{"id":"https://openalex.org/W2087754565","doi":"https://doi.org/10.1093/bioinformatics/btu400","title":"Modeling time-dependent transcription effects of HER2 oncogene and discovery of a role for E2F2 in breast cancer cell-matrix adhesion","display_name":"Modeling time-dependent transcription effects of HER2 oncogene and discovery of a role for E2F2 in breast cancer cell-matrix adhesion","publication_year":2014,"publication_date":"2014-07-15","ids":{"openalex":"https://openalex.org/W2087754565","doi":"https://doi.org/10.1093/bioinformatics/btu400","mag":"2087754565","pmid":"https://pubmed.ncbi.nlm.nih.gov/25028721"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu400","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu400","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/21/3036/48930801/bioinformatics_30_21_3036.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/30/21/3036/48930801/bioinformatics_30_21_3036.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5033688288","display_name":"Aliccia Bollig\u2010Fischer","orcid":"https://orcid.org/0000-0003-4832-9457"},"institutions":[{"id":"https://openalex.org/I119439378","display_name":"University of Verona","ror":"https://ror.org/039bp8j42","country_code":"IT","type":"education","lineage":["https://openalex.org/I119439378"]},{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]},{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]},{"id":"https://openalex.org/I2802934434","display_name":"The Microsoft Research - University of Trento Centre for Computational and Systems Biology","ror":"https://ror.org/04kcgyj43","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I1290206253","https://openalex.org/I193223587","https://openalex.org/I2802934434","https://openalex.org/I4210164937"]},{"id":"https://openalex.org/I4210090317","display_name":"The Barbara Ann Karmanos Cancer Institute","ror":"https://ror.org/00ee40h97","country_code":"US","type":"facility","lineage":["https://openalex.org/I2800590384","https://openalex.org/I4210090317"]}],"countries":["IT","US"],"is_corresponding":true,"raw_author_name":"Aliccia Bollig-Fischer","raw_affiliation_strings":["1 Barbara Ann Karmanos Cancer Institute and 2 Department of Oncology, Wayne State University, Detroit, MI 48201, USA, 3 Department of Computer Science, University of Verona, 37134 Verona, Italy, 4 The Microsoft Research\u2013University of Trento Centre for Computational and Systems Biology, 38068 Rovereto, Italy, 5 Department of Computer Science, Wayne State University and 6 Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Barbara Ann Karmanos Cancer Institute and 2 Department of Oncology, Wayne State University, Detroit, MI 48201, USA, 3 Department of Computer Science, University of Verona, 37134 Verona, Italy, 4 The Microsoft Research\u2013University of Trento Centre for Computational and Systems Biology, 38068 Rovereto, Italy, 5 Department of Computer Science, Wayne State University and 6 Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA","institution_ids":["https://openalex.org/I2802934434","https://openalex.org/I193223587","https://openalex.org/I4210090317","https://openalex.org/I119439378","https://openalex.org/I185443292"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052320095","display_name":"Luca Marchetti","orcid":"https://orcid.org/0000-0001-9043-7705"},"institutions":[{"id":"https://openalex.org/I119439378","display_name":"University of Verona","ror":"https://ror.org/039bp8j42","country_code":"IT","type":"education","lineage":["https://openalex.org/I119439378"]},{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]},{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]},{"id":"https://openalex.org/I2802934434","display_name":"The Microsoft Research - University of Trento Centre for Computational and Systems Biology","ror":"https://ror.org/04kcgyj43","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I1290206253","https://openalex.org/I193223587","https://openalex.org/I2802934434","https://openalex.org/I4210164937"]},{"id":"https://openalex.org/I4210090317","display_name":"The Barbara Ann Karmanos Cancer Institute","ror":"https://ror.org/00ee40h97","country_code":"US","type":"facility","lineage":["https://openalex.org/I2800590384","https://openalex.org/I4210090317"]}],"countries":["IT","US"],"is_corresponding":false,"raw_author_name":"Luca Marchetti","raw_affiliation_strings":["1 Barbara Ann Karmanos Cancer Institute and 2 Department of Oncology, Wayne State University, Detroit, MI 48201, USA, 3 Department of Computer Science, University of Verona, 37134 Verona, Italy, 4 The Microsoft Research\u2013University of Trento Centre for Computational and Systems Biology, 38068 Rovereto, Italy, 5 Department of Computer Science, Wayne State University and 6 Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Barbara Ann Karmanos Cancer Institute and 2 Department of Oncology, Wayne State University, Detroit, MI 48201, USA, 3 