aerospace engineering","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},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[{"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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bty698","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty698","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:30102408","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30102408","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":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5707414633","display_name":"Statistical bioinformatics for network based prognostic and precision therapy in complex disease","funder_award_id":"1111338","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"},{"id":"https://openalex.org/G7630230800","display_name":"Prognosis based network-type feature extraction for complex biological data","funder_award_id":"DP170100654","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"}],"funders":[{"id":"https://openalex.org/F4320334704","display_name":"Australian Research Council","ror":"https://ror.org/05mmh0f86"},{"id":"https://openalex.org/F4320334705","display_name":"National Health and Medical Research Council","ror":"https://ror.org/011kf5r70"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W229097380","https://openalex.org/W1650797637","https://openalex.org/W1899117259","https://openalex.org/W1922783847","https://openalex.org/W1973370947","https://openalex.org/W1981058260","https://openalex.org/W1984883254","https://openalex.org/W1985987855","https://openalex.org/W1991902954","https://openalex.org/W2005794864","https://openalex.org/W2033395428","https://openalex.org/W2039521726","https://openalex.org/W2069733150","https://openalex.org/W2096173332","https://openalex.org/W2102140136","https://openalex.org/W2107665951","https://openalex.org/W2112811019","https://openalex.org/W2114954827","https://openalex.org/W2116531018","https://openalex.org/W2117692326","https://openalex.org/W2120116723","https://openalex.org/W2121110265","https://openalex.org/W2139227366","https://openalex.org/W2153768000","https://openalex.org/W2168264491","https://openalex.org/W2182189596","https://openalex.org/W2230320310","https://openalex.org/W2519004842","https://openalex.org/W2554705260","https://openalex.org/W2576619051"],"related_works":["https://openalex.org/W2188500270","https://openalex.org/W2303858293","https://openalex.org/W2915512527","https://openalex.org/W2798198862","https://openalex.org/W51364034","https://openalex.org/W2798997222","https://openalex.org/W2793336762","https://openalex.org/W2091548507","https://openalex.org/W2368816706","https://openalex.org/W3124253442"],"abstract_inverted_index":{"MOTIVATION:":[0],"Genes":[1],"act":[2],"as":[3,30,115,117],"a":[4,68,118,125,177],"system":[5],"and":[6,83,203,212,237],"not":[7,73],"in":[8,44,87,161,179,191],"isolation.":[9],"Thus,":[10],"it":[11],"is":[12,241],"important":[13],"to":[14,157,173,197],"consider":[15],"coordinated":[16],"changes":[17,43],"of":[18,33,49,55,77,96,99],"gene":[19,65,88,135],"expression":[20],"rather":[21],"than":[22],"single":[23],"genes":[24,50,140],"when":[25],"investigating":[26],"biological":[27,199],"phenomena":[28],"such":[29],"the":[31,45,53,75,97,107,231],"aetiology":[32],"cancer.":[34],"We":[35],"have":[36],"developed":[37],"an":[38],"approach":[39,120],"for":[40,112,122,167],"quantifying":[41],"how":[42],"association":[46],"between":[47,181],"pairs":[48,136],"may":[51],"inform":[52],"outcome":[54,98],"interest":[56],"called":[57],"Differential":[58],"Correlation":[59],"across":[60,67,90,143],"Ranked":[61],"Samples":[62],"(DCARS).":[63],"Modelling":[64],"correlation":[66,89,180],"continuous":[69],"sample":[70,213],"ranking":[71,170],"does":[72],"require":[74],"dichotomisation":[76],"samples":[78],"into":[79],"two":[80],"distinct":[81,165],"classes":[82],"can":[84,188],"identify":[85],"differences":[86],"early,":[91],"mid":[92],"or":[93],"late":[94],"stages":[95],"interest.":[100],"RESULTS:":[101],"When":[102],"we":[103,184],"evaluated":[104],"DCARS":[105,132,154,187,209,238],"against":[106],"typical":[108,119],"Fisher":[109],"Z-transformation":[110],"test":[111],"differential":[113],"correlation,":[114],"well":[116],"testing":[121],"interaction":[123],"within":[124],"linear":[126],"model,":[127],"on":[128],"real":[129],"TCGA":[130],"data,":[131],"significantly":[133],"ranked":[134],"containing":[137],"known":[138],"cancer":[139],"more":[141],"highly":[142],"several":[144,164],"cancers.":[145],"Similar":[146],"results":[147],"are":[148,215,249],"found":[149,172],"with":[150,176,193],"our":[151],"simulation":[152],"study.":[153],"was":[155,171,228],"applied":[156],"13":[158],"cancers":[159],"datasets":[160],"TCGA,":[162],"revealing":[163],"relationships":[166],"which":[168],"survival":[169],"be":[174,189],"associated":[175],"change":[178],"genes.":[182],"Furthermore,":[183],"demonstrated":[185],"that":[186],"used":[190,229],"conjunction":[192],"network":[194],"analysis":[195],"techniques":[196],"extract":[198],"meaning":[200],"from":[201,222],"multi-layered":[202],"complex":[204],"data.":[205],"AVAILABILITY":[206],"AND":[207],"IMPLEMENTATION:":[208],"R":[210,233,239],"package":[211,240],"data":[214,221,248],"available":[216,220,242,250],"at":[217,243,251],"https://github.com/shazanfar/DCARS.":[218,244],"Publicly":[219],"The":[223],"Cancer":[224],"Genome":[225],"Atlas":[226],"(TCGA)":[227],"using":[230],"TCGABiolinks":[232],"package.":[234],"Supplementary":[235,247],"Files":[236],"SUPPLEMENTARY":[245],"INFORMATION:":[246],"Bioinformatics":[252],"online.":[253]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2019-06-27T00:00:00"}
