{"id":"https://openalex.org/W2206131058","doi":"https://doi.org/10.1093/bioinformatics/btv750","title":"MCAST: scanning for cis-regulatory motif clusters","display_name":"MCAST: scanning for cis-regulatory motif clusters","publication_year":2015,"publication_date":"2015-12-24","ids":{"openalex":"https://openalex.org/W2206131058","doi":"https://doi.org/10.1093/bioinformatics/btv750","mag":"2206131058","pmid":"https://pubmed.ncbi.nlm.nih.gov/26704599","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/4907379"},"language":"en","primary_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv750","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/8/1217/16921792/btv750.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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/P4310311647","https://openalex.org/P4310311648"],"host_organization_lineage_names":["University of Oxford","Oxford University Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true},"type":"article","type_crossref":"journal-article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/32/8/1217/16921792/btv750.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5112711469","display_name":"Charles E. Grant","orcid":null},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Charles E. Grant","raw_affiliation_strings":["1 Department of Genome Sciences, University of Washington, Seattle, WA, USA,"],"affiliations":[{"raw_affiliation_string":"1 Department of Genome Sciences, University of Washington, Seattle, WA, USA,","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101686027","display_name":"James Johnson","orcid":"https://orcid.org/0009-0002-9695-0424"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"James Johnson","raw_affiliation_strings":["2 Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia and"],"affiliations":[{"raw_affiliation_string":"2 Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia and","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017222669","display_name":"Timothy L. Bailey","orcid":"https://orcid.org/0000-0002-7018-9342"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Timothy L. Bailey","raw_affiliation_strings":["2 Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia and"],"affiliations":[{"raw_affiliation_string":"2 Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia and","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057375933","display_name":"William Stafford Noble","orcid":"https://orcid.org/0000-0001-7283-4715"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William Stafford Noble","raw_affiliation_strings":["1 Department of Genome Sciences, University of Washington, Seattle, WA, USA,","3 Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Genome Sciences, University of Washington, Seattle, WA, USA,","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"3 Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]}]}],"institution_assertions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618,"provenance":"doaj"},"apc_paid":null,"fwci":0.131,"has_fulltext":true,"fulltext_origin":"pdf","cited_by_count":11,"citation_normalized_percentile":{"value":0.658749,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":86,"max":87},"biblio":{"volume":"32","issue":"8","first_page":"1217","last_page":"1219"},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Regulation of Chromatin Structure and Function","score":1.0,"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":"Regulation of Chromatin Structure and Function","score":1.0,"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":"Microarray Data Analysis and Gene Expression Profiling","score":0.9986,"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/T11468","display_name":"Genetic Architecture of Quantitative Traits","score":0.9982,"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/false-discovery-rate","display_name":"False discovery rate","score":0.57325965},{"id":"https://openalex.org/keywords/genetic-mapping","display_name":"Genetic Mapping","score":0.527308},{"id":"https://openalex.org/keywords/marker-assisted-selection","display_name":"Marker-Assisted Selection","score":0.516958},{"id":"https://openalex.org/keywords/clustering","display_name":"Clustering","score":0.503145},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.4744816},{"id":"https://openalex.org/keywords/epigenomics","display_name":"Epigenomics","score":0.43553573}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.66788065},{"id":"https://openalex.org/C193244246","wikidata":"https://www.wikidata.org/wiki/Q5432696","display_name":"False discovery rate","level":3,"score":0.57325965},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.5349888},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5239689},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.4744816},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.47292453},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.46785647},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.46689093},{"id":"https://openalex.org/C121912465","wikidata":"https://www.wikidata.org/wiki/Q3589153","display_name":"Epigenomics","level":5,"score":0.43553573},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3627624},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3233605},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.24462107},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.09370366},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"","qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv750","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/8/1217/16921792/btv750.