{"id":"https://openalex.org/W2562389674","doi":"https://doi.org/10.4137/grsb.s40768","title":"Identifying Cell Type-Specific Transcription Factors by Integrating ChIP-seq and eQTL Data-Application to Monocyte Gene Regulation","display_name":"Identifying Cell Type-Specific Transcription Factors by Integrating ChIP-seq and eQTL Data-Application to Monocyte Gene Regulation","publication_year":2016,"publication_date":"2016-01-01","ids":{"openalex":"https://openalex.org/W2562389674","doi":"https://doi.org/10.4137/grsb.s40768","mag":"2562389674","pmid":"https://pubmed.ncbi.nlm.nih.gov/28008225","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/5156548"},"language":"en","primary_location":{"id":"doi:10.4137/grsb.s40768","doi":"https://doi.org/10.4137/grsb.s40768","is_oa":true,"landing_page_url":"https://doi.org/10.4137/grsb.s40768","pdf_url":"https://journals.sagepub.com/doi/pdf/10.4137/GRSB.S40768","source":{"id":"https://openalex.org/S2764764968","display_name":"Gene Regulation and Systems Biology","issn_l":"1177-6250","issn":["1177-6250"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","jufo-1","poland-100"],"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Gene Regulation and Systems Biology","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://journals.sagepub.com/doi/pdf/10.4137/GRSB.S40768","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047503323","display_name":"Mudra Choudhury","orcid":"https://orcid.org/0000-0002-7557-4661","observed_orcids":["https://orcid.org/0000-0002-7557-4661"]},"institutions":[{"id":"https://openalex.org/I131249849","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60","country_code":"US","type":"education","lineage":["https://openalex.org/I131249849"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mudra Choudhury","raw_affiliation_strings":["Department of Biomedical Sciences, Oregon State University, Corvallis, OR, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Sciences, Oregon State University, Corvallis, OR, USA","institution_ids":["https://openalex.org/I131249849"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091354698","display_name":"Stephen A. Ramsey","orcid":"https://orcid.org/0000-0002-2168-5403","observed_orcids":["https://orcid.org/0000-0002-2168-5403"]},"institutions":[{"id":"https://openalex.org/I131249849","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60","country_code":"US","type":"education","lineage":["https://openalex.org/I131249849"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Stephen A. Ramsey","raw_affiliation_strings":["Department of Biomedical Sciences, Oregon State University, Corvallis, OR, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Sciences, Oregon State University, Corvallis, OR, USA","institution_ids":["https://openalex.org/I131249849"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5091354698"],"corresponding_institution_ids":["https://openalex.org/I131249849"],"apc_list":null,"apc_paid":null,"fwci":0.1424,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.55345766,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":94},"biblio":{"volume":"10","issue":null,"first_page":"105","last_page":"110"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9711999893188477,"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":0.9711999893188477,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.012799999676644802,"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"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.006099999882280827,"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/transcription-factors","display_name":"transcription factors","score":0.7639999985694885},{"id":"https://openalex.org/keywords/cell-type-specific-gene-regulation","display_name":"cell type-specific gene regulation","score":0.7760000228881836},{"id":"https://openalex.org/keywords/monocytes","display_name":"monocytes","score":0.7770000100135803},{"id":"https://openalex.org/keywords/expression-quantitative-trait-loci","display_name":"expression quantitative trait loci","score":0.906000018119812},{"id":"https://openalex.org/keywords/chip-seq","display_name":"ChIP-seq","score":0.8809999823570251},{"id":"https://openalex.org/keywords/transcription-factor-binding-sites","display_name":"transcription