← Revision 7 as of 2008-08-22 21:26:06
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← Revision 8 as of 2008-08-22 23:21:49 →
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* GMPL Plugin | * GPML Plugin |
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In this example, we are going to use human network data sets (''rual.sif'') and expand this network from public databases. |
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=== Required Plugins === * Advanced Network Merge Plugin * 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 all required plugins. 1. 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 1. Select '''''Import > Import Network from Web Service''''' and choose '''''IntAct Web Service Client''''' 1. Use IntAct plugin to import networks related to ''TP53'' |
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=== Procedure === 1. Start Cytoscape. Assume you have already installed required plugins. 1. Import user network. In this example, use RUAL.sif in the example. 1. Use IntAct plugin to import networks related to ''TP53'' 1. 1. |
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
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
- NCBI Entrez Gene - interaction datasets are taken from HPRD, BioGRID, and BIND
- Annotations from public resources
- Biomart
- NCBI Entrez Gene
Procedure
- Start Cytoscape. Assume you have already installed all required plugins.
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
Select Import > Import Network from Web Service and choose IntAct Web Service Client
Use IntAct plugin to import networks related to TP53
Search
Scinario 2: Merge known pathways onto human interactome data set
Data Source