{"id":"https://openalex.org/W2150520277","doi":"https://doi.org/10.1093/bioinformatics/bti1131","title":"Genome-wide decoding of hierarchical modular structure of transcriptional regulation by <i>cis</i>-element and expression clustering","display_name":"Genome-wide decoding of hierarchical modular structure of transcriptional regulation by <i>cis</i>-element and expression clustering","publication_year":2005,"publication_date":"2005-09-01","ids":{"openalex":"https://openalex.org/W2150520277","doi":"https://doi.org/10.1093/bioinformatics/bti1131","mag":"2150520277","pmid":"https://pubmed.ncbi.nlm.nih.gov/16204103"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti1131","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti1131","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/suppl_2/ii197/6686170/bti1131.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/21/suppl_2/ii197/6686170/bti1131.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048924272","display_name":"Dmitriy Leyfer","orcid":null},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Dmitriy Leyfer","raw_affiliation_strings":["Bioinformatics Program, Boston University, Boston, MA 02215, USA. dleyfer@gnsbiotech.com"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Program, Boston University, Boston, MA 02215, USA. dleyfer@gnsbiotech.com","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084369008","display_name":"Zhiping Weng","orcid":"https://orcid.org/0000-0002-3032-7966"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhiping Weng","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5048924272"],"corresponding_institution_ids":["https://openalex.org/I111088046"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.5023,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.6426775,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"21","issue":"suppl_2","first_page":"ii197","last_page":"ii203"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.8924000263214111,"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":0.8924000263214111,"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/T10268","display_name":"Developmental Biology and Gene Regulation","score":0.03240000084042549,"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":0.020899999886751175,"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/cluster-analysis","display_name":"Cluster analysis","score":0.6753722429275513},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.612832248210907},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6119204163551331},{"id":"https://openalex.org/keywords/hierarchical-clustering","display_name":"Hierarchical clustering","score":0.5776333212852478},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5713198184967041},{"id":"https://openalex.org/keywords/regulatory-sequence","display_name":"Regulatory sequence","score":0.5322142839431763},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.48441368341445923},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.4838246703147888},{"id":"https://openalex.org/keywords/cis-regulatory-module","display_name":"Cis-regulatory module","score":0.46520882844924927},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.46436330676078796},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.45616939663887024},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4399722218513489},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.35272133350372314},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.29927077889442444},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.09537264704704285}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6753722429275513},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.612832248210907},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6119204163551331},{"id":"https://openalex.org/C92835128","wikidata":"https://www.wikidata.org/wiki/Q1277447","display_name":"Hierarchical clustering","level":3,"score":0.5776333212852478},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5713198184967041},{"id":"https://openalex.org/C21592294","wikidata":"https://www.wikidata.org/wiki/Q3238407","display_name":"Regulatory sequence","level":4,"score":0.5322142839431763},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.48441368341445923},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4838246703147888},{"id":"https://openalex.org/C190796033","wikidata":"https://www.wikidata.org/wiki/Q1093165","display_name":"Cis-regulatory module","level":5,"score":0.46520882844924927},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.46436330676078796},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.45616939663887024},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4399722218513489},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.35272133350372314},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.29927077889442444},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.09537264704704285},{"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":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005815","descriptor_name":"Genetic Code","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005815","descriptor_name":"Genetic Code","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005815","descriptor_name":"Genetic Code","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bti1131","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti1131","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/suppl_2/ii197/6686170/bti1131.