{"id":"https://openalex.org/W1976842852","doi":"https://doi.org/10.1109/bibm.2013.6732479","title":"Fast Westfall-Young permutation procedure for combinatorial regulation discovery","display_name":"Fast Westfall-Young permutation procedure for combinatorial regulation discovery","publication_year":2013,"publication_date":"2013-12-01","ids":{"openalex":"https://openalex.org/W1976842852","doi":"https://doi.org/10.1109/bibm.2013.6732479","mag":"1976842852"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2013.6732479","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2013.6732479","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 IEEE International Conference on Bioinformatics and Biomedicine","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5019829876","display_name":"Aika Terada","orcid":null},"institutions":[{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Aika Terada","raw_affiliation_strings":["Dept. of Computer Science, Tokyo Institute of Technology, Tokyo, Japan","Department of Computer Science, Tokyo Institute of Technology, Tokyo, Japan#TAB#"],"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, Tokyo Institute of Technology, Tokyo, Japan","institution_ids":["https://openalex.org/I114531698"]},{"raw_affiliation_string":"Department of Computer Science, Tokyo Institute of Technology, Tokyo, Japan#TAB#","institution_ids":["https://openalex.org/I114531698"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070597006","display_name":"Koji Tsuda","orcid":"https://orcid.org/0000-0002-4288-1606"},"institutions":[{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Koji Tsuda","raw_affiliation_strings":["Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan","Comput. Biol. Res. Center, Nat. Inst. of Adv. Ind. Sci. & Technol., Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan","institution_ids":["https://openalex.org/I73613424"]},{"raw_affiliation_string":"Comput. Biol. Res. Center, Nat. Inst. of Adv. Ind. Sci. & Technol., Tokyo, Japan","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022912020","display_name":"Jun Sese","orcid":"https://orcid.org/0000-0003-3495-4382"},"institutions":[{"id":"https://openalex.org/I4210086780","display_name":"Japan Science and Technology Agency","ror":"https://ror.org/00097mb19","country_code":"JP","type":"government","lineage":["https://openalex.org/I4210086780"]},{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Jun Sese","raw_affiliation_strings":["Minato Discrete Structure Manipulation System Project, Japan Science and Technology Agency, Hokkaido, Japan","Department of Computer Science, Tokyo Institute of Technology, Tokyo, Japan#TAB#"],"affiliations":[{"raw_affiliation_string":"Minato Discrete Structure Manipulation System Project, Japan Science and Technology Agency, Hokkaido, Japan","institution_ids":["https://openalex.org/I4210086780"]},{"raw_affiliation_string":"Department of Computer Science, Tokyo Institute of Technology, Tokyo, Japan#TAB#","institution_ids":["https://openalex.org/I114531698"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5019829876"],"corresponding_institution_ids":["https://openalex.org/I114531698"],"apc_list":null,"apc_paid":null,"fwci":0.5989,"has_fulltext":false,"cited_by_count":36,"citation_normalized_percentile":{"value":0.6781041,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"153","last_page":"158"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9898999929428101,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9898999929428101,"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":0.9656999707221985,"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/T10497","display_name":"Fungal and yeast genetics research","score":0.9527000188827515,"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/computer-science","display_name":"Computer science","score":0.5965297818183899},{"id":"https://openalex.org/keywords/permutation","display_name":"Permutation (music)","score":0.5597598552703857},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.38644978404045105}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5965297818183899},{"id":"https://openalex.org/C21308566","wikidata":"https://www.wikidata.org/wiki/Q7169365","display_name":"Permutation (music)","level":2,"score":0.5597598552703857},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.38644978404045105},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/bibm.2013.6732479","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2013.6732479","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 IEEE International Conference on Bioinformatics and Biomedicine","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.710.1534","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.710.1534","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.seselab.org/papers/BIBM2013-terada.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"},{"id":"https://openalex.org/F4320338075","display_name":"Core Research for Evolutional Science and Technology","ror":"https://ror.org/00097mb19"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W505143","https://openalex.org/W1965138864","https://openalex.org/W1976209715","https://openalex.org/W1980507776","https://openalex.org/W2029817244","https://openalex.org/W2060181803","https://openalex.org/W2064340631","https://openalex.org/W2080498142","https://openalex.org/W2085442947","https://openalex.org/W2097390727","https://openalex.org/W2101759642","https://openalex.org/W2104579579","https://openalex.org/W2118556950","https://openalex.org/W2121044470","https://openalex.org/W2125508747","https://openalex.org/W2137683543","https://openalex.org/W2164683872","https://openalex.org/W2796856748","https://openalex.org/W3047398590","https://openalex.org/W3103280585","https://openalex.org/W6600021472","https://openalex.org/W6678230397"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109"],"abstract_inverted_index":{"Three":[0],"or":[1,49],"more":[2],"transcription":[3],"factors":[4],"(TFs)":[5],"often":[6,62],"work":[7],"together,":[8],"and":[9,174,188],"the":[10,33,36,42,72,75,79,83,111,116,136,140,148,163,167,180],"combinatorial":[11,76,112],"regulations":[12],"are":[13,200],"essential":[14],"in":[15,150],"cellular":[16],"machinery.":[17],"However,":[18,65],"it":[19],"is":[20,183],"impossible":[21],"to":[22,32,97,100,138,160,165],"discover":[23],"statistically":[24,102,192],"significant":[25,103,193],"sets":[26],"of":[27,35,44,74,78,82,127],"TF":[28],"binding":[29],"motifs":[30,80],"due":[31],"necessity":[34],"multiple":[37],"testing":[38],"procedure.":[39],"To":[40],"improve":[41],"sensitivity":[43],"widely":[45],"used":[46,69],"Bonferroni":[47],"correction":[48],"its":[50],"modified":[51],"methods,":[52],"such":[53],"as":[54],"Holm":[55],"procedure,":[56],"Westfall-Young":[57],"permutation":[58],"procedure":[59],"(WY-procedure)":[60],"has":[61,135],"been":[63],"applied.":[64],"few":[66],"studies":[67],"have":[68],"WY-procedure":[70,99,109],"for":[71,110],"discoveries":[73],"effects":[77],"because":[81],"extremely":[84],"large":[85],"computational":[86],"time.":[87,128],"In":[88],"this":[89],"paper,":[90],"we":[91,107],"propose":[92],"an":[93,124],"efficient":[94],"branch-and-bound":[95],"algorithm":[96,159,182],"perform":[98],"enumerate":[101],"motif":[104,194],"combinations.":[105],"When":[106],"use":[108],"regulation":[113],"discovery,":[114],"finding":[115],"minimum":[117,141,168],"P-value":[118,142],"from":[119],"each":[120],"permuted":[121],"dataset":[122],"consumes":[123],"enormous":[125],"amount":[126],"We":[129],"show":[130,178],"that":[131,134,179],"a":[132,155],"combination":[133],"possibility":[137],"achieve":[139,166],"appears":[143],"with":[144],"high":[145],"frequency":[146],"over":[147],"threshold":[149],"dataset.":[151],"This":[152],"property":[153],"enables":[154],"frequent":[156],"itemset":[157],"mining":[158],"efficiently":[161],"select":[162],"candidates":[164],"P-value.":[169],"Our":[170],"demonstrations":[171],"using":[172],"yeast":[173],"human":[175],"transcriptome":[176],"datasets":[177],"proposed":[181],"orders-of-magnitude":[184],"faster":[185],"than":[186],"WY-procedure,":[187],"can":[189],"practically":[190],"list":[191],"combinations":[195,199],"even":[196],"when":[197],"any":[198],"considered.":[201]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":3}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
