{"id":"https://openalex.org/W3083362499","doi":"https://doi.org/10.1093/bioinformatics/btaa765","title":"Characterizing therapeutic signatures of transcription factors in cancer by incorporating profiles in compound treated cells","display_name":"Characterizing therapeutic signatures of transcription factors in cancer by incorporating profiles in compound treated cells","publication_year":2020,"publication_date":"2020-08-26","ids":{"openalex":"https://openalex.org/W3083362499","doi":"https://doi.org/10.1093/bioinformatics/btaa765","mag":"3083362499","pmid":"https://pubmed.ncbi.nlm.nih.gov/32886093"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa765","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa765","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/A5103282907","display_name":"Jin\u2010Myung Jung","orcid":"https://orcid.org/0000-0002-4962-8347"},"institutions":[{"id":"https://openalex.org/I16764540","display_name":"University of Suwon","ror":"https://ror.org/03ysk5e42","country_code":"KR","type":"education","lineage":["https://openalex.org/I16764540"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Jinmyung Jung","raw_affiliation_strings":["Division of Data Science, College of Information and Communication Technology, The University of Suwon , Hwaseong 18323, Republic of Korea"],"raw_orcid":"https://orcid.org/0000-0002-4962-8347","affiliations":[{"raw_affiliation_string":"Division of Data Science, College of Information and Communication Technology, The University of Suwon , Hwaseong 18323, Republic of Korea","institution_ids":["https://openalex.org/I16764540"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5103282907"],"corresponding_institution_ids":["https://openalex.org/I16764540"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.083591,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"37","issue":"7","first_page":"1008","last_page":"1014"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12835","display_name":"FOXO transcription factor regulation","score":0.9085000157356262,"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/T12835","display_name":"FOXO transcription factor regulation","score":0.9085000157356262,"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/T12620","display_name":"Signaling Pathways in Disease","score":0.012299999594688416,"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/T11736","display_name":"Histone Deacetylase Inhibitors Research","score":0.0034000000450760126,"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/runx1","display_name":"RUNX1","score":0.6758003234863281},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.627902626991272},{"id":"https://openalex.org/keywords/cancer-research","display_name":"Cancer research","score":0.5841289162635803},{"id":"https://openalex.org/keywords/crispr","display_name":"CRISPR","score":0.5436922311782837},{"id":"https://openalex.org/keywords/foxo3","display_name":"FOXO3","score":0.5247631072998047},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5217479467391968},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.49073898792266846},{"id":"https://openalex.org/keywords/cancer-cell","display_name":"Cancer cell","score":0.4869752824306488},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.46302786469459534},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3804747760295868},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2403310239315033}],"concepts":[{"id":"https://openalex.org/C2778193527","wikidata":"https://www.wikidata.org/wiki/Q15320451","display_name":"RUNX1","level":4,"score":0.6758003234863281},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.627902626991272},{"id":"https://openalex.org/C502942594","wikidata":"https://www.wikidata.org/wiki/Q3421914","display_name":"Cancer research","level":1,"score":0.5841289162635803},{"id":"https://openalex.org/C98108389","wikidata":"https://www.wikidata.org/wiki/Q412563","display_name":"CRISPR","level":3,"score":0.5436922311782837},{"id":"https://openalex.org/C168003608","wikidata":"https://www.wikidata.org/wiki/Q21101484","display_name":"FOXO3","level":4,"score":0.5247631072998047},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5217479467391968},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.49073898792266846},{"id":"https://openalex.org/C96232424","wikidata":"https://www.wikidata.org/wiki/Q4118072","display_name":"Cancer cell","level":3,"score":0.4869752824306488},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.46302786469459534},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3804747760295868},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2403310239315033}],"mesh":[{"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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"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}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btaa765","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa765","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:32886093","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32886093","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":[{"id":"https://metadata.un.org/sdg/3","score":0.6000000238418579,"display_name":"Good health and