Three-layered models connecting molecular aberrations and gene expressions. Left: layer 1 models connecting mutations, CNVs, DNA methylations with mRNA and protein expressions of the same genes (g1 in the diagram). Solid black lines indicate transcription and translation. Solid green lines indicate layer 1 associations. Associations with mutations or DNA methylations are inhibitory. Middle: layer 2 models connecting internal segment CNVs and transcription factor expressions with expressions of another gene. Here g1 is a known target of transcription factor TF1. Dashed red lines indicate layer 2 associations. Right: layer 3 models connecting external segment CNVs, mutations and DNA methylations with mRNA expressions of a gene on another chromosomal segement. Dotted blue lines indicate layer 3 associations. Associations with external DNA methylations are inhibitory, whereas associations with external gene mutations can be positive or negative.