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Plot Parameters

Plot Type
Data Type
Search case(s)

Plot Parameters

x Axis
y Axis
Plot Type

show mutation data
Search case(s)

Plot Parameters

x Axis

Plot Type


y Axis

Plot Type


show mutation data
Search case(s)

Use the Integrative Genomics Viewer (IGV) to explore and visualize copy number data.

The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated datasets. It supports a wide variety of data types including sequence alignments, gene expression, copy number amplifications and deletions, mutations, and genomic annotations

Clicking the launch button below will:

  • start IGV via Java Web Start.
  • load copy number data (segmented) for your selected cancer study; and
  • automatically highlight your query genes.

Once you click the launch button, you may need to select Open with Java™ Web Start and click OK. If the system displays messages about trusting the application, confirm that you trust the application. Web Start will then download and start IGV. This process can take a few minutes.

For information regarding IGV, please see:

IGV is developed at the Broad Institute of MIT and Harvard.

Overall Survival Kaplan-Meier Estimate

Disease Free Survival Kaplan-Meier Estimate

The query contains gene pair with mutually exclusive alterations ( significant), and gene pair with co-occurrent alterations ( significant).

RPPA ID Gene Alteration Type Target Ave. Abundance p-value data Plot
Protein Residue Unaltered Altered Abs. Diff.
RPPA ID Gene Alteration Type Protein Residue Unaltered Altered Abs. Diff. p-value data Plot

Currently there is no selected node. Please, select a node to see details.

About the Network View

The network view shows the genes you entered (referred to as seed nodes) in the context of biological interactions derived from public pathway databases. Each gene in the network view is color-coded with multi-dimensional genomic data derived from the cancer study you have selected.

Source of Pathway Data

Pathway and interaction data is from HPRD, Reactome, NCI-Nature Pathway Interaction Database, and the MSKCC Cancer Call Map, as derived from Pathway Commons.

Source of Drug Data

Drug data is derived from PiHelper.

Seed Nodes vs. Linker Nodes

A seed node represents a gene that you have entered. A linker node represents a gene that connects to one or more of your seed genes.

Seed nodes are represented with a thick border:

Linker nodes are represented with a thin border:

Visualization Summary of Genomic Data

The exact genomic data displayed on the network depends on the genomic profiles you have selected. For example, you can chose to include mutation, copy number and mRNA expression profiles.

By default, each node is color coded along a white to red color gradient, indicating the total frequency of alteration across the selected case set (deeper red indicates higher frequency of alteration).

For example, EGFR is frequently altered in glibolastoma:

By contrast, STAT3 is not altered at all in glioblastoma:

If you mouse over a node, or select "View::Always Show Profile Data", you will see additional details regarding the genomic alterations affecting the gene. This breaks down into mutation, copy number and mRNA expression changes affecting the gene across all cases.

Click here to see the gene legend.

Drug Information

Drugs targeting genes in the network are hidden by default. If you would like to see them, select "Show All Drugs" or, "Show FDA Approved Drugs" or "Show Cancer Drugs" from the drop-down box under the "Genes & Drugs" tab.

Number of Genes Targeted shown in the drug inspector refers to the total number of genes (regardless of whether or not any such gene is in the current network of interest) targeted by this drug.

Click here to see the drug legend.

Understanding Interaction and Edge Types

The interaction types are derived from the BioPAX to binary interaction mapping rules defined within Pathway Commons. They are encoded by different edge colors and can be seleted on the "Interactions" tab to the right of the network. In addition, if selected, drug-gene interactions are shown as edges in the network. The interaction types are:

  • In same component: Two entities belong to the same molecular complex.
  • Reacts with: The entities participate in a conversion as substrates or products.
  • State change: The first entity controls a reaction that changes the state of the second entity, e.g. by phosphorylation or other posttranslational modification, or by a change in subcellular location.
  • Targeted by drug: The source node (drug) targets the destination node (gene).
  • Other

Click here to see the color codes.

Complete details are available on the Pathway Commons web site.

By default, redundant interactions are merged are merged into a single edge. To see all interactions, uncheck "Merge Interactions" in the "View" menu.

Complexity Management

There are a number of options to better deal with complex networks:

  • Hide Selected/Crop: Selected nodes can be hidden using "Topology::Hide Selected". Alternatively, you can select the set of nodes that you would like to view and hide the rest of the network using "Topology::Show Only Selected". Alternatively, buttons are available for these operations on the "Genes & Drugs" tab.
  • Filter by Interaction Type or Source: If you are interested in only certain types of interactions or interactions from selected sources, you may use the filtering mechanisms on the "Interactions" tab by checking the corresponding check boxes and clicking "Update".
  • Filter by Total Alteration: Networks can be filtered based on alteration frequencies of individual nodes using a slider under the "Genes & Drugs" tab. You can specify a threshold of total alteration frequency - nodes with alteration frequencies below the threshold will be filtered out, but seed nodes are always kept in the network.
  • Filter Drugs by FDA Approval: Networks can be filtered based on whether drugs associated with genes of this network are FDA approved or not.
  • Filter Cancer Drugs: Networks can be filtered based on whether drugs associated with genes of this network are cancer drugs or not. Notice that all cancer drugs are FDA approved.

All filtering can be undone by clicking "Unhide" in the "Topology" menu.

When the flag "Remove Disconnected Nodes on Hide" in the "Topology" menu is checked, an automatic layout is performed upon all changes to the network topology.

Performing Layout

A Force-Directed layout algorithm is used by default. However, you may choose to re-perform the layout with different parameters (by selecting "Layout::Layout Properties ...") or after the topology of the network changes with operations such as hiding or filtering. If you would like the layout to be performed automatically upon such operations simply check "Layout::Auto Layout on Changes".

Exporting Networks

You can export a network to a PNG file. To do so, select "File::Save as Image (PNG)". We do not currently support export to PDF.


Network visualization is powered by Cytoscape Web.

This table lists the genes with the highest expression correlation with the query genes. Click on a row to see the corresponding correlation plot.

    Contents below can be copied and pasted into Excel

    Frequency of Gene Alteration:

    Type of Genetic alterations across all cases: (Alterations are summarized as MUT, Gain, HetLoss, etc.)

    Cases affected: (Only cases with an alteration are included)

    Case matrix: (1= Case harbors alteration in one of the input genes)