Introduction

This is a tutorial how to merge multiple networks from multiple data sources by Advanced Network Merge Plugin.

Examples with Real Data Sets

Scinario 1: Merge existing network file and network imported from web service

This is the most common usecase for this plugin. Supporse users have their own data sets (networks) and want to integrate them with other network data sets available from public databases. This plugin can easily handle this problem.

Data Source

• User network (sif, XGMML, etc.)
• Known interaction data sets from public database

  • IntAct

  • NCBI Entrez Gene - interaction datasets are taken from HPRD, BioGRID, and BIND

  • PathwayCommons

• Annotations from public resources
  • Biomart
  • NCBI Entrez Gene

Required Plugins

• PathwayCommons web service client

• IntAct web service client

• NCBI Entrez Gene web service client
• Biomart plugin

Procedure

1. Start Cytoscape. Assume you have already installed required plugins.
2. Import user network. In this example, use RUAL.sif in the example.

3. Use IntAct plugin to import networks related to TP53

Search

Scinario 2: Merge known pathways onto human interactome data set

Data Source

Scinario 3: Merge network based on user-provided ID mapping file