= Graphical identification of cancer-associated  gene sub-networks based on small proteomics data sets =
== Author ==
||[[http://bioinformatics.tn/|Karim Mezhoud]]||
UR04CNSTN01 - Bio-computing Unit, Life Science Department, National Center for Nuclear Sciences and Technologies ([[http://www.cnstn.rnrt.tn/| CNSTN]]). [[http://www.biotechpole.rnu.tn/en/default.aspx|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  [[http://www.liebertpub.com/OMI|OMICS: A Journal of integrative Biology]].

== Figures ==
||[[https://wiki.ubuntu.com/kmezhoud/supplemental_material?action=AttachFile&do=get&target=Figure+1.eps|Figure 1.eps]]: Legend is available in main text.||
||[[https://wiki.ubuntu.com/kmezhoud/supplemental_material?action=AttachFile&do=get&target=Figure+2.eps|Figure 2.eps]]: Legend is available in main text.||
||[[https://wiki.ubuntu.com/kmezhoud/supplemental_material?action=AttachFile&do=get&target=Figure+3.eps|Figure 3.eps]]: Legend is available in main text.||

== Supplemental files ==
||[[https://wiki.ubuntu.com/kmezhoud/supplemental_material?action=AttachFile&do=get&target=Supplemental_Tutorial.pdf|Supplemental_Tutorial.pdf]]: This tutorial describes the main steps used to construct an enriched network from a list of genes with their expression values.||
||[[https://wiki.ubuntu.com/kmezhoud/supplemental_material?action=AttachFile&do=get&target=only_modulated_symbol.txt|only_modulated_symbol.txt]]: The list of select genes after proteomics analysis.||
||[[https://wiki.ubuntu.com/kmezhoud/supplemental_material?action=AttachFile&do=get&target=Correlation_Network.txt|Correlation_Network.txt]]: This file connect genes (pp) that have expressions correlation.||
||[[https://wiki.ubuntu.com/kmezhoud/supplemental_material?action=AttachFile&do=get&target=Fold_Change.txt|Fold_change.txt]]: This file attributes genes (nodes) with their fold change.||
||[[https://wiki.ubuntu.com/kmezhoud/supplemental_material?action=AttachFile&do=get&target=FDR.txt|FDR.txt]]: This file attributes genes (nodes) with their False Discovery Rate (FDR).||
||[[https://wiki.ubuntu.com/kmezhoud/supplemental_material?action=AttachFile&do=get&target=Correlation%2BCancers.txt|Correlation+Cancers.txt]]: This file attributes values to interactions (Edges). There is two types of interactions: gene-gene and gene-cancer.||
||[[https://wiki.ubuntu.com/kmezhoud/supplemental_material?action=AttachFile&do=get&target=Cancer_Network.txt|Cancer_Network.txt]]: This file connects genes with cancers which are modulated.||
||[[https://wiki.ubuntu.com/kmezhoud/supplemental_material?action=AttachFile&do=get&target=Cancer_frequency.txt|Cancer_frequency.txt]]: This file attributes Cancers (nodes) with their frequency.||
||[[https://wiki.ubuntu.com/kmezhoud/supplemental_material?action=AttachFile&do=get&target=Edge_Disease.txt|Edge_Disease.txt]]: This file attributes Cancers (nodes) with their frequency.||
||[[https://wiki.ubuntu.com/kmezhoud/supplemental_material?action=AttachFile&do=get&target=network.cys|network.cys]]: This file is the Cytoscape session of this work. It is readable only by Cytoscape software.||
||[[https://wiki.ubuntu.com/kmezhoud/supplemental_material?action=AttachFile&do=get&target=proteinEXP.txt|proteinEXP.txt]]: This is an example of proteomic data that used for this work. It is consist of 3 replicates and two conditions.||
||[[https://wiki.ubuntu.com/kmezhoud/supplemental_material?action=AttachFile&do=get&target=Patient-profile.png|Patient-profile.png]]: The general characteristics of the patients/volunteers are described here.||
||[[https://wiki.ubuntu.com/kmezhoud/supplemental_material?action=AttachFile&do=get&target=only_modulatedEXP.txt|only_modulatedEXP.txt]]: This file was submitted to the [[http://www.cbioportal.org/public-portal/|cBio Cancer genomics portal]] (Figure 2, supplemental Tutorial).||
||[[https://wiki.ubuntu.com/kmezhoud/supplemental_material?action=AttachFile&do=get&target=Supplemental_Table1.pdf|Supplemantal_Table1.pdf]]:  The features of the discussed bioinfomatic tools.||
||[[https://wiki.ubuntu.com/kmezhoud/supplemental_material?action=AttachFile&do=get&target=Supplemental_Table+2.pdf|Supplemental_Table2.pdf]]: Non exhaustive list of important protein from Figure 2.||
||[[http://youtu.be/7E4Q_JyTyWw|Supplemental_Video]]: This video shows all steps with comments.||



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CategoryScience