{"id":"https://openalex.org/W2150894805","doi":"https://doi.org/10.1093/bioinformatics/bts112","title":"Deriving transcriptional programs and functional processes from gene expression databases","display_name":"Deriving transcriptional programs and functional processes from gene expression databases","publication_year":2012,"publication_date":"2012-03-08","ids":{"openalex":"https://openalex.org/W2150894805","doi":"https://doi.org/10.1093/bioinformatics/bts112","mag":"2150894805","pmid":"https://pubmed.ncbi.nlm.nih.gov/22408194"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts112","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts112","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/8/1122/48930321/bioinformatics_28_8_1122.pdf","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","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":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/28/8/1122/48930321/bioinformatics_28_8_1122.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004242684","display_name":"Jeffrey T. Chang","orcid":"https://orcid.org/0000-0002-4578-5636"},"institutions":[{"id":"https://openalex.org/I4210159031","display_name":"The University of Texas Health Science Center","ror":"https://ror.org/05cwbxa29","country_code":"US","type":"education","lineage":["https://openalex.org/I4210159031"]},{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jeffrey T. Chang","raw_affiliation_strings":["Department of Integrative Biology and Pharmacology, The University of Texas Health Science Center in Houston, Houston, TX 77030, USA. jeffrey.t.chang@uth.tmc.edu","Department of Integrative Biology and Pharmacology, The University of Texas Health Science Center in Houston, Houston, TX 77030, USA"],"affiliations":[{"raw_affiliation_string":"Department of Integrative Biology and Pharmacology, The University of Texas Health Science Center in Houston, Houston, TX 77030, USA. jeffrey.t.chang@uth.tmc.edu","institution_ids":["https://openalex.org/I4210159031","https://openalex.org/I919571938"]},{"raw_affiliation_string":"Department of Integrative Biology and Pharmacology, The University of Texas Health Science Center in Houston, Houston, TX 77030, USA","institution_ids":["https://openalex.org/I919571938"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5004242684"],"corresponding_institution_ids":["https://openalex.org/I4210159031","https://openalex.org/I919571938"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.2627,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.58355619,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"28","issue":"8","first_page":"1122","last_page":"1129"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9987999796867371,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9984999895095825,"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/database","display_name":"Database","score":0.6721081137657166},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.6060431599617004},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6060030460357666},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5744717121124268},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.5508532524108887},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5245782732963562},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4911169707775116},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.471037894487381},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.4584178328514099},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.442328542470932},{"id":"https://openalex.org/keywords/gene-nomenclature","display_name":"Gene nomenclature","score":0.42866894602775574},{"id":"https://openalex.org/keywords/transcriptional-regulation","display_name":"Transcriptional regulation","score":0.4274613857269287},{"id":"https://openalex.org/keywords/biological-pathway","display_name":"Biological pathway","score":0.4253963530063629},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3397296667098999},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.317885160446167}],"concepts":[{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.6721081137657166},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.6060431599617004},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6060030460357666},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5744717121124268},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.5508532524108887},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5245782732963562},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4911169707775116},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.471037894487381},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.4584178328514099},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.442328542470932},{"id":"https://openalex.org/C62177273","wikidata":"https://www.wikidata.org/wiki/Q5531556","display_name":"Gene nomenclature","level":4,"score":0.42866894602775574},{"id":"https://openalex.org/C27153228","wikidata":"https://www.wikidata.org/wiki/Q3787274","display_name":"Transcriptional regulation","level":4,"score":0.4274613857269287},{"id":"https://openalex.org/C9927688","wikidata":"https://www.wikidata.org/wiki/Q4915012","display_name":"Biological pathway","level":4,"score":0.4253963530063629},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3397296667098999},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.317885160446167},{"id":"https://openalex.org/C58642233","wikidata":"https://www.wikidata.org/wiki/Q8269924","display_name":"Taxonomy (biology)","level":2,"score":0.0},{"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/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C514705636","wikidata":"https://www.wikidata.org/wiki/Q863247","display_name":"Nomenclature","level":3,"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":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D002453","descriptor_name":"Cell