{"id":"https://openalex.org/W2949327634","doi":"https://doi.org/10.1093/bioinformatics/btz398","title":"Accurate differential analysis of transcription factor activity from gene expression","display_name":"Accurate differential analysis of transcription factor activity from gene expression","publication_year":2019,"publication_date":"2019-05-08","ids":{"openalex":"https://openalex.org/W2949327634","doi":"https://doi.org/10.1093/bioinformatics/btz398","mag":"2949327634","pmid":"https://pubmed.ncbi.nlm.nih.gov/31099391"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz398","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz398","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086187149","display_name":"Viren Amin","orcid":null},"institutions":[{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Viren Amin","raw_affiliation_strings":["Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center , Dallas, TX, USA"],"affiliations":[{"raw_affiliation_string":"Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center , Dallas, TX, USA","institution_ids":["https://openalex.org/I867280407"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021497280","display_name":"Didem A\u011fa\u00e7 \u00c7obano\u011flu","orcid":"https://orcid.org/0000-0002-3493-7024"},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Didem A\u011fa\u00e7","raw_affiliation_strings":["Department of Immunology, University of Texas MD Anderson Cancer Center , Houston, TX, USA"],"affiliations":[{"raw_affiliation_string":"Department of Immunology, University of Texas MD Anderson Cancer Center , Houston, TX, USA","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085558566","display_name":"Spencer Barnes","orcid":"https://orcid.org/0000-0003-1103-0953"},"institutions":[{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Spencer D Barnes","raw_affiliation_strings":["Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center , Dallas, TX, USA"],"affiliations":[{"raw_affiliation_string":"Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center , Dallas, TX, USA","institution_ids":["https://openalex.org/I867280407"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042634777","display_name":"Murat Can \u00c7obano\u011flu","orcid":"https://orcid.org/0000-0002-0622-0376"},"institutions":[{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Murat Can \u00c7obano\u011flu","raw_affiliation_strings":["Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center , Dallas, TX, USA"],"affiliations":[{"raw_affiliation_string":"Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center , Dallas, TX, USA","institution_ids":["https://openalex.org/I867280407"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5042634777","https://openalex.org/A5086187149"],"corresponding_institution_ids":["https://openalex.org/I867280407"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.3436,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.59189144,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":"35","issue":"23","first_page":"5018","last_page":"5029"},"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/T10604","display_name":"RNA Research and Splicing","score":0.9940999746322632,"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":0.9699000120162964,"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/regulon","display_name":"Regulon","score":0.6828263998031616},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6050337553024292},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.5652902722358704},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5631447434425354},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5521685481071472},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.4499753415584564},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3852316737174988},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2892630696296692},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2715933918952942},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.16577911376953125},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1370006501674652}],"concepts":[{"id":"https://openalex.org/C62361671","wikidata":"https://www.wikidata.org/wiki/Q1754612","display_name":"Regulon","level":4,"score":0.6828263998031616},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6050337553024292},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5652902722358704},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5631447434425354},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5521685481071472},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.4499753415584564},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3852316737174988},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2892630696296692},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2715933918952942},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.16577911376953125},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1370006501674652},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018085","descriptor_name":"Regulon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018085","descriptor_name":"Regulon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018085","descriptor_name":"Regulon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btz398","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz398","pdf_url":null,"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:31099391","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31099391","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":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3884107769","display_name":null,"funder_award_id":"RP150596","funder_id":"https://openalex.org/F4320308129","funder_display_name":"Cancer Prevention and Research Institute of Texas"}],"funders":[{"id":"https://openalex.org/F4320308129","display_name":"Cancer Prevention and Research Institute of Texas","ror":"https://ror.org/0003xa228"},{"id":"https://openalex.org/F4320310169","display_name":"University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":63,"referenced_works":["https://openalex.org/W105302811","https://openalex.org/W284239745","https://openalex.org/W1572656384","https://openalex.org/W1602470456","https://openalex.org/W1934094702","https://openalex.org/W1967261754","https://openalex.org/W1970554427","https://openalex.org/W1986223165","https://openalex.org/W1988271142","https://openalex.org/W1993420755","https://openalex.org/W1994041743","https://openalex.org/W2001713238","https://openalex.org/W2002168324","https://openalex.org/W2002186586","https://openalex.org/W2025143086","https://openalex.org/W2027994854","https://openalex.org/W2029860358","https://openalex.org/W2040407706","https://openalex.org/W2044555648","https://openalex.org/W2045049295","https://openalex.org/W2045362835","https://openalex.org/W2058593261","https://openalex.org/W2070085523","https://openalex.org/W2070494252","https://openalex.org/W2074660641","https://openalex.org/W2074693857","https://openalex.org/W2091451666","https://openalex.org/W2093213568","https://openalex.org/W2105031411","https://openalex.org/W2107665951","https://openalex.org/W2112484474","https://openalex.org/W2115260093","https://openalex.org/W2116634113","https://openalex.org/W2127300249","https://openalex.org/W2128648326","https://openalex.org/W2129441797","https://openalex.org/W2130410032","https://openalex.org/W2139280965","https://openalex.org/W2140514146","https://openalex.org/W2144710927","https://openalex.org/W2144803920","https://openalex.org/W2155978263","https://openalex.org/W2157908534","https://openalex.org/W2158485828","https://openalex.org/W2163296115","https://openalex.org/W2166992988","https://openalex.org/W2185207072","https://openalex.org/W2190954851","https://openalex.org/W2262414037","https://openalex.org/W2288260164","https://openalex.org/W2295275561","https://openalex.org/W2329801343","https://openalex.org/W2335309161","https://openalex.org/W2340473927","https://openalex.org/W2347110697","https://openalex.org/W2395900612","https://openalex.org/W2472255748","https://openalex.org/W2530630735","https://openalex.org/W2620721366","https://openalex.org/W2785792383","https://openalex.org/W2894573839","https://openalex.org/W3099289621","https://openalex.org/W3133236490"],"related_works":["https://openalex.org/W61127607","https://openalex.org/W1984136937","https://openalex.org/W1786268878","https://openalex.org/W2794893700","https://openalex.org/W4281651837","https://openalex.org/W4313622135","https://openalex.org/W4362693150","https://openalex.org/W4282031271","https://openalex.org/W2164421791","https://openalex.org/W4220701345"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1}],"updated_date":"2026-04-17T18:11:37.981687","created_date":"2025-10-10T00:00:00"}