Department of Computer Science, University of Verona, 37134 Verona, Italy, 4 The Microsoft Research\u2013University of Trento Centre for Computational and Systems Biology, 38068 Rovereto, Italy, 5 Department of Computer Science, Wayne State University and 6 Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA","institution_ids":["https://openalex.org/I2802934434","https://openalex.org/I193223587","https://openalex.org/I4210090317","https://openalex.org/I119439378","https://openalex.org/I185443292"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071747191","display_name":"Cristina Mitrea","orcid":null},"institutions":[{"id":"https://openalex.org/I119439378","display_name":"University of Verona","ror":"https://ror.org/039bp8j42","country_code":"IT","type":"education","lineage":["https://openalex.org/I119439378"]},{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]},{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]},{"id":"https://openalex.org/I2802934434","display_name":"The Microsoft Research - University of Trento Centre for Computational and Systems Biology","ror":"https://ror.org/04kcgyj43","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I1290206253","https://openalex.org/I193223587","https://openalex.org/I2802934434","https://openalex.org/I4210164937"]},{"id":"https://openalex.org/I4210090317","display_name":"The Barbara Ann Karmanos Cancer Institute","ror":"https://ror.org/00ee40h97","country_code":"US","type":"facility","lineage":["https://openalex.org/I2800590384","https://openalex.org/I4210090317"]}],"countries":["IT","US"],"is_corresponding":false,"raw_author_name":"Cristina Mitrea","raw_affiliation_strings":["1 Barbara Ann Karmanos Cancer Institute and 2 Department of Oncology, Wayne State University, Detroit, MI 48201, USA, 3 Department of Computer Science, University of Verona, 37134 Verona, Italy, 4 The Microsoft Research\u2013University of Trento Centre for Computational and Systems Biology, 38068 Rovereto, Italy, 5 Department of Computer Science, Wayne State University and 6 Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Barbara Ann Karmanos Cancer Institute and 2 Department of Oncology, Wayne State University, Detroit, MI 48201, USA, 3 Department of Computer Science, University of Verona, 37134 Verona, Italy, 4 The Microsoft Research\u2013University of Trento Centre for Computational and Systems Biology, 38068 Rovereto, Italy, 5 Department of Computer Science, Wayne State University and 6 Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA","institution_ids":["https://openalex.org/I2802934434","https://openalex.org/I193223587","https://openalex.org/I4210090317","https://openalex.org/I119439378","https://openalex.org/I185443292"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091252490","display_name":"Jiusheng Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I119439378","display_name":"University of Verona","ror":"https://ror.org/039bp8j42","country_code":"IT","type":"education","lineage":["https://openalex.org/I119439378"]},{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]},{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]},{"id":"https://openalex.org/I2802934434","display_name":"The Microsoft Research - University of Trento Centre for Computational and Systems Biology","ror":"https://ror.org/04kcgyj43","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I1290206253","https://openalex.org/I193223587","https://openalex.org/I2802934434","https://openalex.org/I4210164937"]},{"id":"https://openalex.org/I4210090317","display_name":"The Barbara Ann Karmanos Cancer Institute","ror":"https://ror.org/00ee40h97","country_code":"US","type":"facility","lineage":["https://openalex.org/I2800590384","https://openalex.org/I4210090317"]}],"countries":["IT","US"],"is_corresponding":false,"raw_author_name":"Jiusheng Wu","raw_affiliation_strings":["1 Barbara Ann Karmanos Cancer Institute and 2 Department of Oncology, Wayne State University, Detroit, MI 48201, USA, 3 Department of Computer Science, University of Verona, 37134 Verona, Italy, 4 The Microsoft Research\u2013University of Trento Centre for Computational and Systems Biology, 38068 Rovereto, Italy, 5 Department of Computer Science, Wayne State University and 6 Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Barbara Ann Karmanos Cancer Institute and 2 Department of Oncology, Wayne State University, Detroit, MI 48201, USA, 3 Department of Computer Science, University of Verona, 37134 Verona, Italy, 4 The Microsoft Research\u2013University of Trento Centre for Computational and Systems Biology, 38068 Rovereto, Italy, 5 Department of Computer Science, Wayne State University and 6 Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA","institution_ids":["https://openalex.org/I2802934434","https://openalex.org/I193223587","https://openalex.org/I4210090317","https://openalex.org/I119439378","https://openalex.org/I185443292"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081482723","display_name":"Ad\u00e9le