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:16204103","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16204103","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bti1131","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti1131","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/suppl_2/ii197/6686170/bti1131.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/G4603274807","display_name":null,"funder_award_id":"R01 HG03110","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W1595688369","https://openalex.org/W1988303029","https://openalex.org/W1991770658","https://openalex.org/W1995409627","https://openalex.org/W2000495354","https://openalex.org/W2008491350","https://openalex.org/W2013089038","https://openalex.org/W2018045523","https://openalex.org/W2025146617","https://openalex.org/W2046374070","https://openalex.org/W2053126761","https://openalex.org/W2053360677","https://openalex.org/W2053852189","https://openalex.org/W2058682865","https://openalex.org/W2062055237","https://openalex.org/W2062872358","https://openalex.org/W2080278541","https://openalex.org/W2099950599","https://openalex.org/W2101345690","https://openalex.org/W2109327803","https://openalex.org/W2112221859","https://openalex.org/W2114459488","https://openalex.org/W2117549173","https://openalex.org/W2119022656","https://openalex.org/W2119104284","https://openalex.org/W2124637492","https://openalex.org/W2124821604","https://openalex.org/W2125508747","https://openalex.org/W2126449841","https://openalex.org/W2126602684","https://openalex.org/W2127053639","https://openalex.org/W2129422961","https://openalex.org/W2133147430","https://openalex.org/W2136726922","https://openalex.org/W2143274936","https://openalex.org/W2145333821","https://openalex.org/W2150926065","https://openalex.org/W2158128075","https://openalex.org/W2161646573","https://openalex.org/W2163157163","https://openalex.org/W2163480486","https://openalex.org/W2165011536","https://openalex.org/W2165228646","https://openalex.org/W2167190345"],"related_works":["https://openalex.org/W2084309586","https://openalex.org/W2010571965","https://openalex.org/W2153800196","https://openalex.org/W2277277196","https://openalex.org/W2043274041","https://openalex.org/W2294194070","https://openalex.org/W2083342336","https://openalex.org/W2172096124","https://openalex.org/W1538019557","https://openalex.org/W2167190345"],"abstract_inverted_index":{"MOTIVATION:":[0],"A":[1],"holistic":[2],"approach":[3],"to":[4,45,73,91,111],"the":[5,74,100,127],"study":[6],"of":[7,32,38,78,116,119,131,175,183,188,195],"cellular":[8],"processes":[9,23,177],"is":[10,67,171],"identifying":[11],"both":[12],"gene-expression":[13],"changes":[14],"and":[15,60,102,129,150],"regulatory":[16,22,117,179],"elements":[17],"promoting":[18],"such":[19],"changes.":[20],"Cellular":[21],"can":[24],"be":[25],"viewed":[26],"as":[27],"transcriptional":[28,196],"modules":[29,154],"(TMs),":[30],"groups":[31,37,89],"coexpressed":[33],"genes":[34,79],"regulated":[35],"by":[36,69,94,145],"transcription":[39],"factors":[40],"(TFs).":[41],"We":[42,136],"set":[43],"out":[44],"devise":[46],"a":[47,186],"method":[48,124],"that":[49,64,71,138,169],"would":[50],"identify":[51],"TMs":[52,132,141,161],"while":[53],"avoiding":[54],"arbitrary":[55],"thresholds":[56],"on":[57,81,133],"TM":[58,113],"sizes":[59,130],"number.":[61],"METHOD:":[62],"Assuming":[63],"gene":[65,88,95,104],"expression":[66,96,101],"determined":[68],"TFs":[70],"bind":[72],"gene's":[75],"promoter,":[76],"clustering":[77],"based":[80],"TF":[82],"binding":[83],"sites":[84],"(cis-elements)":[85],"should":[86],"create":[87],"similar":[90],"those":[92],"obtained":[93],"clustering.":[97],"Intersections":[98],"between":[99],"cis-element-based":[103],"clusters":[105],"reveal":[106],"TMs.":[107],"Statistical":[108],"significance":[109],"assigned":[110],"each":[112,181],"allows":[114],"identification":[115],"units":[118],"any":[120],"size.":[121],"RESULTS:":[122],"Our":[123,153],"correctly":[125],"identifies":[126],"number":[128],"simulated":[134],"datasets.":[135],"demonstrate":[137],"yeast":[139],"experimental":[140],"are":[142,155],"biologically":[143],"relevant":[144],"comparing":[146],"them":[147],"with":[148,160],"MIPS":[149],"GO":[151],"categories.":[152],"in":[156],"statistically":[157],"significant":[158],"agreement":[159],"from":[162],"other":[163],"research":[164],"groups.":[165],"This":[166],"work":[167],"suggests":[168],"there":[170],"no":[172],"preferential":[173],"division":[174],"biological":[176,189],"into":[178],"units;":[180],"degree":[182],"partitioning":[184],"exhibits":[185],"slice":[187],"network":[190],"revealing":[191],"hierarchical":[192],"modular":[193],"organization":[194],"regulation.":[197]},"counts_by_year":[{"year":2018,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2016-06-24T00:00:00"}