{"id":"https://openalex.org/W2114788499","doi":"https://doi.org/10.1093/bioinformatics/bth011","title":"Finding coexpressed genes in counts-based data: an improved measure with validation experiments","display_name":"Finding coexpressed genes in counts-based data: an improved measure with validation experiments","publication_year":2004,"publication_date":"2004-01-29","ids":{"openalex":"https://openalex.org/W2114788499","doi":"https://doi.org/10.1093/bioinformatics/bth011","mag":"2114788499","pmid":"https://pubmed.ncbi.nlm.nih.gov/14751974"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bth011","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth011","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/A5072368469","display_name":"Morgan N. Price","orcid":"https://orcid.org/0000-0002-4251-0362"},"institutions":[{"id":"https://openalex.org/I26274970","display_name":"FX Palo Alto Laboratory","ror":"https://ror.org/05ef4zt88","country_code":"US","type":"facility","lineage":["https://openalex.org/I26274970"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Morgan N. Price","raw_affiliation_strings":["FX Palo Alto Laboratory, 3400 Hillview Avenue Building 4, Palo Alto, CA 94304, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"FX Palo Alto Laboratory, 3400 Hillview Avenue Building 4, Palo Alto, CA 94304, USA","institution_ids":["https://openalex.org/I26274970"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023002743","display_name":"Eleanor Rieffel","orcid":"https://orcid.org/0009-0005-2957-9372"},"institutions":[{"id":"https://openalex.org/I26274970","display_name":"FX Palo Alto Laboratory","ror":"https://ror.org/05ef4zt88","country_code":"US","type":"facility","lineage":["https://openalex.org/I26274970"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eleanor Rieffel","raw_affiliation_strings":["FX Palo Alto Laboratory, 3400 Hillview Avenue Building 4, Palo Alto, CA 94304, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"FX Palo Alto Laboratory, 3400 Hillview Avenue Building 4, Palo Alto, CA 94304, USA","institution_ids":["https://openalex.org/I26274970"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5072368469"],"corresponding_institution_ids":["https://openalex.org/I26274970"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.5987,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.65522632,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"20","issue":"6","first_page":"945","last_page":"952"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","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/T10887","display_name":"Bioinformatics and Genomic Networks","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/T10885","display_name":"Gene expression and cancer classification","score":0.9983000159263611,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9513999819755554,"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/gene-ontology","display_name":"Gene ontology","score":0.6580014824867249},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6316269040107727},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6090003848075867},{"id":"https://openalex.org/keywords/uncorrelated","display_name":"Uncorrelated","score":0.6074382662773132},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.510321319103241},{"id":"https://openalex.org/keywords/measure","display_name":"Measure (data warehouse)","score":0.44879570603370667},{"id":"https://openalex.org/keywords/false-discovery-rate","display_name":"False discovery rate","score":0.4426393210887909},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4103028178215027},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.33435508608818054},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2626626491546631},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.26171422004699707},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.19789201021194458},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1032501757144928}],"concepts":[{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.6580014824867249},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6316269040107727},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6090003848075867},{"id":"https://openalex.org/C169345407","wikidata":"https://www.wikidata.org/wiki/Q8216221","display_name":"Uncorrelated","level":2,"score":0.6074382662773132},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.510321319103241},{"id":"https://openalex.org/C2780009758","wikidata":"https://www.wikidata.org/wiki/Q6804172","display_name":"Measure (data warehouse)","level":2,"score":0.44879570603370667},{"id":"https://openalex.org/C193244246","wikidata":"https://www.wikidata.org/wiki/Q5432696","display_name":"False discovery rate","level":3,"score":0.4426393210887909},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4103028178215027},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.33435508608818054},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2626626491546631},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.26171422004699707},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.19789201021194458},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1032501757144928}],"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":"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":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bth011","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth011","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:14751974","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/14751974","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W1512809401","https://openalex.org/W1594655861","https://openalex.org/W1982428412","https://openalex.org/W1998251495","https://openalex.org/W1998415512","https://openalex.org/W2004850055","https://openalex.org/W2006368694","https://openalex.org/W2046863812","https://openalex.org/W2061439657","https://openalex.org/W2063106517","https://openalex.org/W2072032642","https://openalex.org/W2074027785","https://openalex.org/W2101595316","https://openalex.org/W2133743912","https://openalex.org/W2151253576","https://openalex.org/W2152689720","https://openalex.org/W2156031219","https://openalex.org/W2162691829","https://openalex.org/W2164891186","https://openalex.org/W2165532730","https://openalex.org/W2170040895","https://openalex.org/W2172049947","https://openalex.org/W2403035479"],"related_works":["https://openalex.org/W2389124870","https://openalex.org/W1921844237","https://openalex.org/W4300887971","https://openalex.org/W2360779366","https://openalex.org/W2168149717","https://openalex.org/W200978175","https://openalex.org/W2178204436","https://openalex.org/W2113356685","https://openalex.org/W4293336298","https://openalex.org/W2467227750"],"abstract_inverted_index":{"MOTIVATION:":[0],"Expressed":[1],"sequence":[2],"tag":[3],"(EST)":[4],"data":[5,20],"reflects":[6],"variation":[7],"in":[8,18,52],"gene":[9,96],"expression,":[10],"but":[11,116],"previous":[12,57,66,109],"methods":[13,67],"for":[14],"finding":[15],"coexpressed":[16,33,93],"genes":[17,90],"EST":[19],"are":[21],"subject":[22],"to":[23,95,126],"bias":[24],"and":[25,46,99],"vastly":[26],"overstate":[27],"the":[28,85,107,139],"statistical":[29],"significance":[30,81],"of":[31,120,141],"putatively":[32],"genes.":[34],"RESULTS:":[35],"We":[36,83,111],"introduce":[37],"a":[38,114,135],"new":[39],"method":[40,131],"(LNP)":[41],"that":[42,101],"reports":[43,80],"reasonable":[44],"p-values":[45,69],"also":[47,112],"detects":[48],"more":[49,104],"biological":[50],"relationships":[51],"human":[53,62,89],"dbEST":[54,63],"than":[55,106],"do":[56],"methods.":[58,110],"In":[59],"simulations":[60],"with":[61],"library":[64],"sizes,":[65],"report":[68],"as":[70,72],"low":[71],"10(-30)":[73],"on":[74,87,134,138],"1/1000":[75],"uncorrelated":[76],"pairs,":[77],"while":[78],"LNP":[79,102,130],"correctly.":[82],"validate":[84],"analysis":[86],"real":[88],"by":[91],"comparing":[92],"pairs":[94],"ontology":[97],"annotations":[98],"find":[100,113],"is":[103,132],"sensitive":[105],"three":[108],"small":[115],"statistically":[117],"significant":[118],"level":[119],"coexpression":[121],"between":[122],"interacting":[123],"proteins":[124],"relative":[125],"randomized":[127],"controls.":[128],"The":[129],"based":[133],"log-normal":[136],"prior":[137],"distribution":[140],"expression":[142],"levels.":[143]},"counts_by_year":[{"year":2016,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
