{"id":"https://openalex.org/W2101135336","doi":"https://doi.org/10.1093/bioinformatics/bti140","title":"Probabilities of spurious connections in gene networks: application to expression time series","display_name":"Probabilities of spurious connections in gene networks: application to expression time series","publication_year":2004,"publication_date":"2004-11-16","ids":{"openalex":"https://openalex.org/W2101135336","doi":"https://doi.org/10.1093/bioinformatics/bti140","mag":"2101135336","pmid":"https://pubmed.ncbi.nlm.nih.gov/15546939"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti140","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti140","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/7/1121/48966868/bioinformatics_21_7_1121.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":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/21/7/1121/48966868/bioinformatics_21_7_1121.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038684006","display_name":"David R. Bickel","orcid":"https://orcid.org/0000-0002-9623-3946"},"institutions":[{"id":"https://openalex.org/I25041050","display_name":"Augusta University","ror":"https://ror.org/012mef835","country_code":"US","type":"education","lineage":["https://openalex.org/I25041050"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"David R. Bickel","raw_affiliation_strings":["Office of Biostatistics and Bioinformatics, Medical College of Georgia Augusta, GA 30912-4900, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Office of Biostatistics and Bioinformatics, Medical College of Georgia Augusta, GA 30912-4900, USA","institution_ids":["https://openalex.org/I25041050"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5038684006"],"corresponding_institution_ids":["https://openalex.org/I25041050"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.8382,"has_fulltext":true,"cited_by_count":26,"citation_normalized_percentile":{"value":0.70689859,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"21","issue":"7","first_page":"1121","last_page":"1128"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9994000196456909,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9994000196456909,"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":0.9987000226974487,"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":0.998199999332428,"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/spurious-relationship","display_name":"Spurious relationship","score":0.8247498273849487},{"id":"https://openalex.org/keywords/false-discovery-rate","display_name":"False discovery rate","score":0.6310871243476868},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.566824197769165},{"id":"https://openalex.org/keywords/estimator","display_name":"Estimator","score":0.5457912087440491},{"id":"https://openalex.org/keywords/randomness","display_name":"Randomness","score":0.517616868019104},{"id":"https://openalex.org/keywords/conditional-probability","display_name":"Conditional probability","score":0.45341476798057556},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3470649719238281},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.34387731552124023},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.32156527042388916},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.30040475726127625},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.27571040391921997},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22303161025047302},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.21542295813560486},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.21452990174293518}],"concepts":[{"id":"https://openalex.org/C97256817","wikidata":"https://www.wikidata.org/wiki/Q1462316","display_name":"Spurious relationship","level":2,"score":0.8247498273849487},{"id":"https://openalex.org/C193244246","wikidata":"https://www.wikidata.org/wiki/Q5432696","display_name":"False discovery rate","level":3,"score":0.6310871243476868},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.566824197769165},{"id":"https://openalex.org/C185429906","wikidata":"https://www.wikidata.org/wiki/Q1130160","display_name":"Estimator","level":2,"score":0.5457912087440491},{"id":"https://openalex.org/C125112378","wikidata":"https://www.wikidata.org/wiki/Q176640","display_name":"Randomness","level":2,"score":0.517616868019104},{"id":"https://openalex.org/C44492722","wikidata":"https://www.wikidata.org/wiki/Q327069","display_name":"Conditional probability","level":2,"score":0.45341476798057556},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3470649719238281},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.34387731552124023},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.32156527042388916},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.30040475726127625},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.27571040391921997},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22303161025047302},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21542295813560486},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.21452990174293518}],"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":"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":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","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":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","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":"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":3,"locations":[{"id":"doi:10.1093/bioinformatics/bti140","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti140","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/7/1121/48966868/bioinformatics_21_7_1121.