{"id":"https://openalex.org/W2143489962","doi":"https://doi.org/10.1093/bioinformatics/btm482","title":"Extracting three-way gene interactions from microarray data","display_name":"Extracting three-way gene interactions from microarray data","publication_year":2007,"publication_date":"2007-10-05","ids":{"openalex":"https://openalex.org/W2143489962","doi":"https://doi.org/10.1093/bioinformatics/btm482","mag":"2143489962","pmid":"https://pubmed.ncbi.nlm.nih.gov/17921496"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btm482","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm482","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/21/2903/1064175/btm482.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":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":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/23/21/2903/1064175/btm482.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062057879","display_name":"Jiexin Zhang","orcid":"https://orcid.org/0000-0001-9526-6730"},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jiexin Zhang","raw_affiliation_strings":["Department of Bioinformatics and Computational Biology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 237, Houston, TX 77030-4009, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Computational Biology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 237, Houston, TX 77030-4009, USA","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102011950","display_name":"Yuan Ji","orcid":"https://orcid.org/0000-0002-2631-9082"},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuan Ji","raw_affiliation_strings":["Department of Bioinformatics and Computational Biology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 237, Houston, TX 77030-4009, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Computational Biology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 237, Houston, TX 77030-4009, USA","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100425554","display_name":"Li Zhang","orcid":"https://orcid.org/0000-0002-3617-2627"},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Li Zhang","raw_affiliation_strings":["Department of Bioinformatics and Computational Biology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 237, Houston, TX 77030-4009, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Computational Biology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 237, Houston, TX 77030-4009, USA","institution_ids":["https://openalex.org/I1343551460"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100425554"],"corresponding_institution_ids":["https://openalex.org/I1343551460"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":1.5104,"has_fulltext":true,"cited_by_count":50,"citation_normalized_percentile":{"value":0.81704013,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"23","issue":"21","first_page":"2903","last_page":"2909"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9416000247001648,"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":0.9416000247001648,"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":0.030700000002980232,"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":0.00559999980032444,"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/microarray-analysis-techniques","display_name":"Microarray analysis techniques","score":0.5664474368095398},{"id":"https://openalex.org/keywords/microarray-databases","display_name":"Microarray databases","score":0.5537845492362976},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5296922326087952},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5179038047790527},{"id":"https://openalex.org/keywords/microarray","display_name":"Microarray","score":0.48464900255203247},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4270618259906769},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38932204246520996},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3017256259918213},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24589648842811584},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2121838927268982}],"concepts":[{"id":"https://openalex.org/C8415881","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Microarray analysis techniques","level":4,"score":0.5664474368095398},{"id":"https://openalex.org/C548314002","wikidata":"https://www.wikidata.org/wiki/Q6839218","display_name":"Microarray databases","level":5,"score":0.5537845492362976},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5296922326087952},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5179038047790527},{"id":"https://openalex.org/C186836561","wikidata":"https://www.wikidata.org/wiki/Q1931516","display_name":"Microarray","level":4,"score":0.48464900255203247},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4270618259906769},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38932204246520996},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3017256259918213},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24589648842811584},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2121838927268982}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D003198","descriptor_name":"Computer Simulation","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":"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":"D009363","descriptor_name":"Neoplasm Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009363","descriptor_name":"Neoplasm Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009363","descriptor_name":"Neoplasm Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btm482","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm482","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/21/2903/1064175/btm482.