{"id":"https://openalex.org/W2149420772","doi":"https://doi.org/10.1093/bioinformatics/btn009","title":"fdrMotif: identifying<i>cis</i>-elements by an EM algorithm coupled with false discovery rate control","display_name":"fdrMotif: identifying<i>cis</i>-elements by an EM algorithm coupled with false discovery rate control","publication_year":2008,"publication_date":"2008-02-23","ids":{"openalex":"https://openalex.org/W2149420772","doi":"https://doi.org/10.1093/bioinformatics/btn009","mag":"2149420772","pmid":"https://pubmed.ncbi.nlm.nih.gov/18296465"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn009","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn009","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/5/629/16886451/btn009.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/24/5/629/16886451/btn009.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100408451","display_name":"Leping Li","orcid":"https://orcid.org/0000-0003-4208-0259"},"institutions":[{"id":"https://openalex.org/I4210095140","display_name":"National Institute of Environmental Health Sciences","ror":"https://ror.org/00j4k1h63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210095140"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Leping Li","raw_affiliation_strings":["1 Biostatistics Branch and 2Computational Biology Facility, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Biostatistics Branch and 2Computational Biology Facility, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA","institution_ids":["https://openalex.org/I4210095140"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078723626","display_name":"Robert L. Bass","orcid":null},"institutions":[{"id":"https://openalex.org/I4210095140","display_name":"National Institute of Environmental Health Sciences","ror":"https://ror.org/00j4k1h63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210095140"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert L. Bass","raw_affiliation_strings":["1 Biostatistics Branch and 2Computational Biology Facility, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Biostatistics Branch and 2Computational Biology Facility, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA","institution_ids":["https://openalex.org/I4210095140"]}]},{"author_position":"last","author":{"id":null,"display_name":"Yu Liang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210095140","display_name":"National Institute of Environmental Health Sciences","ror":"https://ror.org/00j4k1h63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210095140"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yu Liang","raw_affiliation_strings":["1 Biostatistics Branch and 2Computational Biology Facility, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Biostatistics Branch and 2Computational Biology Facility, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA","institution_ids":["https://openalex.org/I4210095140"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100408451"],"corresponding_institution_ids":["https://openalex.org/I4210095140"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.7526,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.73747732,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"24","issue":"5","first_page":"629","last_page":"636"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10583","display_name":"Cancer-related Molecular Pathways","score":0.9351999759674072,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10583","display_name":"Cancer-related Molecular Pathways","score":0.9351999759674072,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.010700000450015068,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.004900000058114529,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/normalization","display_name":"Normalization (sociology)","score":0.6225292682647705},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5860151052474976},{"id":"https://openalex.org/keywords/false-discovery-rate","display_name":"False discovery rate","score":0.5779181122779846},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4779277443885803},{"id":"https://openalex.org/keywords/statistic","display_name":"Statistic","score":0.44887542724609375},{"id":"https://openalex.org/keywords/statistical-hypothesis-testing","display_name":"Statistical hypothesis testing","score":0.4258831739425659},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.36247318983078003},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.3469582200050354},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3385506272315979},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14082694053649902},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09127810597419739}],"concepts":[{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.6225292682647705},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5860151052474976},{"id":"https://openalex.org/C193244246","wikidata":"https://www.wikidata.org/wiki/Q5432696","display_name":"False discovery rate","level":3,"score":0.5779181122779846},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4779277443885803},{"id":"https://openalex.org/C89128539","wikidata":"https://www.wikidata.org/wiki/Q1949963","display_name":"Statistic","level":2,"score":0.44887542724609375},{"id":"https://openalex.org/C87007009","wikidata":"https://www.wikidata.org/wiki/Q210832","display_name":"Statistical hypothesis testing","level":2,"score":0.4258831739425659},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.36247318983078003},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.3469582200050354},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3385506272315979},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14082694053649902},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09127810597419739},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btn009","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn009","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/5/629/16886451/btn009.