Kruger","orcid":null},"institutions":[{"id":"https://openalex.org/I119439378","display_name":"University of Verona","ror":"https://ror.org/039bp8j42","country_code":"IT","type":"education","lineage":["https://openalex.org/I119439378"]},{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]},{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]},{"id":"https://openalex.org/I2802934434","display_name":"The Microsoft Research - University of Trento Centre for Computational and Systems Biology","ror":"https://ror.org/04kcgyj43","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I1290206253","https://openalex.org/I193223587","https://openalex.org/I2802934434","https://openalex.org/I4210164937"]},{"id":"https://openalex.org/I4210090317","display_name":"The Barbara Ann Karmanos Cancer Institute","ror":"https://ror.org/00ee40h97","country_code":"US","type":"facility","lineage":["https://openalex.org/I2800590384","https://openalex.org/I4210090317"]}],"countries":["IT","US"],"is_corresponding":false,"raw_author_name":"Ad\u00e9le Kruger","raw_affiliation_strings":["1 Barbara Ann Karmanos Cancer Institute and 2 Department of Oncology, Wayne State University, Detroit, MI 48201, USA, 3 Department of Computer Science, University of Verona, 37134 Verona, Italy, 4 The Microsoft Research\u2013University of Trento Centre for Computational and Systems Biology, 38068 Rovereto, Italy, 5 Department of Computer Science, Wayne State University and 6 Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Barbara Ann Karmanos Cancer Institute and 2 Department of Oncology, Wayne State University, Detroit, MI 48201, USA, 3 Department of Computer Science, University of Verona, 37134 Verona, Italy, 4 The Microsoft Research\u2013University of Trento Centre for Computational and Systems Biology, 38068 Rovereto, Italy, 5 Department of Computer Science, Wayne State University and 6 Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA","institution_ids":["https://openalex.org/I2802934434","https://openalex.org/I193223587","https://openalex.org/I4210090317","https://openalex.org/I119439378","https://openalex.org/I185443292"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025588068","display_name":"Vincenzo Manca","orcid":"https://orcid.org/0000-0002-1304-0277"},"institutions":[{"id":"https://openalex.org/I119439378","display_name":"University of Verona","ror":"https://ror.org/039bp8j42","country_code":"IT","type":"education","lineage":["https://openalex.org/I119439378"]},{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]},{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]},{"id":"https://openalex.org/I2802934434","display_name":"The Microsoft Research - University of Trento Centre for Computational and Systems Biology","ror":"https://ror.org/04kcgyj43","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I1290206253","https://openalex.org/I193223587","https://openalex.org/I2802934434","https://openalex.org/I4210164937"]},{"id":"https://openalex.org/I4210090317","display_name":"The Barbara Ann Karmanos Cancer Institute","ror":"https://ror.org/00ee40h97","country_code":"US","type":"facility","lineage":["https://openalex.org/I2800590384","https://openalex.org/I4210090317"]}],"countries":["IT","US"],"is_corresponding":false,"raw_author_name":"Vincenzo Manca","raw_affiliation_strings":["1 Barbara Ann Karmanos Cancer Institute and 2 Department of Oncology, Wayne State University, Detroit, MI 48201, USA, 3 Department of Computer Science, University of Verona, 37134 Verona, Italy, 4 The Microsoft Research\u2013University of Trento Centre for Computational and Systems Biology, 38068 Rovereto, Italy, 5 Department of Computer Science, Wayne State University and 6 Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Barbara Ann Karmanos Cancer Institute and 2 Department of Oncology, Wayne State University, Detroit, MI 48201, USA, 3 Department of Computer Science, University of Verona, 37134 Verona, Italy, 4 The Microsoft Research\u2013University of Trento Centre for Computational and Systems Biology, 38068 Rovereto, Italy, 5 Department of Computer Science, Wayne State University and 6 Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA","institution_ids":["https://openalex.org/I2802934434","https://openalex.org/I193223587","https://openalex.org/I4210090317","https://openalex.org/I119439378","https://openalex.org/I185443292"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006190733","display_name":"Sorin Dr\u0103ghici","orcid":"https://orcid.org/0000-0002-0786-8377"},"institutions":[{"id":"https://openalex.org/I119439378","display_name":"University of Verona","ror":"https://ror.org/039bp8j42","country_code":"IT","type":"education","lineage":["https://openalex.org/I119439378"]},{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]},{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]},{"id":"https://openalex.org/I2802934434","display_name":"The