{"id":"https://openalex.org/W2577402342","doi":"https://doi.org/10.1371/journal.pcbi.1005340","title":"Contextual Refinement of Regulatory Targets Reveals Effects on Breast Cancer Prognosis of the Regulome","display_name":"Contextual Refinement of Regulatory Targets Reveals Effects on Breast Cancer Prognosis of the Regulome","publication_year":2017,"publication_date":"2017-01-19","ids":{"openalex":"https://openalex.org/W2577402342","doi":"https://doi.org/10.1371/journal.pcbi.1005340","mag":"2577402342","pmid":"https://pubmed.ncbi.nlm.nih.gov/28103241"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1005340","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005340","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005340&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005340&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5033559836","display_name":"Erik Andrews","orcid":null},"institutions":[{"id":"https://openalex.org/I107672454","display_name":"Dartmouth College","ror":"https://ror.org/049s0rh22","country_code":"US","type":"education","lineage":["https://openalex.org/I107672454"]},{"id":"https://openalex.org/I126688049","display_name":"Dartmouth Institute for Health Policy and Clinical Practice","ror":"https://ror.org/0511yej17","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I126688049"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Erik Andrews","raw_affiliation_strings":["Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America","Institute for Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America","institution_ids":["https://openalex.org/I107672454"]},{"raw_affiliation_string":"Institute for Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America","institution_ids":["https://openalex.org/I126688049"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100372068","display_name":"Yue Wang","orcid":"https://orcid.org/0000-0002-7761-2721"},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]},{"id":"https://openalex.org/I107672454","display_name":"Dartmouth College","ror":"https://ror.org/049s0rh22","country_code":"US","type":"education","lineage":["https://openalex.org/I107672454"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Yue Wang","raw_affiliation_strings":["Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America","School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan, Hubei, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America","institution_ids":["https://openalex.org/I107672454"]},{"raw_affiliation_string":"School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan, Hubei, China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054677999","display_name":"Tian Xia","orcid":"https://orcid.org/0000-0002-0097-6949"},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tian Xia","raw_affiliation_strings":["School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan, Hubei, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan, Hubei, China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056643192","display_name":"Wenqing Cheng","orcid":"https://orcid.org/0000-0001-7840-1195"},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenqing Cheng","raw_affiliation_strings":["School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan, Hubei, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan, Hubei, China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082582585","display_name":"Chao Cheng","orcid":"https://orcid.org/0000-0002-5002-3417"},"institutions":[{"id":"https://openalex.org/I126688049","display_name":"Dartmouth Institute for Health Policy and Clinical Practice","ror":"https://ror.org/0511yej17","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I126688049"]},{"id":"https://openalex.org/I107672454","display_name":"Dartmouth College","ror":"https://ror.org/049s0rh22","country_code":"US","type":"education","lineage":["https://openalex.org/I107672454"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Chao Cheng","raw_affiliation_strings":["Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America","Institute for Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America","Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America","institution_ids":["https://openalex.org/I107672454"]},{"raw_affiliation_string":"Institute for Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America","institution_ids":["https://openalex.org/I126688049"]},{"raw_affiliation_string":"Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America","institution_ids":["https://openalex.org/I107672454"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5082582585"],"corresponding_institution_ids":["https://openalex.org/I107672454","https://openalex.org/I126688049"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.5465,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.64296987,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"13","issue":"1","first_page":"e1005340","last_page":"e1005340"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9988999962806702,"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":0.9986000061035156,"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/regulator","display_name":"Regulator","score":0.8047144412994385},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6163320541381836},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5925309658050537},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.5072102546691895},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.4964504837989807},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.49134841561317444},{"id":"https://openalex.org/keywords/microrna","display