well-being"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322120","display_name":"National Research Foundation of Korea","ror":"https://ror.org/013aysd81"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W639218804","https://openalex.org/W1516269154","https://openalex.org/W1851611944","https://openalex.org/W1888680490","https://openalex.org/W1976271079","https://openalex.org/W1978477477","https://openalex.org/W1980480652","https://openalex.org/W2016464448","https://openalex.org/W2018796139","https://openalex.org/W2023546573","https://openalex.org/W2024011783","https://openalex.org/W2032058375","https://openalex.org/W2036104550","https://openalex.org/W2062989416","https://openalex.org/W2076851669","https://openalex.org/W2077135823","https://openalex.org/W2108068107","https://openalex.org/W2115075151","https://openalex.org/W2146980885","https://openalex.org/W2154139219","https://openalex.org/W2163413675","https://openalex.org/W2177605184","https://openalex.org/W2217264961","https://openalex.org/W2252568502","https://openalex.org/W2317542146","https://openalex.org/W2472255748","https://openalex.org/W2519635945","https://openalex.org/W2602892063","https://openalex.org/W2604095865","https://openalex.org/W2612467560","https://openalex.org/W2613445794","https://openalex.org/W2736453173","https://openalex.org/W2772692099","https://openalex.org/W2782454362","https://openalex.org/W2787229753","https://openalex.org/W2791178241","https://openalex.org/W2792052154","https://openalex.org/W2801284408","https://openalex.org/W2804749440","https://openalex.org/W2896634772","https://openalex.org/W2904153084","https://openalex.org/W2917858269","https://openalex.org/W2945883683","https://openalex.org/W2994177398","https://openalex.org/W3028373440","https://openalex.org/W3045153201","https://openalex.org/W3095691412","https://openalex.org/W3165669824","https://openalex.org/W4233120011","https://openalex.org/W6639547688","https://openalex.org/W6699882801"],"related_works":["https://openalex.org/W2079505765","https://openalex.org/W4306247897","https://openalex.org/W2315442591","https://openalex.org/W2510125591","https://openalex.org/W2580195473","https://openalex.org/W2888308691","https://openalex.org/W2082395362","https://openalex.org/W1963681345","https://openalex.org/W2794294196","https://openalex.org/W2044068920"],"abstract_inverted_index":{"MOTIVATION:":[0],"Cancers":[1],"are":[2,102,233,241],"promoted":[3],"by":[4,56,80,141],"abnormal":[5],"alterations":[6],"in":[7,36,70,223],"biological":[8],"processes,":[9],"such":[10,45],"as":[11,41,46,98,122,167,176],"cell":[12,149],"cycle":[13],"and":[14,48,73,86,135,152,169,171,178,185,203,230],"apoptosis.":[15],"An":[16],"immediate":[17],"reason":[18],"for":[19,219],"those":[20],"aberrant":[21],"processes":[22],"is":[23],"the":[24,33,92,99,114,123,133,163,172,186,189,196,214],"deregulation":[25],"of":[26,65,68],"their":[27],"involved":[28],"transcription":[29],"factors":[30],"(TFs).":[31],"Thus,":[32],"deregulated":[34],"TFs":[35,69,94,100],"cancer":[37,76],"have":[38],"been":[39],"experimented":[40],"successful":[42],"therapeutic":[43,51,66,93,198,220],"targets,":[44,199],"RARA":[47],"RUNX1.":[49],"This":[50],"strategy":[52],"can":[53],"be":[54],"accelerated":[55],"characterizing":[57],"new":[58],"potential":[59],"TF":[60,82,117,124,221],"targets.":[61],"RESULTS:":[62],"Two":[63],"kinds":[64],"signatures":[67],"A375":[71],"(skin)":[72],"HT29":[74],"(colon)":[75],"cells":[77],"were":[78,96,120,181,193],"characterized":[79],"analyzing":[81],"activities":[83],"under":[84,107],"effective":[85,108,134],"ineffective":[87,111,136],"compounds":[88],"to":[89,110],"cancer.":[90,224],"First,":[91],"(TTs)":[95],"identified":[97],"that":[101,213],"significantly":[103],"activated":[104],"or":[105],"repressed":[106],"compared":[109,194],"compounds.":[112,137],"Second,":[113],"therapeutically":[115],"correlated":[116],"pairs":[118,125],"(TCPs)":[119],"determined":[121],"whose":[126],"activity":[127],"correlations":[128],"show":[129],"substantial":[130],"discrepancy":[131],"between":[132,191],"It":[138],"was":[139],"facilitated":[140],"incorporating":[142],"(i)compound-induced":[143],"gene":[144],"expressions":[145],"(LINCS),":[146],"(ii)":[147],"compound-induced":[148],"viabilities":[150],"(GDSC)":[151],"(iii)":[153],"TF-target":[154],"interactions":[155],"(TRUST2).":[156],"As":[157],"a":[158],"result,":[159],"among":[160],"627":[161],"TFs,":[162],"35":[164],"TTs":[165,184],"(such":[166,175],"MYCN":[168],"TP53)":[170],"214":[173],"TCPs":[174,192],"FOXO3":[177],"POU2F2":[179],"pair)":[180],"identified.":[182],"The":[183,228],"proteins":[187],"on":[188],"paths":[190],"with":[195],"known":[197],"tumor":[200],"suppressors,":[201],"oncogenes":[202],"CRISPR-Cas9":[204],"knockout":[205],"screening,":[206],"which":[207],"yielded":[208],"significant":[209],"consequences.":[210],"We":[211],"expect":[212],"results":[215],"provide":[216],"good":[217],"candidates":[218],"targets":[222],"AVAILABILITY":[225],"AND":[226],"IMPLEMENTATION:":[227],"data":[229,240],"Python":[231],"implementations":[232],"available":[234,242],"at":[235,243],"https://github.com/jmjung83/TT_and_TCP.":[236],"SUPPLEMENTARY":[237],"INFORMATION:":[238],"Supplementary":[239],"Bioinformatics":[244],"online.":[245]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
