{"id":"https://openalex.org/W2163988673","doi":"https://doi.org/10.1093/bioinformatics/bth354","title":"Biologically valid linear factor models of gene expression","display_name":"Biologically valid linear factor models of gene expression","publication_year":2004,"publication_date":"2004-06-16","ids":{"openalex":"https://openalex.org/W2163988673","doi":"https://doi.org/10.1093/bioinformatics/bth354","mag":"2163988673","pmid":"https://pubmed.ncbi.nlm.nih.gov/15201181"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bth354","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth354","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/A5045384249","display_name":"Mark Girolami","orcid":"https://orcid.org/0000-0003-3008-253X"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Mark Girolami","raw_affiliation_strings":["Bioinformatics Research Centre, Department of Computing Science, University of Glasgow, UK. girolami@dcs.gla.ac.uk"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Centre, Department of Computing Science, University of Glasgow, UK. girolami@dcs.gla.ac.uk","institution_ids":["https://openalex.org/I7882870"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070145336","display_name":"Rainer Breitling","orcid":"https://orcid.org/0000-0001-7173-0922"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Rainer Breitling","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5045384249"],"corresponding_institution_ids":["https://openalex.org/I7882870"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":2.1685,"has_fulltext":false,"cited_by_count":31,"citation_normalized_percentile":{"value":0.87321123,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"20","issue":"17","first_page":"3021","last_page":"3033"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9591000080108643,"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":0.9591000080108643,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.00800000037997961,"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/T12867","display_name":"Advanced Biosensing Techniques and Applications","score":0.002199999988079071,"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/expression","display_name":"Expression (computer science)","score":0.5678310394287109},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5443165302276611},{"id":"https://openalex.org/keywords/factor","display_name":"Factor (programming language)","score":0.5426471829414368},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.46807560324668884},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4516758322715759},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.44740796089172363},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.35651296377182007},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.34747830033302307},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.34696322679519653},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09823858737945557}],"concepts":[{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.5678310394287109},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5443165302276611},{"id":"https://openalex.org/C2781039887","wikidata":"https://www.wikidata.org/wiki/Q1391724","display_name":"Factor (programming language)","level":2,"score":0.5426471829414368},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.46807560324668884},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4516758322715759},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.44740796089172363},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.35651296377182007},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.34747830033302307},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.34696322679519653},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09823858737945557}],"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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018384","descriptor_name":"Oxidative Stress","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D018384","descriptor_name":"Oxidative Stress","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D018384","descriptor_name":"Oxidative Stress","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D018797","descriptor_name":"Cell Cycle Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018797","descriptor_name":"Cell Cycle Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018797","descriptor_name":"Cell Cycle Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","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},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bth354","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth354","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:15201181","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15201181","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":"Comparative Study"},{"id":"pmh:oai:pure.atira.dk:openaire_cris_publications/5c077a2d-aa70-4417-9c1f-5163deb0a3a3","is_oa":false,"landing_page_url":"https://research.manchester.ac.uk/en/publications/5c077a2d-aa70-4417-9c1f-5163deb0a3a3","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Girolami, M & Breitling, R 2004, 'Biologically valid linear factor models of gene expressions', Bioinformatics, vol. 20, no. 17, pp. 3021-3033. https://doi.org/10.1093/bioinformatics/bth354","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pure.atira.dk:publications/5c077a2d-aa70-4417-9c1f-5163deb0a3a3","is_oa":false,"landing_page_url":"https://www.research.manchester.ac.uk/portal/en/publications/biologically-valid-linear-factor-models-of-gene-expressions(5c077a2d-aa70-4417-9c1f-5163deb0a3a3).html","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Girolami, M & Breitling, R 2004, 'Biologically valid linear factor models of gene expressions', Bioinformatics, vol. 20, no. 17, pp. 3021-3033. https://doi.org/10.1093/bioinformatics/bth354","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1216003154","https://openalex.org/W1527042480","https://openalex.org/W1548802052","https://openalex.org/W1586727544","https://openalex.org/W2063111759","https://openalex.org/W2075665712","https://openalex.org/W2085702771","https://openalex.org/W2095109339","https://openalex.org/W2103453943","https://openalex.org/W2121824548","https://openalex.org/W2125027820","https://openalex.org/W2125512776","https://openalex.org/W2126662731","https://openalex.org/W2130470264","https://openalex.org/W2137683543","https://openalex.org/W2146264532","https://openalex.org/W2148541040","https://openalex.org/W2150926065","https://openalex.org/W2151797745","https://openalex.org/W2155386706","https://openalex.org/W2158128075","https://openalex.org/W2162491638"],"related_works":["https://openalex.org/W2392243736","https://openalex.org/W86652014","https://openalex.org/W2328518092","https://openalex.org/W3101249758","https://openalex.org/W2382079200","https://openalex.org/W2374091470","https://openalex.org/W3032874291","https://openalex.org/W2005057264","https://openalex.org/W2363156284","https://openalex.org/W2415025170"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"The":[2,144],"identification":[3],"of":[4,47,67,74,103,129,136],"physiological":[5],"processes":[6,50],"underlying":[7,62],"and":[8,105,131,154,160],"generating":[9],"the":[10,53,59,75,100,127,132,137,166],"expression":[11],"pattern":[12],"observed":[13],"in":[14],"microarray":[15,80,124],"experiments":[16],"is":[17,25,32,88],"a":[18,26,41,89],"major":[19],"challenge.":[20],"Principal":[21],"component":[22],"analysis":[23,91],"(PCA)":[24],"linear":[27,108,138],"multivariate":[28],"statistical":[29],"method":[30],"that":[31,36],"regularly":[33],"employed":[34],"for":[35,44],"purpose":[37],"as":[38,151,156,158],"it":[39],"provides":[40],"reduced-dimensional":[42],"representation":[43,82],"subsequent":[45],"study":[46,120],"possible":[48],"biological":[49,68,72,86,116,134],"responding":[51],"to":[52],"particular":[54],"experimental":[55],"conditions.":[56],"Making":[57],"explicit":[58],"data":[60,81,159],"assumptions":[61],"PCA":[63,104,130],"highlights":[64,126],"their":[65],"lack":[66],"validity":[69],"thus":[70],"making":[71],"interpretation":[73,87,102],"principal":[76],"components":[77],"problematic.":[78],"A":[79,118],"which":[83,111],"enables":[84],"clear":[85],"desirable":[90],"tool.":[92],"Results:":[93],"We":[94],"address":[95],"this":[96],"issue":[97],"by":[98],"employing":[99],"probabilistic":[101],"proposing":[106],"alternative":[107],"factor":[109],"models":[110,139],"are":[112,148,163],"based":[113],"on":[114,121],"refined":[115],"assumptions.":[117],"practical":[119],"two":[122],"well-understood":[123],"datasets":[125],"weakness":[128],"greater":[133],"interpretability":[135],"we":[140],"have":[141],"developed.":[142],"Availability:":[143],"model":[145],"estimation":[146],"routines":[147,153],"currently":[149],"implemented":[150],"Matlab":[152],"these,":[155],"well":[157],"results":[161],"reported,":[162],"available":[164],"from":[165],"following":[167],"URL:":[168],"http://www.dcs.gla.ac.uk/~girolami/lfm/index.html":[169]},"counts_by_year":[{"year":2015,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