Microsoft Research - University of Trento Centre for Computational and Systems Biology","ror":"https://ror.org/04kcgyj43","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I1290206253","https://openalex.org/I193223587","https://openalex.org/I2802934434","https://openalex.org/I4210164937"]},{"id":"https://openalex.org/I4210090317","display_name":"The Barbara Ann Karmanos Cancer Institute","ror":"https://ror.org/00ee40h97","country_code":"US","type":"facility","lineage":["https://openalex.org/I2800590384","https://openalex.org/I4210090317"]}],"countries":["IT","US"],"is_corresponding":false,"raw_author_name":"Sorin Dr\u0103ghici","raw_affiliation_strings":["1 Barbara Ann Karmanos Cancer Institute and 2 Department of Oncology, Wayne State University, Detroit, MI 48201, USA, 3 Department of Computer Science, University of Verona, 37134 Verona, Italy, 4 The Microsoft Research\u2013University of Trento Centre for Computational and Systems Biology, 38068 Rovereto, Italy, 5 Department of Computer Science, Wayne State University and 6 Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Barbara Ann Karmanos Cancer Institute and 2 Department of Oncology, Wayne State University, Detroit, MI 48201, USA, 3 Department of Computer Science, University of Verona, 37134 Verona, Italy, 4 The Microsoft Research\u2013University of Trento Centre for Computational and Systems Biology, 38068 Rovereto, Italy, 5 Department of Computer Science, Wayne State University and 6 Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA","institution_ids":["https://openalex.org/I2802934434","https://openalex.org/I193223587","https://openalex.org/I4210090317","https://openalex.org/I119439378","https://openalex.org/I185443292"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5033688288"],"corresponding_institution_ids":["https://openalex.org/I119439378","https://openalex.org/I185443292","https://openalex.org/I193223587","https://openalex.org/I2802934434","https://openalex.org/I4210090317"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.5652,"has_fulltext":false,"cited_by_count":33,"citation_normalized_percentile":{"value":0.82729291,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"30","issue":"21","first_page":"3036","last_page":"3043"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.46560001373291016,"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":0.46560001373291016,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.09510000050067902,"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":0.08560000360012054,"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/oncogene","display_name":"Oncogene","score":0.6803935170173645},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5832661390304565},{"id":"https://openalex.org/keywords/gene-knockdown","display_name":"Gene knockdown","score":0.5568317174911499},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.4599965512752533},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.458479642868042},{"id":"https://openalex.org/keywords/kras","display_name":"KRAS","score":0.44032636284828186},{"id":"https://openalex.org/keywords/cancer-research","display_name":"Cancer research","score":0.4149152934551239},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3939973711967468},{"id":"https://openalex.org/keywords/cell-cycle","display_name":"Cell cycle","score":0.24223467707633972},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23751497268676758},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.07917609810829163}],"concepts":[{"id":"https://openalex.org/C2781018059","wikidata":"https://www.wikidata.org/wiki/Q207609","display_name":"Oncogene","level":4,"score":0.6803935170173645},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5832661390304565},{"id":"https://openalex.org/C173396325","wikidata":"https://www.wikidata.org/wiki/Q1501275","display_name":"Gene knockdown","level":3,"score":0.5568317174911499},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.4599965512752533},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.458479642868042},{"id":"https://openalex.org/C2781187634","wikidata":"https://www.wikidata.org/wiki/Q20969980","display_name":"KRAS","level":4,"score":0.44032636284828186},{"id":"https://openalex.org/C502942594","wikidata":"https://www.wikidata.org/wiki/Q3421914","display_name":"Cancer research","level":1,"score":0.4149152934551239},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3939973711967468},{"id":"https://openalex.org/C29537977","wikidata":"https://www.wikidata.org/wiki/Q188941","display_name":"Cell cycle","level":3,"score":0.24223467707633972},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23751497268676758},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.07917609810829163}],"mesh":[{"descriptor_ui":"D000090063","descriptor_name":"Proto-Oncogene Mas","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000090063","descriptor_name":"Proto-Oncogene