Overview of our approach.

(A) Collect gene expression data obtained from microarray and RNA-Seq platforms for paired samples, and calculate the log2 ratios between tumor samples and the average of normal samples. (B) Compare gene expression data of the microarray and RNA-Seq datasets. (C) Construct FGMD modules using the microarray and RNA-Seq gene expression data. Further details are provided in Fig 2. (D) Compare the modules constructed by FGMD to those constructed by other methods. PCC, Pearson correlation coefficient; TF, transcription factor.