2. Tutorial

This chapter provides step-by-step tutorials for the Case Study and more.


Input data files to be imported into the MONGKIE in this tutorial were generated by the extractAlteredNet_GBM.R. Refer to Case Study for details about the method. Briefly, starting with somatic mutations, CNAs, and gene expression data sets downloaded from UCSC Cancer Browser, the R script does the following tasks.

  • Calculate expression log2FCs of each gene in normal vs. tumor conditions.
  • Calculate expression means of each gene in 4 GBM subtypes.
  • Extract a sub-network of altered (somatic mutation or CNV) genes in STRING.
  • Calculate expression correlations between each pair of genes in the extracted network.
  • Write vertices, edges, and expression related data files.

You can download the R script and generated input files in supplementary_data.zip.