查看文章

Complex diseases such as cancers usually result from accumulated disturbance of pathways instead of the disruptions of one or a few major genes. As opposed to single-platform analyses, it is likely that integrating diverse molecular regulatory elements and their interactions can lead to more insights on pathway-level disturbances of biological systems and their potential consequences in disease development and progression. To explore the benefit of pathway-based analysis, we focus on multi-platform genomics, epigenomics, and transcriptomics (-omics, for short) from 11 cancer types collected by The Cancer Genome Atlas project. Specifically, we use a well-studied oncogenic pathway, the BRAF pathway, to investigate the relevant copy number variants (CNVs), methylations, and gene expressions, and quantify their effects on discovering tumor-specific aberrations across multiple tumor lineages. We …