factor binding sites","score":0.7990000247955322},{"id":"https://openalex.org/keywords/bclaf1","display_name":"BCLAF1","score":0.8519999980926514},{"id":"https://openalex.org/keywords/sin3a","display_name":"SIN3A","score":1.0},{"id":"https://openalex.org/keywords/protein-protein-interaction-network","display_name":"protein-protein interaction network","score":0.8220000267028809},{"id":"https://openalex.org/keywords/data-integration","display_name":"data integration","score":0.47600001096725464}],"concepts":[{"id":"https://openalex.org/C168393362","wikidata":"https://www.wikidata.org/wiki/Q5421706","display_name":"Expression quantitative trait loci","level":5,"score":0.8715255260467529},{"id":"https://openalex.org/C134320426","wikidata":"https://www.wikidata.org/wiki/Q901026","display_name":"Chromatin immunoprecipitation","level":5,"score":0.7158395051956177},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6382876634597778},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.6303658485412598},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5551144480705261},{"id":"https://openalex.org/C2781184567","wikidata":"https://www.wikidata.org/wiki/Q107244","display_name":"Monocyte","level":2,"score":0.4829818308353424},{"id":"https://openalex.org/C189014844","wikidata":"https://www.wikidata.org/wiki/Q189118","display_name":"Cell type","level":3,"score":0.47462356090545654},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.44824936985969543},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4429607391357422},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3951093554496765},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3625461459159851},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.28797489404678345},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.21263441443443298},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.1768110692501068},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.06146612763404846},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.4137/grsb.s40768","doi":"https://doi.org/10.4137/grsb.s40768","is_oa":true,"landing_page_url":"https://doi.org/10.4137/grsb.s40768","pdf_url":"https://journals.sagepub.com/doi/pdf/10.4137/GRSB.S40768","source":{"id":"https://openalex.org/S2764764968","display_name":"Gene Regulation and Systems Biology","issn_l":"1177-6250","issn":["1177-6250"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","jufo-1","poland-100"],"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Gene Regulation and Systems Biology","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5156548","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5156548","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,"listed_in":[],"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":"Gene Regul Syst Bio","raw_type":"Text"},{"id":"pmid:28008225","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28008225","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,"listed_in":[],"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":"Gene regulation and systems biology","raw_type":"Journal Article"},{"id":"pmh:oai:libertasacademica.com/6085","doi":null,"is_oa":false,"landing_page_url":"http://insights.sagepub.com/redirect_file.php?fileId=8069&filename=6085-GRSB-Identifying-Cell-Type-Specific-Transcription-Factors-by-Integrating-Ch.pdf&fileType=pdf","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://insights.sagepub.com/identifying-cell-type-specific-transcription-factors-by-integrating-ch-article-a6085","raw_type":null}],"best_oa_location":{"id":"doi:10.4137/grsb.s40768","doi":"https://doi.org/10.4137/grsb.s40768","is_oa":true,"landing_page_url":"https://doi.org/10.4137/grsb.s40768","pdf_url":"https://journals.sagepub.com/doi/pdf/10.4137/GRSB.S40768","source":{"id":"https://openalex.org/S2764764968","display_name":"Gene Regulation and Systems Biology","issn_l":"1177-6250","issn":["1177-6250"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","jufo-1","poland-100"],"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Gene Regulation and Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.6240000128746033}],"study_designs":[],"awards":[{"id":"https://openalex.org/G5164921321","display_name":"Systems