Karim Mezhoud

Figure 1.eps: Legend is available in main text.

Figure 2.eps: Legend is available in main text.

Figure 3.eps: Legend is available in main text.

Supplemental_Tutorial.pdf: This tutorial describes the main steps used to construct an enriched network from a list of genes with their expression values.

only_modulated_symbol.txt: The list of select genes after proteomics analysis.

Correlation_Network.txt: This file connect genes (pp) that have expressions correlation.

Fold_change.txt: This file attributes genes (nodes) with their fold change.

FDR.txt: This file attributes genes (nodes) with their False Discovery Rate (FDR).

Correlation+Cancers.txt: This file attributes values to interactions (Edges). There is two types of interactions: gene-gene and gene-cancer.

Cancer_Network.txt: This file connects genes with cancers which are modulated.

Cancer_frequency.txt: This file attributes Cancers (nodes) with their frequency.

Edge_Disease.txt: This file attributes Cancers (nodes) with their frequency.

network.cys: This file is the Cytoscape session of this work. It is readable only by Cytoscape software.

proteinEXP.txt: This is an example of proteomic data that used for this work. It is consist of 3 replicates and two conditions.

Patient-profile.png: The general characteristics of the patients/volunteers are described here.

only_modulatedEXP.txt: This file was submitted to the cBio Cancer genomics portal (Figure 2, supplemental Tutorial).

Supplemantal_Table1.pdf: The features of the discussed bioinfomatic tools.

Supplemental_Table2.pdf: Non exhaustive list of important protein from Figure 2.

Supplemental_Video: This video shows all steps with comments.