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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/P4310311647","https://openalex.org/P4310311648"],"host_organization_lineage_names":["University of Oxford","Oxford University Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":true,"landing_page_url":"https://europepmc.org/articles/pmc4907379","pdf_url":"https://europepmc.org/articles/pmc4907379?pdf=render","source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":true,"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":["European Bioinformatics Institute"],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4907379","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":["National Institutes of Health"],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26704599","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":["National Institutes of Health"],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false}],"best_oa_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv750","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/8/1217/16921792/btv750.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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/P4310311647","https://openalex.org/P4310311648"],"host_organization_lineage_names":["University of Oxford","Oxford University Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true},"sustainable_development_goals":[{"score":0.45,"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17"}],"grants":[],"datasets":[],"versions":[],"referenced_works_count":6,"referenced_works":["https://openalex.org/W1971578941","https://openalex.org/W2068011423","https://openalex.org/W2095791120","https://openalex.org/W2105381419","https://openalex.org/W2151845703","https://openalex.org/W2171365066"],"related_works":["https://openalex.org/W4300887971","https://openalex.org/W4231704780","https://openalex.org/W2389124870","https://openalex.org/W2178204436","https://openalex.org/W2168149717","https://openalex.org/W2162436860","https://openalex.org/W2083794993","https://openalex.org/W200978175","https://openalex.org/W2000109482","https://openalex.org/W1921844237"],"abstract_inverted_index":{"Precise":[0],"regulatory":[1],"control":[2],"of":[3,13,46,72,74,99,146,154,162],"genes,":[4],"particularly":[5],"in":[6,40,157],"eukaryotes,":[7],"frequently":[8],"requires":[9],"the":[10,59,122,144,152,163],"joint":[11],"action":[12],"multiple":[14,35],"sequence-specific":[15],"transcription":[16,36,48],"factors.":[17],"A":[18,168],"cis-regulatory":[19],"module":[20],"(CRM)":[21],"is":[22,27,160],"a":[23,44,66,80,85,96,106],"genomic":[24,67],"locus":[25],"that":[26,33,101],"responsible":[28],"for":[29,63],"gene":[30],"regulation":[31],"and":[32,151,171,178],"contains":[34],"factor":[37,49],"binding":[38,50],"sites":[39],"close":[41],"proximity.":[42],"Given":[43],"collection":[45],"known":[47],"motifs,":[51],"many":[52],"bioinformatics":[53],"methods":[54],"have":[55],"been":[56],"proposed":[57],"over":[58],"past":[60],"15":[61],"years":[62],"identifying":[64,158],"within":[65],"sequence":[68],"candidate":[69,91],"CRMs":[70,126],"consisting":[71],"clusters":[73],"those":[75],"motifs.The":[76],"MCAST":[77,100],"algorithm":[78],"uses":[79],"hidden":[81],"Markov":[82],"model":[83],"with":[84],"P-value-based":[86],"scoring":[87],"scheme":[88],"to":[89,124],"identify":[90],"CRMs.":[92],"Here,":[93],"we":[94],"introduce":[95],"new":[97],"version":[98],"offers":[102],"improved":[103],"graphical":[104],"output,":[105],"dynamic":[107],"background":[108],"model,":[109],"statistical":[110,148],"confidence":[111,149],"estimates":[112,150],"based":[113],"on":[114],"false":[115],"discovery":[116],"rate":[117],"estimation":[118],"and,":[119],"most":[120],"significantly,":[121],"ability":[123],"predict":[125],"while":[127],"taking":[128],"into":[129],"account":[130],"epigenomic":[131,155],"data":[132,182],"such":[133],"as":[134],"DNase":[135],"I":[136],"sensitivity":[137],"or":[138,180],"histone":[139],"modification":[140],"data.":[141],"We":[142],"demonstrate":[143],"validity":[145],"MCAST's":[147],"utility":[153],"priors":[156],"CRMs.MCAST":[159],"part":[161],"MEME":[164],"Suite":[165],"software":[166],"toolkit.":[167],"web":[169],"server":[170],"source":[172],"code":[173],"are":[174,183],"available":[175,184],"at":[176,185],"http://meme-suite.org":[177],"http://alternate.meme-suite.orgt.bailey@imb.uq.edu.au":[179],"william-noble@uw.eduSupplementary":[181],"Bioinformatics":[186],"online.":[187]},"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W2206131058","counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2016,"cited_by_count":1}],"updated_date":"2024-10-17T10:38:29.071873","created_date":"2016-06-24"}
