Subnetwork analysis on proteomics data

Question

[ahmedakhokhar]

Background: I have proteomics data from seven samples (pvalue/ log-score of fold change), I want to analyze the data by network (interactome) analyses.

Question: I like to create an interactome of all the proteins from the data, and map the proteins to this network that have significant pvalue (compare to control), after that I like to create subnetwork(s); also like to add the pathways enrichments to the subnetwork(s).

Request: please suggest online or standalone tools (or algorithm) that fits my requirements.

Thanks !

Answer 1

[Khader Shameer]

We have done something similar to do what you are looking for to identify essential proteins for downstream analyses of human proteome-nanoparticle interactions, and it's biological significance.

• Proteomics: MS-MS > Protein List > FDR filtering
• Canonical or contextual networks: Proteins to Networks using STRING/GeneMania > Full or pruned network
• Network analyses: Cytoscape for network analyses and visualisation > NetworkAnalyzer > Network parameters. Another option is to run module detection algorithms to detect cliques or graphlets in your network using GraphletCounter, MCODE etc.
• Biological inferences: Use the node-based scores or module-set/subnetworks/cliques to run enrichment analyses for biological inferences

Manuscript on protein-nanoparticle proteomics + network analyses paper here: Understanding protein-nanoparticle interaction: a new gateway to disease therapeutics.

Manuscript discussing application of graphlet/clique analyses using plant stress network here: Network Modules Driving Plant Stress Response, Tolerance and Adaptation: A case study using Abscisic acid Induced Protein-protein Interactome of Arabidopsis thaliana