BioMonth - CSC supercomputing and data management for bioscientists

Proteome Network analysis using containerised webapplication

Phosphoproteomic experiments typically identify sites within a protein that are differentially phosphorylated between two or more cell states. However, the interpretation of these data is hampered by the lack of methods that can translate site-specific information into global maps of active proteins and signaling networks, especially as the phosphoproteome is often undersampled. Here, we use PHOTON, a method for interpreting phosphorylation data within their signaling context, as captured by protein-protein interaction networks, to identify active proteins and pathways and pinpoint functional phosphosites.

Learning Objectives

• Start a containerised webb app for analysing phosphoproteomics dataset
• Perform analysis using a test dataset

Basic usage of docker

• Explore more about photon here
• Pull docker image from dockerhub

docker pull jdrudolph/photon:dev

• Launch web-application as below:

 docker run -d -p 5000:5000 jdrudolph/photon:dev

Now you can access PHOTON from your browser at: http://localhost:5000

1. Construct a phosphoproteomics signaling networks and identify the positively regulated neighbours of EGFR protein?
2. Explain your experience of using a containerised web-application like Photon. How easy or hard it would be if you were to install all dependencies of photon to get it work?

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