ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles

Autor(es)

Silva, Tiago C. ^{[1, 2]} ; Coetzee, Simon G. ^[2] ; Gull, Nicole ^[2] ; Yao, Lijing ^[3] ; Hazelett, Dennis J. ^[2] ; Noushmehr, Houtan ^{[1, 4]} ; Lin, De-Chen ^[5] ; Berman, Benjamin R. ^{[2, 5]}

Afiliação do(s) autor(es)

^[1] Univ Sao Paulo, Ribeirao Preto Med Sch, Dept Genet, Ribeirao Preto - Brazil

^[2] Cedars Sinai Med Ctr, Ctr Bioinformat & Funct Genom, Dept Biomed Sci, Los Angeles, CA 90048 - USA

^[3] Bioinformat Res & Early Dev Roche Sequencing Solu, Belmont, CA - USA

^[4] Henry Ford Hosp, Dept Neurosurg, Detroit, MI 48202 - USA

^[5] Cedars Sinai Med Ctr, Dept Med, Los Angeles, CA 90048 - USA

• Tipo de documento: Artigo Científico
• Fonte: Bioinformatics; v. 35, n. 11, p. 1974-1977, JUN 1 2019.
• Citações Web of Science: 5

Resumo

Motivation: DNA methylation has been used to identify functional changes at transcriptional enhancers and other cis-regulatory modules (CRMs) in tumors and other disease tissues. Our R/Bioconductor package ELMER (Enhancer Linking by Methylation/Expression Relationships) provides a systematic approach that reconstructs altered gene regulatory networks (GRNs) by combining enhancer methylation and gene expression data derived from the same sample set. Results: We present a completely revised version 2 of ELMER that provides numerous new features including an optional web-based interface and a new Supervised Analysis mode to use predefined sample groupings. We show that Supervised mode significantly increases statistical power and identifies additional GRNs and associated Master Regulators, such as SOX11 and KLF5 in Basal-like breast cancer. (AU)

• Processo FAPESP: 16/01389-7 - Ferramenta de bioinformática para integrar e compreender as mudanças epigenômicas e genômicas aberrantes associadas com câncer: métodos, desenvolvimento e análise
• Beneficiário: Tiago Chedraoui Silva
• Modalidade de apoio: Bolsas no Brasil - Doutorado Direto
• Processo FAPESP: 15/07925-5 - Softwares de código aberto contendo ferramentas estatísticas para análise e integração de conjuntos de dados epigenômicos produzidos em alta escala, a fim de decifrar e entender redes reguladoras de câncer
• Beneficiário: Houtan Noushmehr
• Modalidade de apoio: Auxílio à Pesquisa - Jovens Pesquisadores