Mas","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000090063","descriptor_name":"Proto-Oncogene Mas","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D002448","descriptor_name":"Cell Adhesion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002448","descriptor_name":"Cell Adhesion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002448","descriptor_name":"Cell Adhesion","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":"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":"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":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015854","descriptor_name":"Up-Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015854","descriptor_name":"Up-Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015854","descriptor_name":"Up-Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018734","descriptor_name":"Genes, erbB-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018734","descriptor_name":"Genes, erbB-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018734","descriptor_name":"Genes, erbB-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D021982","descriptor_name":"Cell-Matrix Junctions","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D021982","descriptor_name":"Cell-Matrix Junctions","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D021982","descriptor_name":"Cell-Matrix Junctions","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D050703","descriptor_name":"E2F2 Transcription Factor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D050703","descriptor_name":"E2F2 Transcription Factor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D050703","descriptor_name":"E2F2 Transcription Factor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D050703","descriptor_name":"E2F2 Transcription Factor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D050703","descriptor_name":"E2F2 Transcription Factor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D050703","descriptor_name":"E2F2 Transcription Factor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D050703","descriptor_name":"E2F2 Transcription Factor","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D050703","descriptor_name":"E2F2 Transcription Factor","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D050703","descriptor_name":"E2F2 Transcription Factor","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D055785","descriptor_name":"Gene Knockdown Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055785","descriptor_name":"Gene Knockdown Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055785","descriptor_name":"Gene Knockdown Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btu400","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu400","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/21/3036/48930801/bioinformatics_30_21_3036.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:25028721","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25028721","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},{"id":"pmh:oai:europepmc.org:3598357","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4201152","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:iris.unitn.it:11572/326060","is_oa":false,"landing_page_url":"http://hdl.handle.net/11572/326060","pdf_url":null,"source":{"id":"https://openalex.org/S4377196320","display_name":"Iris (University of Trento)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I193223587","host_organization_name":"University of Trento","host_organization_lineage":["https://openalex.org/I193223587"],"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":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btu400","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu400","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/21/3036/48930801/bioinformatics_30_21_3036.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":[{"score":0.6700000166893005,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G2279343672","display_name":null,"funder_award_id":"42GM087013","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2720309917","display_name":null,"funder_award_id":"R01 CA140314","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G3507318458","display_name":null,"funder_award_id":"R01 DK089167","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G5509426373","display_name":null,"funder_award_id":"P30 CA022453","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G6529076551","display_name":null,"funder_award_id":"P30CA022453","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337357","display_name":"National Institute of Diabetes and Digestive and Kidney