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:15546939","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15546939","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:arXiv.org:q-bio/0404033","is_oa":true,"landing_page_url":"http://arxiv.org/abs/q-bio/0404033","pdf_url":"https://arxiv.org/pdf/q-bio/0404033","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bti140","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti140","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/7/1121/48966868/bioinformatics_21_7_1121.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":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2101135336.pdf","grobid_xml":"https://content.openalex.org/works/W2101135336.grobid-xml"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W1601744694","https://openalex.org/W1637056484","https://openalex.org/W1693940118","https://openalex.org/W1992452843","https://openalex.org/W1995945562","https://openalex.org/W1999621686","https://openalex.org/W2047968474","https://openalex.org/W2056574935","https://openalex.org/W2058221907","https://openalex.org/W2059238813","https://openalex.org/W2074089196","https://openalex.org/W2083675953","https://openalex.org/W2091841926","https://openalex.org/W2093463665","https://openalex.org/W2105381419","https://openalex.org/W2110065044","https://openalex.org/W2125905177","https://openalex.org/W2130618490","https://openalex.org/W2134696273","https://openalex.org/W2137952433","https://openalex.org/W2166525781"],"related_works":["https://openalex.org/W3113091479","https://openalex.org/W2162899405","https://openalex.org/W941090075","https://openalex.org/W2044987316","https://openalex.org/W3134374554","https://openalex.org/W2237480245","https://openalex.org/W2075065631","https://openalex.org/W2519167559","https://openalex.org/W1857488133","https://openalex.org/W2011096102"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"The":[2,22,128,145,159,187],"reconstruction":[3],"of":[4,24,81,98,108,118,124,226],"gene":[5,100,115,196,206],"networks":[6,26],"from":[7,41,46,220,241],"gene-expression":[8],"microarrays":[9],"is":[10,38,68,87,156,169,218],"gaining":[11],"popularity":[12],"as":[13,17],"methods":[14],"improve":[15],"and":[16,57,194,198,216],"more":[18],"data":[19],"become":[20],"available.":[21],"reliability":[23],"such":[25,142],"could":[27],"be":[28,136],"judged":[29],"by":[30],"the":[31,53,62,79,92,96,106,119,199],"probability":[32,74,107,129,146,160,189,214],"that":[33,130,133,147,161],"a":[34,47,72,109,113,148,162,183,224,230],"connection":[35,111],"between":[36],"genes":[37,132,155,168],"spurious,":[39],"resulting":[40],"chance":[42],"fluctuations":[43],"rather":[44],"than":[45],"true":[48],"biological":[49],"relationship.":[50],"Results:":[51],"Unlike":[52],"false":[54,59,64],"discovery":[55,60,65],"rate":[56,66],"positive":[58],"rate,":[61],"decisive":[63],"(dFDR)":[67],"exactly":[69],"equal":[70],"to":[71,95,135,191,204],"conditional":[73],"without":[75,182],"assuming":[76],"independence":[77],"or":[78,177],"randomness":[80],"hypothesis":[82],"truth":[83],"values.":[84],"This":[85],"property":[86],"useful":[88],"not":[89,175],"only":[90,202],"in":[91,104,112,185,222],"common":[93],"application":[94],"detection":[97],"differential":[99],"expression,":[101],"but":[102],"also":[103],"determining":[105],"spurious":[110],"reconstructed":[114],"network.":[116],"Estimators":[117],"dFDR":[120],"can":[121],"estimate":[122],"each":[123,139],"three":[125],"probabilities:":[126],"(1)":[127],"two":[131,153,167,201],"appear":[134],"associated":[137,154,176,181],"with":[138,229],"other":[140,200],"lack":[141],"association.":[143],"(2)":[144],"time":[149,163],"ordering":[150,164],"observed":[151,165],"for":[152,166,211],"misleading.":[157],"(3)":[158],"misleading,":[170],"either":[171],"because":[172,178],"they":[173,179],"are":[174,180,239],"lag":[184],"time.":[186],"first":[188],"applies":[190],"both":[192],"static":[193],"dynamic":[195,205],"networks,":[197],"apply":[203],"networks.":[207],"Availability:":[208],"Cross-platform":[209],"software":[210],"network":[212],"reconstruction,":[213],"estimation,":[215],"plotting":[217],"free":[219],"http://www.davidbickel.com":[221,242],"Statomics,":[223],"suite":[225],"R":[227],"functions":[228],"Java":[231],"application.":[232],"Contact:":[233],"bickel@prueba.info":[234],"Supplementary":[235],"information:":[236],"Color":[237],"figures":[238],"available":[240]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":3},{"year":2012,"cited_by_count":2}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}