<> = 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. 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 et al. (rual.sif)''''' dataset. Then press Import 1. Select '''''Import > Network from Web Services...''''' 1. For ''Data Source'', select '''''IntAct Web Service Client''''' 1. Type '''''TP53 AND human''''' in the ''Query'' field, then press ''Search'' 1. When you asked to enter network name, type ''TP53 from IntAct'' 1. Select '''''Import > Network from Web Services...''''' 1. For ''Data Source'', select '''''NCBI Entrez Eutilities Web Service Client''''' 1. Type '''''TP53 AND human''''' then press search. 1. Name the network (''TP53 from Entrez'') 1. Apply layouts for each networks 1. Select '''''View > Arrange Network Windows > Tiled'''''. At this point, your workspace looks like the following: {{attachment:merge1.png}} (Under construction) ==== Search ==== == Scinario 2: Merge known pathways onto human interactome data set == === Data Source === == Scinario 3: Merge network based on user-provided ID mapping file ==