Diseases","ror":"https://ror.org/00adh9b73"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2087754565.pdf"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W198928030","https://openalex.org/W1975387345","https://openalex.org/W1976020443","https://openalex.org/W1976203623","https://openalex.org/W1977918192","https://openalex.org/W1984252723","https://openalex.org/W1992053143","https://openalex.org/W1992858142","https://openalex.org/W2017187984","https://openalex.org/W2018716739","https://openalex.org/W2022397091","https://openalex.org/W2026403124","https://openalex.org/W2029485495","https://openalex.org/W2029742759","https://openalex.org/W2033672070","https://openalex.org/W2044527070","https://openalex.org/W2067815025","https://openalex.org/W2075614349","https://openalex.org/W2077813812","https://openalex.org/W2081755394","https://openalex.org/W2084054884","https://openalex.org/W2089448177","https://openalex.org/W2106195342","https://openalex.org/W2110326852","https://openalex.org/W2115108153","https://openalex.org/W2116934284","https://openalex.org/W2117250543","https://openalex.org/W2117692326","https://openalex.org/W2117954572","https://openalex.org/W2123326378","https://openalex.org/W2126382397","https://openalex.org/W2133609791","https://openalex.org/W2134099461","https://openalex.org/W2136020634","https://openalex.org/W2137476312","https://openalex.org/W2141452279","https://openalex.org/W2146078095","https://openalex.org/W2150926065","https://openalex.org/W2154972152","https://openalex.org/W2156246479","https://openalex.org/W2166898290","https://openalex.org/W2172161723","https://openalex.org/W2412476799","https://openalex.org/W4254445705","https://openalex.org/W6679724817"],"related_works":["https://openalex.org/W3030972949","https://openalex.org/W4306404900","https://openalex.org/W4229832877","https://openalex.org/W3111812619","https://openalex.org/W4248366929","https://openalex.org/W2590035663","https://openalex.org/W2914997899","https://openalex.org/W4229670017","https://openalex.org/W4226309907","https://openalex.org/W2603467863"],"abstract_inverted_index":{"MOTIVATION:":[0],"Oncogenes":[1],"are":[2],"known":[3],"drivers":[4],"of":[5,10,47,66,83,113,126,150,171,226],"cancer":[6,56,130,208],"phenotypes":[7],"and":[8,16,23,98,133,219],"targets":[9],"molecular":[11],"therapies;":[12],"however,":[13],"the":[14,48,95,103,109,114,124,202,233],"complex":[15],"diverse":[17],"signaling":[18,163,188],"mechanisms":[19,45],"regulated":[20],"by":[21],"oncogenes":[22,218],"potential":[24],"routes":[25],"to":[26,31,42,75,108,184,196,200,215],"targeted":[27,119],"therapy":[28],"resistance":[29],"remain":[30],"be":[32,182],"fully":[33],"understood.":[34],"To":[35],"this":[36,146],"end,":[37],"we":[38,122],"present":[39],"an":[40],"approach":[41],"infer":[43],"regulatory":[44,79,90],"downstream":[46,187],"HER2":[49,104,159,203],"driver":[50],"oncogene":[51,204],"in":[52,94,145,157,231],"SUM-225":[53],"metastatic":[54],"breast":[55],"cells":[57],"from":[58],"dynamic":[59],"gene":[60,120,161,173],"expression":[61,112,174],"patterns":[62],"using":[63],"a":[64,70,99,153,158,206],"succession":[65],"analytical":[67],"techniques,":[68],"including":[69],"novel":[71,100],"MP":[72],"grammars":[73],"method":[74,88,193],"mathematically":[76],"model":[77,220],"putative":[78],"interactions":[80,91],"among":[81],"sets":[82],"clustered":[84],"genes.":[85],"RESULTS:":[86],"Our":[87],"highlighted":[89],"previously":[92],"identified":[93],"cell":[96,209],"line":[97],"finding":[101],"that":[102,129,148],"oncogene,":[105],"as":[106,199],"opposed":[107],"proto-oncogene,":[110],"upregulates":[111],"E2F2":[115,139,151],"transcription":[116],"factor.":[117],"By":[118],"knockdown":[121],"show":[123],"significance":[125],"this,":[127],"demonstrating":[128],"cell-matrix":[131],"adhesion":[132],"outgrowth":[134],"were":[135,141],"markedly":[136],"inhibited":[137],"when":[138],"levels":[140],"reduced.":[142],"Thus,":[143],"validating":[144],"context":[147],"upregulation":[149],"represents":[152],"key":[154],"intermediate":[155],"event":[156],"oncogene-directed":[160],"expression-based":[162],"circuit.":[164],"This":[165],"work":[166],"demonstrates":[167],"how":[168,201],"predictive":[169],"modeling":[170],"longitudinal":[172],"data":[175],"combined":[176],"with":[177],"multiple":[178],"systems-level":[179],"analyses":[180],"can":[181],"used":[183],"accurately":[185],"predict":[186],"pathways.":[189],"Here,":[190],"our":[191],"integrated":[192],"was":[194],"applied":[195],"reveal":[197],"insights":[198],"drives":[205],"specific":[207],"phenotype,":[210],"but":[211],"it":[212],"is":[213,229,238],"adaptable":[214],"investigate":[216],"other":[217],"systems.":[221],"AVAILABILITY":[222],"AND":[223],"IMPLEMENTATION:":[224],"Accessibility":[225],"various":[227],"tools":[228],"listed":[230],"methods;":[232],"Log-Gain":[234],"Stoichiometric":[235],"Stepwise":[236],"algorithm":[237],"accessible":[239],"at":[240],"http://www.cbmc.it/software/Software.php.":[241]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":5},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":4},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":3}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}