_name":"microRNA","score":0.4859844148159027},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4775058627128601},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3348262310028076},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.3324812054634094}],"concepts":[{"id":"https://openalex.org/C6929976","wikidata":"https://www.wikidata.org/wiki/Q3771881","display_name":"Regulator","level":3,"score":0.8047144412994385},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6163320541381836},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5925309658050537},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.5072102546691895},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4964504837989807},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.49134841561317444},{"id":"https://openalex.org/C145059251","wikidata":"https://www.wikidata.org/wiki/Q310899","display_name":"microRNA","level":3,"score":0.4859844148159027},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4775058627128601},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3348262310028076},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3324812054634094},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","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":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011379","descriptor_name":"Prognosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011379","descriptor_name":"Prognosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011379","descriptor_name":"Prognosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1371/journal.pcbi.1005340","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005340","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005340&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:28103241","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28103241","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":"PLoS computational biology","raw_type":null},{"id":"pmh:ark:/13030/qt71v5q9g5","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:RePEc:plo:pcbi00:1005340","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005340","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:3c83d102d6a44462be7dadcb1b507df0","is_oa":false,"landing_page_url":"https://doaj.org/article/3c83d102d6a44462be7dadcb1b507df0","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 13, Iss 1, p e1005340 (2017)","raw_type":"article"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt71v5q9g5","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/71v5q9g5","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLOS Computational Biology, vol 13, iss 1","raw_type":"article"},{"id":"pmh:oai:europepmc.org:4172259","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5289608","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"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":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/4570609","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Contextual_Refinement_of_Regulatory_Targets_Reveals_Effects_on_Breast_Cancer_Prognosis_of_the_Regulome/4570609","pdf_url":null,"source":{"id":"https://openalex.org/S4306402621","display_name":"INDIGO (University of Illinois at Chicago)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I39422238","host_organization_name":"University of Illinois Chicago","host_organization_lineage":["https://openalex.org/I39422238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1005340","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005340","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005340&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.5400000214576721,"display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G1588133564","display_name":null,"funder_award_id":"KL2 TR001088","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"},{"id":"https://openalex.org/G2805242875","display_name":"\u9ad8\u901a\u91cf\u9057\u4f20\u76f8\u4e92\u4f5c\u7528\u7f51\u7edc\u5efa\u6a21\u6280\u672f\u7814\u7a76","funder_award_id":"61571202","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3158680667","display_name":null,"funder_award_id":"KL2TR001088","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"},{"id":"https://openalex.org/G3242082962","display_name":null,"funder_award_id":"UL1 TR001086","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"},{"id":"https://openalex.org/G5204542997","display_name":null,"funder_award_id":"UL1TR001086","funder_id":"https://openalex.org/F4320310400","funder_display_name":"Dartmouth College"},{"id":"https://openalex.org/G5668804095","display_name":null,"funder_award_id":"P20 GM103534","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6157900747","display_name":null,"funder_award_id":"UL1TR001086","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7965638068","display_name":null,"funder_award_id":"GM103534","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8084936081","display_name":null,"funder_award_id":"KL2TR001088","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8211238123","display_name":null,"funder_award_id":"UL1TR001086","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"}],"funders":[{"id":"https://openalex.org/F4320310400","display_name":"Dartmouth College","ror":"https://ror.org/049s0rh22"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320326701","display_name":"Recruitment Program of Global Experts","ror":null},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332818","display_name":"Audrey and Theodor Geisel School of Medicine at Dartmouth","ror":"https://ror.org/049s0rh22"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337472","display_name":"National