A Practical Guide to Cancer Systems Biology

6. Proteomic Data Analysis 67

Set parameters and Run (Fig. 4). Figure 4.

SetparametersappliedforGSEA.1.Click“RunGSEA”;2.Selec

t expression file; 3. Select the gene set of interests from

the gene set database; 4. Select the phenotype labels for comparison; 5. Select “false” of collapse dataset to gene symbols; 6. Select“GENE

SYMBOL.chip” for annotation; 7. Select “Signal2Noise” for raw value or “Diff

of

Classes” for logarithm value to generate metric

for ranking genes; 8. Click “Run”; 9. After the program is executed, the status of current jobs will be shown.