analysis of transcriptional interactions underlying foam cell formation","funder_award_id":"K25HL098807","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"}],"funders":[{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2562389674.pdf"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W1533942137","https://openalex.org/W1931807888","https://openalex.org/W1973064777","https://openalex.org/W1977099733","https://openalex.org/W1984939442","https://openalex.org/W2001554877","https://openalex.org/W2013898117","https://openalex.org/W2017526442","https://openalex.org/W2035451872","https://openalex.org/W2066465196","https://openalex.org/W2072999024","https://openalex.org/W2079674166","https://openalex.org/W2080806096","https://openalex.org/W2085964485","https://openalex.org/W2090602346","https://openalex.org/W2098412979","https://openalex.org/W2104549677","https://openalex.org/W2109108939","https://openalex.org/W2110065044","https://openalex.org/W2112293785","https://openalex.org/W2116634411","https://openalex.org/W2118608526","https://openalex.org/W2124649441","https://openalex.org/W2128476271","https://openalex.org/W2128965269","https://openalex.org/W2130410032","https://openalex.org/W2138636722","https://openalex.org/W2145221987","https://openalex.org/W2159675211","https://openalex.org/W2230245649","https://openalex.org/W2302719675","https://openalex.org/W2333617152","https://openalex.org/W2336882982","https://openalex.org/W2343932903","https://openalex.org/W2433959401","https://openalex.org/W2501634966","https://openalex.org/W2533463607","https://openalex.org/W2537643963","https://openalex.org/W4245023496","https://openalex.org/W4313347709"],"related_works":["https://openalex.org/W584413499","https://openalex.org/W2814473043","https://openalex.org/W2964526879","https://openalex.org/W4237992946","https://openalex.org/W2901678069","https://openalex.org/W1967735816","https://openalex.org/W4225777909","https://openalex.org/W4251774738","https://openalex.org/W4393277980","https://openalex.org/W1973064777"],"abstract_inverted_index":{"We":[0,115,147],"describe":[1],"a":[2,16,63,161],"novel":[3,169],"computational":[4],"approach":[5,23,177],"to":[6,58,121,182],"identify":[7,183],"transcription":[8],"factors":[9],"(TFs)":[10],"that":[11,73,109,134,151,186],"are":[12,110,137,198],"candidate":[13,170,184],"regulators":[14,81],"in":[15,42,56,85],"human":[17,54],"cell":[18,26,43,78],"type":[19,193],"of":[20,65,77,88,93,106],"interest.":[21],"Our":[22,165,176],"involves":[24],"integrating":[25],"type-specific":[27,79],"expression":[28],"quantitative":[29],"trait":[30],"locus":[31],"(eQTL)":[32],"data":[33,36,52,96,118,197],"and":[34,128,157,174],"TF":[35,80],"from":[37,53,129],"chromatin":[38],"immunoprecipitation-to-tag-sequencing":[39],"(ChIP-seq)":[40],"experiments":[41],"lines.":[44],"To":[45],"test":[46],"the":[47,71,74,86,104],"method,":[48],"we":[49,69,98,132],"used":[50,189],"eQTL":[51,126,196],"monocytes":[55],"order":[57],"screen":[59],"for":[60,103,125,190,194],"TFs.":[61],"Using":[62],"list":[64],"known":[66],"monocyte-regulating":[67,135,171],"TFs,":[68,172],"tested":[70],"hypothesis":[72],"binding":[75],"sites":[76],"would":[82,142],"be":[83,143,188],"concentrated":[84],"vicinity":[87],"monocyte":[89,113,154],"eQTLs.":[90,114],"For":[91],"each":[92],"397":[94],"ChIP-seq":[95,107,117],"sets,":[97],"obtained":[99],"an":[100,179],"enrichment":[101,155],"ratio":[102],"number":[105],"peaks":[108],"located":[111],"within":[112],"ranked":[116,140],"sets":[119],"according":[120],"their":[122],"statistical":[123],"significances":[124],"overlap,":[127],"this":[130],"ranking,":[131],"observed":[133],"TFs":[136,150,185],"more":[138],"highly":[139],"than":[141],"expected":[144],"by":[145],"chance.":[146],"identified":[148],"27":[149],"had":[152],"significant":[153],"scores":[156],"mapped":[158],"them":[159],"into":[160],"protein":[162],"interaction":[163],"network.":[164],"analysis":[166],"uncovered":[167],"two":[168],"BCLAF1":[173],"SIN3A.":[175],"is":[178],"efficient":[180],"method":[181],"can":[187],"any":[191],"cell/tissue":[192],"which":[195],"available.":[199]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2017-01-06T00:00:00"}