Center for Advancing Translational Sciences","ror":"https://ror.org/04pw6fb54"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2577402342.pdf","grobid_xml":"https://content.openalex.org/works/W2577402342.grobid-xml"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W17966160","https://openalex.org/W1969012014","https://openalex.org/W1986707106","https://openalex.org/W1988393300","https://openalex.org/W1995082021","https://openalex.org/W2005895632","https://openalex.org/W2008951807","https://openalex.org/W2010457001","https://openalex.org/W2017199818","https://openalex.org/W2026918499","https://openalex.org/W2035329335","https://openalex.org/W2044702943","https://openalex.org/W2044832480","https://openalex.org/W2049658618","https://openalex.org/W2050869737","https://openalex.org/W2053835153","https://openalex.org/W2067527491","https://openalex.org/W2070159701","https://openalex.org/W2074174832","https://openalex.org/W2077327925","https://openalex.org/W2078429592","https://openalex.org/W2083381199","https://openalex.org/W2084379028","https://openalex.org/W2085442947","https://openalex.org/W2086893629","https://openalex.org/W2087011329","https://openalex.org/W2088160256","https://openalex.org/W2090757807","https://openalex.org/W2096079397","https://openalex.org/W2096283457","https://openalex.org/W2098023402","https://openalex.org/W2108539079","https://openalex.org/W2112192177","https://openalex.org/W2128648326","https://openalex.org/W2128937741","https://openalex.org/W2131638827","https://openalex.org/W2133658633","https://openalex.org/W2135030836","https://openalex.org/W2139522545","https://openalex.org/W2142890842","https://openalex.org/W2147703218","https://openalex.org/W2148929244","https://openalex.org/W2149785901","https://openalex.org/W2150671673","https://openalex.org/W2154085311","https://openalex.org/W2160450758","https://openalex.org/W2160913143","https://openalex.org/W2163563958","https://openalex.org/W2171622167","https://openalex.org/W2259938310","https://openalex.org/W2402362653","https://openalex.org/W2560367415","https://openalex.org/W4245024447","https://openalex.org/W6662071483"],"related_works":["https://openalex.org/W2128583238","https://openalex.org/W2010571965","https://openalex.org/W2034377088","https://openalex.org/W3151254369","https://openalex.org/W2002709996","https://openalex.org/W2613929436","https://openalex.org/W3128451840","https://openalex.org/W2347793859","https://openalex.org/W4387092964","https://openalex.org/W2103471012"],"abstract_inverted_index":{"Gene":[0],"expression":[1,103,125],"regulators,":[2],"such":[3],"as":[4],"transcription":[5],"factors":[6],"(TFs)":[7],"and":[8,19,98,126,140,156,172,217,225],"microRNAs":[9],"(miRNAs),":[10],"have":[11,65],"varying":[12],"regulatory":[13,131],"targets":[14],"based":[15],"on":[16],"the":[17,29,36,118,127,134,138,142,165,223,228],"tissue":[18],"physiological":[20],"state":[21],"(context)":[22],"within":[23],"which":[24],"they":[25],"are":[26,53,61],"expressed.":[27],"While":[28],"emergence":[30],"of":[31,39,83,130,150,169,238],"regulator-characterizing":[32],"experiments":[33],"has":[34],"inferred":[35],"target":[37,49,57,95,123,152,175,245],"genes":[38,50,136,246],"many":[40,43,204,250],"regulators":[41,207],"across":[42,51,249],"contexts,":[44],"methods":[45],"for":[46,112,178,186,247],"transferring":[47],"regulator":[48,56,244],"contexts":[52],"lacking.":[54],"Further,":[55],"gene":[58,96,102,176],"lists":[59,177],"frequently":[60],"not":[62],"curated":[63],"or":[64],"permissive":[66],"inclusion":[67],"criteria,":[68],"impairing":[69],"their":[70],"use.":[71],"Here,":[72],"we":[73,160],"present":[74],"a":[75,92,106,147,219],"method":[76],"called":[77],"iterative":[78],"Contextual":[79],"Transcriptional":[80],"Activity":[81],"Inference":[82],"Regulators":[84],"(icTAIR)":[85],"to":[86,163,212],"resolve":[87],"these":[88],"issues.":[89],"icTAIR":[90,235,253],"takes":[91],"regulator's":[93,110],"previously-identified":[94],"list":[97,149],"combines":[99],"it":[100,145,162],"with":[101,189],"data":[104],"from":[105,137,258],"context,":[107],"quantifying":[108],"that":[109,113,208],"activity":[111],"context.":[114],"It":[115],"then":[116,182],"calculates":[117],"correlation":[119],"between":[120],"each":[121],"listed":[122],"gene's":[124],"quantitative":[128],"score":[129],"activity,":[132],"removes":[133],"uncorrelated":[135],"list,":[139],"iterates":[141],"process":[143],"until":[144],"derives":[146],"stable":[148],"refined":[151],"genes.":[153],"To":[154],"validate":[155],"demonstrate":[157],"icTAIR's":[158],"power,":[159],"use":[161,183,240],"refine":[164],"MSigDB":[166],"c3":[167],"database":[168],"TF,":[170],"miRNA":[171],"unclassified":[173],"motif":[174],"breast":[179,196,229],"cancer.":[180],"We":[181,202,233],"its":[184],"output":[185],"survival":[187],"analysis":[188],"clinicopathological":[190],"multivariable":[191],"adjustment":[192],"in":[193,214,241],"7":[194],"independent":[195],"cancer":[197,230],"datasets":[198],"covering":[199],"3,430":[200],"patients.":[201],"uncover":[203],"novel":[205],"prognostic":[206,231],"were":[209],"obscured":[210],"prior":[211],"refinement,":[213],"particular":[215],"NFY,":[216],"offer":[218],"detailed":[220],"look":[221],"at":[222],"composition":[224],"relationships":[226],"among":[227],"regulome.":[232],"anticipate":[234],"will":[236],"be":[237,256],"general":[239],"contextually":[242],"refining":[243],"discoveries":[248],"contexts.":[251],"The":[252],"algorithm":[254],"can":[255],"downloaded":[257],"https://github.com/icTAIR.":[259]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}