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:18296465","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18296465","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:1928713","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2376047","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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btn009","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn009","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/5/629/16886451/btn009.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/G3907148169","display_name":null,"funder_award_id":"Z01 ES101765","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8340615800","display_name":null,"funder_award_id":"Z99 ES999999","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337361","display_name":"National Institute of Environmental Health Sciences","ror":"https://ror.org/00j4k1h63"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W1592870802","https://openalex.org/W1596515083","https://openalex.org/W1969423031","https://openalex.org/W1980124153","https://openalex.org/W1981367467","https://openalex.org/W1994755936","https://openalex.org/W1995674377","https://openalex.org/W2003967338","https://openalex.org/W2029722028","https://openalex.org/W2035462635","https://openalex.org/W2073116379","https://openalex.org/W2073850887","https://openalex.org/W2077013196","https://openalex.org/W2084620487","https://openalex.org/W2084908610","https://openalex.org/W2094231493","https://openalex.org/W2105381419","https://openalex.org/W2108757877","https://openalex.org/W2110065044","https://openalex.org/W2121356022","https://openalex.org/W2126558916","https://openalex.org/W2136434805","https://openalex.org/W2141408320","https://openalex.org/W2149680578","https://openalex.org/W2158266834","https://openalex.org/W2158962723","https://openalex.org/W2171407623","https://openalex.org/W4300819821","https://openalex.org/W6635200387","https://openalex.org/W6649055232","https://openalex.org/W6669145357"],"related_works":["https://openalex.org/W1995992573","https://openalex.org/W154531455","https://openalex.org/W3172121640","https://openalex.org/W3008469829","https://openalex.org/W1986765826","https://openalex.org/W3000705684","https://openalex.org/W3174861742","https://openalex.org/W2088387197","https://openalex.org/W1976797354","https://openalex.org/W2278145554"],"abstract_inverted_index":{"MOTIVATION:":[0],"Most":[1],"de":[2],"novo":[3],"motif":[4,9,21,28],"identification":[5],"methods":[6],"optimize":[7],"the":[8,16,20,24,38,48,106,120,123,146,150,158,162,181,285],"model":[10,91,127,159],"first":[11,25],"and":[12,98,135,199,284],"then":[13,129],"separately":[14],"test":[15,49],"statistical":[17],"significance":[18,99],"of":[19,108,115,164,242],"score.":[22],"In":[23,37,223],"stage,":[26,40],"a":[27,41,63,79,141,167,196],"abundance":[29],"parameter":[30],"needs":[31],"to":[32,180,254,268],"be":[33,301],"specified":[34],"or":[35,43,161],"modeled.":[36],"second":[39],"Z-score":[42],"P-value":[44],"is":[45,128,154,266],"used":[46,189],"as":[47,71,75],"statistic.":[50],"Error":[51],"rates":[52],"under":[53],"multiple":[54],"comparisons":[55],"are":[56],"not":[57],"fully":[58],"considered.":[59],"METHODOLOGY:":[60],"We":[61,139,288],"propose":[62,140],"simple":[64],"but":[65,230],"novel":[66],"approach,":[67],"fdrMotif,":[68,252],"that":[69,173,290],"selects":[70],"many":[72,113],"binding":[73,109,182,211,217,228,250,274],"sites":[74,110,183,218,229,275],"possible":[76],"while":[77],"controlling":[78],"user-specified":[80,197],"false":[81],"discovery":[82],"rate":[83],"(FDR).":[84],"Unlike":[85],"existing":[86],"iterative":[87],"methods,":[88],"fdrMotif":[89,118,193,213,265,291],"combines":[90],"optimization":[92],"[e.g.":[93],"position":[94],"weight":[95],"matrix":[96],"(PWM)]":[97],"testing":[100],"at":[101],"each":[102],"step.":[103],"By":[104],"monitoring":[105],"proportion":[107],"selected":[111,271],"in":[112,122,145,219,231,276],"sets":[114,241],"background":[116,282],"sequences,":[117],"controls":[119],"FDR":[121,198],"original":[124],"data.":[125,287],"The":[126],"updated":[130],"using":[131],"an":[132,200,293],"expectation":[133],"(E)-":[134],"maximization":[136],"(M)-like":[137],"procedure.":[138],"new":[142],"normalization":[143,175,190],"procedure":[144,176],"E-step":[147],"for":[148],"updating":[149],"model.":[151],"This":[152],"process":[153],"repeated":[155],"until":[156],"either":[157],"converges":[160],"number":[163],"iterations":[165],"exceeds":[166],"maximum.":[168],"RESULTS:":[169],"Simulation":[170],"studies":[171],"suggest":[172,289],"our":[174],"assigns":[177],"larger":[178],"weights":[179],"than":[184,235],"do":[185],"two":[186],"other":[187],"commonly":[188],"procedures.":[191],"Furthermore,":[192,264],"requires":[194],"only":[195],"initial":[201],"PWM.":[202],"When":[203,237],"tested":[204,238],"on":[205,239],"542":[206],"high":[207],"confidence":[208],"experimental":[209],"p53":[210,216,249],"loci,":[212],"identified":[214,226],"569":[215],"505":[220],"(93.2%)":[221],"sequences.":[222],"comparison,":[224],"MEME":[225],"more":[227],"fewer":[232],"ChIP":[233],"sequences":[234,245,283],"fdrMotif.":[236],"500":[240],"simulated":[243],"'ChIP'":[244],"with":[246,259,279],"embedded":[247],"known":[248],"sites,":[251],"compared":[253],"MEME,":[255],"has":[256],"higher":[257],"sensitivity":[258],"similar":[260],"positive":[261],"predictive":[262],"value.":[263],"robust":[267],"noise:":[269],"it":[270],"nearly":[272],"identical":[273],"data":[277],"adulterated":[278],"50%":[280],"added":[281],"unadulterated":[286],"represents":[292],"improvement":[294],"over":[295],"MEME.":[296],"AVAILABILITY:":[297],"C":[298],"code":[299],"can":[300],"found":[302],"at:":[303],"http://www.niehs.nih.gov/research/resources/software/fdrMotif/.":[304]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2016-06-24T00:00:00"}
