Fig. 1

Overview of the elastic-net analysis pipeline. Genomic data was downloaded from Broad Firehose and analyzed in three separate groups. Gene-oriented analysis relied on samples with data for mutations, copy number alterations, RNA-Seq, and methylation. The genes, miRs, and proteins with >3 % missing values were excluded; otherwise missing values were imputed using the median sample value. MicroRNA (miR) and proteins (reverse phase protein array, RPPA) were analyzed separately given the smaller number of genes and targets that came from these analysis platforms. Integrated genomic/proteomic matrices were associated with clinical outcomes by elastic-net across all 25 type of cancer. SNP single nucleotide polymorphism