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
- 2.1. Import a GBM-altered network
- 2.2. Data-to-Visual mapping
- 2.3. Network clustering
- 2.4. Make a new network from a cluster
- 2.5. Import expression log2FCs in normal vs. tumor
- 2.6. Functional annotation of a cluster
- 2.7. Import expression profiles for 4 GBM subtypes
- 2.8. Save as a image, CSV files, GraphML, and a VLG (Visualized Graph) file