Cycle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002453","descriptor_name":"Cell Cycle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002453","descriptor_name":"Cell Cycle","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"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":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D050684","descriptor_name":"E2F Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D050684","descriptor_name":"E2F Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D050684","descriptor_name":"E2F Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bts112","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts112","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/8/1122/48930321/bioinformatics_28_8_1122.pdf","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22408194","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22408194","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:europepmc.org:2620016","is_oa":false,"landing_page_url":"http://europepmc.org/articles/PMC3324522","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3324522","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3324522","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts112","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts112","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/8/1122/48930321/bioinformatics_28_8_1122.pdf","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.41999998688697815}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2150894805.pdf","grobid_xml":"https://content.openalex.org/works/W2150894805.grobid-xml"},"referenced_works_count":59,"referenced_works":["https://openalex.org/W88518327","https://openalex.org/W1517579686","https://openalex.org/W1607267312","https://openalex.org/W1730877038","https://openalex.org/W1753047181","https://openalex.org/W1976209715","https://openalex.org/W2010457001","https://openalex.org/W2016311718","https://openalex.org/W2020859582","https://openalex.org/W2023720844","https://openalex.org/W2043653128","https://openalex.org/W2048066878","https://openalex.org/W2058451329","https://openalex.org/W2065343028","https://openalex.org/W2068858902","https://openalex.org/W2073727170","https://openalex.org/W2078202582","https://openalex.org/W2080152736","https://openalex.org/W2080498142","https://openalex.org/W2082668371","https://openalex.org/W2088468751","https://openalex.org/W2092224388","https://openalex.org/W2094678200","https://openalex.org/W2095718954","https://openalex.org/W2097168572","https://openalex.org/W2097255042","https://openalex.org/W2099101879","https://openalex.org/W2101155068","https://openalex.org/W2101696428","https://openalex.org/W2102614435","https://openalex.org/W2103017472","https://openalex.org/W2104357712","https://openalex.org/W2105712639","https://openalex.org/W2110065044","https://openalex.org/W2112464428","https://openalex.org/W2114381883","https://openalex.org/W2116961371","https://openalex.org/W2120261416","https://openalex.org/W2121604817","https://openalex.org/W2123879591","https://openalex.org/W2124711114","https://openalex.org/W2125508747","https://openalex.org/W2128540871","https://openalex.org/W2129795133","https://openalex.org/W2130410032","https://openalex.org/W2133465414","https://openalex.org/W2135000328","https://openalex.org/W2135030836","https://openalex.org/W2146264532","https://openalex.org/W2157132621","https://openalex.org/W2158217645","https://openalex.org/W2160073543","https://openalex.org/W2162874742","https://openalex.org/W2165232124","https://openalex.org/W2166103265","https://openalex.org/W2168459422","https://openalex.org/W2791873134","https://openalex.org/W6603590815","https://openalex.org/W6635882816"],"related_works":["https://openalex.org/W1515070932","https://openalex.org/W4243726184","https://openalex.org/W2159799774","https://openalex.org/W3130139893","https://openalex.org/W1973260612","https://openalex.org/W2620422757","https://openalex.org/W2092671888","https://openalex.org/W2132025459","https://openalex.org/W2006820294","https://openalex.org/W2745533986"],"abstract_inverted_index":{"To":[0],"address":[1,55,126],"this":[2],"issue,":[3],"we":[4,26,51,60,81],"have":[5],"developed":[6],"a":[7,22,73,78,88,108],"high-throughput":[8],"method":[9],"to":[10,42,54,93,125],"mine":[11],"gene":[12,19,31,91,116],"expression":[13,32,117],"databases":[14],"for":[15,36,122],"the":[16,49,62,83,105,112,120],"regulation":[17,86],"of":[18,24,38,85,90,99,107,111],"sets.":[20],"Given":[21],"set":[23],"genes,":[25],"scored":[27],"it":[28,53],"against":[29],"each":[30],"dataset":[33],"by":[34],"looking":[35],"enrichment":[37],"co-regulated":[39],"genes":[40],"relative":[41],"an":[43,95],"empirical":[44],"null":[45],"distribution.":[46],"After":[47],"validating":[48],"method,":[50],"applied":[52],"two":[56],"biological":[57,100,127],"problems.":[58],"First,":[59],"deciphered":[61],"E2F":[63],"transcriptional":[64,70],"network.":[65],"We":[66],"confirmed":[67],"that":[68],"true":[69],"targets":[71],"exhibit":[72],"distinct":[74],"regulatory":[75],"profile":[76],"across":[77,87],"database.":[79],"Second,":[80],"leveraged":[82],"patterns":[84],"database":[89],"sets":[92],"produce":[94],"automatically":[96],"generated":[97],"catalog":[98],"processes.":[101],"These":[102],"demonstrations":[103],"revealed":[104],"power":[106],"global":[109],"analysis":[110],"data":[113],"contained":[114],"within":[115],"databases,":[118],"and":[119],"potential":[121],"using":[123],"them":[124],"questions.":[128]},"counts_by_year":[{"year":2018,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
