{"id":"https://openalex.org/W2000515602","doi":"https://doi.org/10.1093/bib/bbu034","title":"Predictive modelling of gene expression from transcriptional regulatory elements","display_name":"Predictive modelling of gene expression from transcriptional regulatory elements","publication_year":2014,"publication_date":"2014-09-16","ids":{"openalex":"https://openalex.org/W2000515602","doi":"https://doi.org/10.1093/bib/bbu034","mag":"2000515602","pmid":"https://pubmed.ncbi.nlm.nih.gov/25231769"},"language":"en","primary_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbu034","pdf_url":"https://academic.oup.com/bib/article-pdf/16/4/616/1003334/bbu034.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":false,"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/bib/article-pdf/16/4/616/1003334/bbu034.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003238807","display_name":"David Budden","orcid":"https://orcid.org/0000-0003-4372-8985"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"David M. Budden","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054811862","display_name":"Daniel Hurley","orcid":"https://orcid.org/0000-0003-0171-1982"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Daniel G. Hurley","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5083478373","display_name":"Edmund J. Crampin","orcid":"https://orcid.org/0000-0001-6569-9543"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Edmund J. Crampin","raw_affiliation_strings":[],"affiliations":[]}],"institution_assertions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011,"provenance":"doaj"},"apc_paid":null,"fwci":3.001,"has_fulltext":true,"fulltext_origin":"pdf","cited_by_count":38,"citation_normalized_percentile":{"value":0.735016,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":95},"biblio":{"volume":"16","issue":"4","first_page":"616","last_page":"628"},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","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":"Genomics and Chromatin Dynamics","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/T10604","display_name":"RNA Research and Splicing","score":0.9966,"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/T13157","display_name":"Cancer-related gene regulation","score":0.9951,"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/chromatin-immunoprecipitation","display_name":"Chromatin immunoprecipitation","score":0.59342015},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.52655935}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6554407},{"id":"https://openalex.org/C134320426","wikidata":"https://www.wikidata.org/wiki/Q901026","display_name":"Chromatin immunoprecipitation","level":5,"score":0.59342015},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.52655935},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.52047634},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.5181514},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49169117},{"id":"https://openalex.org/C64927066","wikidata":"https://www.wikidata.org/wiki/Q36293","display_name":"Histone","level":3,"score":0.46238604},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.43929252},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.39738607},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38961163},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3531785},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2471956},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.13600498}],"mesh":[{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","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":"D051379","descriptor_name":"Mice","qualifier_ui":"","qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbu034","pdf_url":"https://academic.oup.com/bib/article-pdf/16/4/616/1003334/bbu034.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":false,"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":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25231769","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/bib/bbu034","pdf_url":"https://academic.oup.com/bib/article-pdf/16/4/616/1003334/bbu034.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":false,"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":[],"grants":[],"datasets":[],"versions":[],"referenced_works_count":71,"referenced_works":["https://openalex.org/W1963553964","https://openalex.org/W1964963969","https://openalex.org/W1966083128","https://openalex.org/W1969323007","https://openalex.org/W1969451832","https://openalex.org/W1974463674","https://openalex.org/W1977729188","https://openalex.org/W1984097115","https://openalex.org/W1985444222","https://openalex.org/W1987777080","https://openalex.org/W1988294855","https://openalex.org/W2001554877","https://openalex.org/W2015416439","https://openalex.org/W2017840637","https://openalex.org/W2026865241","https://openalex.org/W2035180740","https://openalex.org/W2039313637","https://openalex.org/W2042930277","https://openalex.org/W2053421436","https://openalex.org/W2057119701","https://openalex.org/W2060392690","https://openalex.org/W2061834804","https://openalex.org/W2063333928","https://openalex.org/W2072492970","https://openalex.org/W2081000967","https://openalex.org/W2086411786","https://openalex.org/W2089689396","https://openalex.org/W2089817566","https://openalex.org/W2089865437","https://openalex.org/W2095791120","https://openalex.org/W2096083625","https://openalex.org/W2096139934","https://openalex.org/W2098412979","https://openalex.org/W2105776281","https://openalex.org/W2105924780","https://openalex.org/W2108381095","https://openalex.org/W2109384743","https://openalex.org/W2113387206","https://openalex.org/W2121295901","https://openalex.org/W2121607820","https://openalex.org/W2126917138","https://openalex.org/W2127081697","https://openalex.org/W2127851640","https://openalex.org/W2129795133","https://openalex.org/W2133452708","https://openalex.org/W2134087142","https://openalex.org/W2135423581","https://openalex.org/W2137226992","https://openalex.org/W2139617657","https://openalex.org/W2140952049","https://openalex.org/W2141458291","https://openalex.org/W2142570576","https://openalex.org/W2144792857","https://openalex.org/W2146053439","https://openalex.org/W2146634563","https://openalex.org/W2148541040","https://openalex.org/W2149974435","https://openalex.org/W2151656460","https://openalex.org/W2152296813","https://openalex.org/W2154431984","https://openalex.org/W2155725346","https://openalex.org/W2156909104","https://openalex.org/W2158850335","https://openalex.org/W2159164310","https://openalex.org/W2161224111","https://openalex.org/W2164116506","https://openalex.org/W2166898290","https://openalex.org/W2169053773","https://openalex.org/W2169389191","https://openalex.org/W2259938310","https://openalex.org/W4210767115"],"related_works":["https://openalex.org/W61640353","https://openalex.org/W3129816939","https://openalex.org/W2912862995","https://openalex.org/W2790955376","https://openalex.org/W2468279273","https://openalex.org/W2417693299","https://openalex.org/W2354198838","https://openalex.org/W2103419012","https://openalex.org/W2101501829","https://openalex.org/W1989130879"],"abstract_inverted_index":{"Predictive":[0],"modelling":[1,61,141],"of":[2,23,29,38,52,58,75,139,152,167,177],"gene":[3,30,168],"expression":[4,33,169],"provides":[5],"a":[6,55,212],"powerful":[7],"framework":[8,202],"for":[9,84],"exploring":[10],"the":[11,21,49,59,86,148],"regulatory":[12,150],"logic":[13],"underpinning":[14],"transcriptional":[15],"regulation.":[16],"Recent":[17],"studies":[18],"have":[19],"demonstrated":[20],"utility":[22],"such":[24,53],"models":[25,106],"in":[26,128,137],"identifying":[27],"dysregulation":[28],"and":[31,63,71,80,96,102,114,123,144,155,162,183,187,197,208],"miRNA":[32],"associated":[34],"with":[35],"abnormal":[36],"patterns":[37,92],"transcription":[39],"factor":[40],"(TF)":[41],"binding":[42,91],"or":[43,179],"nucleosomal":[44],"histone":[45],"modifications":[46],"(HMs).":[47],"Despite":[48],"growing":[50],"popularity":[51],"approaches,":[54],"comparative":[56],"review":[57],"various":[60,108],"algorithms":[62,133],"feature":[64],"extraction":[65],"methods":[66,74],"is":[67,203],"lacking.":[68],"We":[69,98],"define":[70],"compare":[72],"three":[73],"quantifying":[76],"pairwise":[77],"gene-TF/HM":[78],"interactions":[79],"discuss":[81],"their":[82,140],"suitability":[83],"integrating":[85],"heterogeneous":[87],"chromatin":[88],"immunoprecipitation":[89],"(ChIP)-seq":[90],"exhibited":[93],"by":[94,172],"TFs":[95,154],"HMs.":[97,156],"then":[99],"construct":[100],"log-linear":[101],"\u03f5-support":[103],"vector":[104],"regression":[105],"from":[107],"mouse":[109],"embryonic":[110],"stem":[111],"cell":[112,180],"(mESC)":[113],"human":[115],"lymphoblastoid":[116],"(GM12878)":[117],"data":[118],"sets,":[119],"considering":[120,184],"both":[121,136,185],"ChIP-seq-":[122],"position":[124],"weight":[125],"matrix-":[126],"(PWM)-derived":[127],"silico":[129],"TF-binding.":[130,189],"The":[131],"two":[132],"are":[134,164],"evaluated":[135],"terms":[138],"prediction":[142],"accuracy":[143],"ability":[145],"to":[146,195],"identify":[147],"established":[149],"roles":[151],"individual":[153],"Our":[157],"results":[158],"demonstrate":[159],"that":[160],"TF-binding":[161],"HMs":[163],"highly":[165],"predictive":[166],"as":[170,211],"measured":[171],"mRNA":[173],"transcript":[174],"abundance,":[175],"irrespective":[176],"algorithm":[178],"type":[181],"selection":[182],"ChIP-seq":[186],"PWM-derived":[188],"As":[190],"we":[191],"encourage":[192],"other":[193],"researchers":[194],"explore":[196],"develop":[198],"these":[199],"results,":[200],"our":[201],"implemented":[204],"using":[205],"open-source":[206],"software":[207],"made":[209],"available":[210],"preconfigured":[213],"bootable":[214],"virtual":[215],"environment.":[216]},"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W2000515602","counts_by_year":[{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":3}],"updated_date":"2024-12-15T02:41:37.598694","created_date":"2016-06-24"}