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:17921496","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17921496","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":{"id":"doi:10.1093/bioinformatics/btm482","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm482","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/21/2903/1064175/btm482.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2873061488","display_name":null,"funder_award_id":"P-01 CA049639","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G5620134746","display_name":null,"funder_award_id":"CA016672-28","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G6736661663","display_name":null,"funder_award_id":"CA- 016672","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8890603225","display_name":null,"funder_award_id":"CA108558-01","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2143489962.pdf","grobid_xml":"https://content.openalex.org/works/W2143489962.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W139767586","https://openalex.org/W1519855763","https://openalex.org/W1893505266","https://openalex.org/W2006145698","https://openalex.org/W2009358682","https://openalex.org/W2011832962","https://openalex.org/W2022756254","https://openalex.org/W2030165415","https://openalex.org/W2062233253","https://openalex.org/W2067745031","https://openalex.org/W2068275331","https://openalex.org/W2070491426","https://openalex.org/W2079231943","https://openalex.org/W2084833542","https://openalex.org/W2087430129","https://openalex.org/W2103717646","https://openalex.org/W2104385125","https://openalex.org/W2106620396","https://openalex.org/W2120865735","https://openalex.org/W2121158863","https://openalex.org/W2135000328","https://openalex.org/W2135871131","https://openalex.org/W2139807849","https://openalex.org/W2139845570","https://openalex.org/W2141823231","https://openalex.org/W2144792853","https://openalex.org/W2150249052","https://openalex.org/W2150926065","https://openalex.org/W2152027317","https://openalex.org/W2158128075","https://openalex.org/W2167190345","https://openalex.org/W2169012810","https://openalex.org/W2170704198","https://openalex.org/W2284706217","https://openalex.org/W2312735157","https://openalex.org/W2495373072","https://openalex.org/W4256140420","https://openalex.org/W6605808646","https://openalex.org/W6675612979"],"related_works":["https://openalex.org/W3152114242","https://openalex.org/W2796636403","https://openalex.org/W2028324514","https://openalex.org/W2074092657","https://openalex.org/W2065186132","https://openalex.org/W1889322612","https://openalex.org/W2911678823","https://openalex.org/W2367975718","https://openalex.org/W2152648570","https://openalex.org/W2489437692"],"abstract_inverted_index":{"MOTIVATION:":[0],"It":[1],"is":[2,20,34],"an":[3],"important":[4],"and":[5,112,127],"difficult":[6],"task":[7],"to":[8,21,38,52],"extract":[9],"gene":[10,66,79,135,172,178,233],"network":[11,234],"information":[12],"from":[13,146,170],"high-throughput":[14],"genomic":[15],"data.":[16],"A":[17,163],"common":[18],"approach":[19],"cluster":[22],"genes":[23,45,98,186],"using":[24,224],"pairwise":[25,32,212],"correlation":[26,33],"as":[27,227],"a":[28,53,64,78,85,100,124,128],"distance":[29],"metric.":[30],"However,":[31],"clearly":[35],"too":[36],"simplistic":[37],"describe":[39],"the":[40,71,82,110,121,134,138,143,151,156,160,176,183,203],"complex":[41],"relationships":[42,48],"among":[43,96],"real":[44],"since":[46],"co-expression":[47,75],"are":[49],"often":[50],"restricted":[51],"specific":[54],"set":[55,126,153],"of":[56,74,84,115,166,196,199],"biological":[57],"conditions/processes.":[58],"In":[59],"this":[60],"study,":[61],"we":[62,118],"described":[63],"three-way":[65,94,167,206,216],"interaction":[67,168],"model":[68],"that":[69,133,231],"captures":[70],"dynamic":[72],"nature":[73],"relationship":[76],"between":[77],"pair":[80],"through":[81],"introduction":[83],"controller":[86],"gene.":[87],"RESULTS:":[88],"We":[89,131],"surveyed":[90],"0.4":[91],"billion":[92],"possible":[93],"interactions":[95,140,158,207,217],"1000":[97],"in":[99,150,159],"microarray":[101],"dataset":[102],"containing":[103],"678":[104],"human":[105],"cancer":[106],"samples.":[107],"To":[108],"test":[109],"reproducibility":[111],"statistical":[113,148],"significance":[114],"our":[116],"results,":[117],"randomly":[119],"split":[120],"samples":[122],"into":[123],"training":[125,152],"testing":[129,161],"set.":[130,162],"found":[132],"triplets":[136],"with":[137,142],"strongest":[139,157],"(i.e.":[141,194],"smallest":[144],"P-values":[145],"appropriate":[147],"tests)":[149],"also":[154],"had":[155],"distinctive":[164],"pattern":[165],"emerged":[169],"these":[171],"triplets:":[173],"depending":[174],"on":[175],"third":[177],"being":[179],"expressed":[180],"or":[181,191,235],"not,":[182],"remaining":[184],"two":[185],"can":[187,208],"be":[188,238],"either":[189,197],"co-expressed":[190],"mutually":[192],"exclusive":[193],"expression":[195],"one":[198],"them":[200],"would":[201],"repress":[202],"other).":[204],"Such":[205],"exist":[209],"without":[210],"apparent":[211],"correlations.":[213],"The":[214],"identified":[215],"may":[218],"constitute":[219],"candidates":[220],"for":[221],"further":[222],"experimentation":[223],"techniques":[225],"such":[226],"RNA":[228],"interference,":[229],"so":[230],"novel":[232],"pathways":[236],"could":[237],"identified.":[239]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":6}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
