Mondrian, the Genome Data Mapper Software: Retrieving Pathway Data

Introduction

The Mondrian Software can be used in conjunction with pathway data retrieved from Pathway Commons. Pathway Commons is a convenient, single point of access for browsing and searching freely available pathway and interaction data sets. It currently provides access to multiple data sources, including: Reactome, the Human Protein Reference Database (HPRD), the MSKCC Cancer Cell Map, HumanCyc, and the Nature/NCI Pathway Interaction Database (PID).

This page provides a tutorial in retrieving interaction data from Pathway Commons and mapping genomic profiling data onto the retrieved interaction network. By example, we show how to retrieve a network of protein-protein interactions for BRCA1 from HPRD.

Getting Started

To get started, click the webstart button on the Getting Started page.

Retrieving Pathway Data: BRCA1 Network from HPRD

To search Pathway Commons directly from within Cytoscape:

  • Select: File → Import → Network from web services...
  • From the pull-down menu, select the Pathway Commons Web Service Client.

Importing networks via the Cytoscape web services framework

Then, follow the three steps outlined below:

Three-step process for searching Pathway Commons

  • Step 1: Enter your search term and organism filter; for example: BRCA1 [Human].
  • Step 2: Select the protein or small molecule of interest. Full details regarding each molecule is shown in the bottom left panel. For example, select the first hit: "Breast cancer type 1 susceptibility protein".
  • Step 3: Download a specific pathway or interaction network.

In Step 3, you can simply double-click on a pathway of interest, or click on the "Interaction Networks" tab. This tab enables you to filter interactions by data source and/or interaction type.

For our tutorial, restrict your network to interactions derived from HPRD only, and click the "Retrieve Interactions" button.

Interaction Filters

You should now see a network similar to one below:

BRCA1 Network from HPRD

Visualizing Genomic Profile Data

If you haven't already done so, download the sample mondrian-sample-data.zip file. This archive contains several sample data files including: copy_number_pc.gbm. This file contains "dummy" copy number data specifically tailored to the BRCA1 network from HPRD.

To load it, follow these steps:

  • In the right hand panel, under "Load Data File", click the "Browse" button.
  • Navigate to: copy_number_pc.gbm.

    The plugin will automatically load the copy number data and overlay it onto the BRCA1 network:

    BRCA1 Network from HPRD, w/ sample copy number data

    Additional Information