A Novel Strategy to Identify Prognosis Relevant Gene Sets in Cancers

Step 1: Single-gene survival analysis

#Check code/Step1.survival.R

Step 2: GSEA based on single gene survival analysis results

#Check code/Step2.fgsea.R

Step 3: Gene set survival analysis based on CGES

#Check code/Step3.gsea_flow2_CGES.R

Step 4: Crosstalk analysis using DCGL & CSPN

#Check code/Step4.crosstalk.R #Unzip cspn
cd cspn
#Deploy three aspects of files in cspn
##background gene-gene network @ cspn/reference/PPI_network/
##Gene set definition identified with EntrezGeneIDs @ cspn/reference/original_gene_sets/
##Concerned pathway list @ cspn/reference/concerned_pathway_list/
#$nw is project keyword
#$nwFile designates file name for background network (say, DCLi.all.txt or DCLd.all.txt)
perl ./cspn.pl $nwFile ./reference/concerned_pathway_list/sigPWs.27.lst ./result/$nw.ctalk ./result/$nw.clink