Your browser doesn't support javascript.
loading
Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network.
Dhingra, Priyanka; Martinez-Fundichely, Alexander; Berger, Adeline; Huang, Franklin W; Forbes, Andre Neil; Liu, Eric Minwei; Liu, Deli; Sboner, Andrea; Tamayo, Pablo; Rickman, David S; Rubin, Mark A; Khurana, Ekta.
Afiliação
  • Dhingra P; Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, 10065, USA.
  • Martinez-Fundichely A; Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, 10021, USA.
  • Berger A; Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, 10065, USA.
  • Huang FW; Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, 10021, USA.
  • Forbes AN; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, 10065, USA.
  • Liu EM; Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.
  • Liu D; Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA.
  • Sboner A; Cancer Program, The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, 02142, USA.
  • Tamayo P; Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, 10065, USA.
  • Rickman DS; Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, 10021, USA.
  • Rubin MA; Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, 10065, USA.
  • Khurana E; Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, 10021, USA.
Genome Biol ; 18(1): 141, 2017 07 27.
Article em En | MEDLINE | ID: mdl-28750683
ABSTRACT
We report a novel computational method, RegNetDriver, to identify tumorigenic drivers using the combined effects of coding and non-coding single nucleotide variants, structural variants, and DNA methylation changes in the DNase I hypersensitivity based regulatory network. Integration of multi-omics data from 521 prostate tumor samples indicated a stronger regulatory impact of structural variants, as they affect more transcription factor hubs in the tissue-specific network. Moreover, crosstalk between transcription factor hub expression modulated by structural variants and methylation levels likely leads to the differential expression of target genes. We report known prostate tumor regulatory drivers and nominate novel transcription factors (ERF, CREB3L1, and POU2F2), which are supported by functional validation.
Assuntos
Palavras-chave
Texto completo
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Neoplasias da Próstata / Proteínas Repressoras / Algoritmos / Regulação Neoplásica da Expressão Gênica / Proteína de Ligação ao Elemento de Resposta ao AMP Cíclico / Fator 2 de Transcrição de Octâmero / Carcinogênese / Proteínas do Tecido Nervoso Tipo de estudo: Diagnostic_studies / Prognostic_studies Limite: Humans / Male Idioma: En Revista: Genome Biol Assunto da revista: BIOLOGIA MOLECULAR / GENETICA Ano de publicação: 2017 Tipo de documento: Article País de afiliação: Estados Unidos
Texto completo
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Neoplasias da Próstata / Proteínas Repressoras / Algoritmos / Regulação Neoplásica da Expressão Gênica / Proteína de Ligação ao Elemento de Resposta ao AMP Cíclico / Fator 2 de Transcrição de Octâmero / Carcinogênese / Proteínas do Tecido Nervoso Tipo de estudo: Diagnostic_studies / Prognostic_studies Limite: Humans / Male Idioma: En Revista: Genome Biol Assunto da revista: BIOLOGIA MOLECULAR / GENETICA Ano de publicação: 2017 Tipo de documento: Article País de afiliação: Estados Unidos