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Introduction

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

Examples

Setup

You need to install following plugins to try this tutorial.

Required

• Advanced Network Merge Plugin

• PathwayCommons web service client

• IntAct web service client

• NCBI Entrez Gene web service client
• GPML Plugin
• Biomart Client plugin

Optional

• Scripting Engine Manager

• RubyScriptingEngine

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.

In this example, we are going to use human network data sets (rual.sif) and expand this network from public databases.

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

Procedure

1. Start Cytoscape. Assume you have already installed all required plugins.

2. Import user network. In this example, use RUAL.sif in the example. Import > Network and select URL. From the plull-down menu, select rual.sif dataset. Then press import

3. Select Import > Import Network from Web Service and choose IntAct Web Service Client

4. 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