Graphical identification of cancer-associated gene sub-networks based on small proteomics data sets
Author
UR04CNSTN01 - Bio-computing Unit, Life Science Department, National Center for Nuclear Sciences and Technologies (CNSTN). Sidi Thabet BioTechPole, 2020, Ariana, Tunisia. Email: kmezhoud(at)bioinformatics.tn
Description
These supplemental files allow reader to follow the Methodology described in the paper accepted in OMICS: A Journal of integrative Biology.
Figures
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 files
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. |