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Horizontal Axis

Genetic Profile Clinical Attribute

Vertical Axis

Genetic Profile Clinical Attribute

Utilities



Download

    Download a copy number segment file for the selected samples

    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).

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    Currently there is no selected node/edge. Please, select a node/edge 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:

    seed node

    Linker nodes are represented with a thin border:

    linker node

    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:

    altered node

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

    not altered node

    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:

    • Controls-state-change-of: First protein controls a reaction that changes the state of the second protein.
    • Controls-transport-of: First protein controls a reaction that changes the cellular location of the second protein.
    • Controls-phosphorylation-of: First protein controls a reaction that changes the phosphorylation status of the second protein.
    • Controls-expression-of: First protein controls a conversion or a template reaction that changes expression of the second protein.
    • Catalysis-precedes: First protein controls a reaction whose output molecule is input to another reaction controled by the second protein.
    • In-complex-with: Proteins are members of the same complex.
    • Interacts-with: Proteins are participants of the same MolecularInteraction.
    • Neighbor-of: Proteins are participants or controlers of the same interaction.
    • Consumption-controled-by: The small molecule is consumed by a reaction that is controled by a protein
    • Controls-production-of: The protein controls a reaction of which the small molecule is an output.
    • Controls-transport-of-chemical: The protein controls a reaction that changes cellular location of the small molecule.
    • Chemical-affects: A small molecule has an effect on the protein state.
    • Reacts-with: Small molecules are input to a biochemical reaction.
    • Used-to-produce: A reaction consumes a small molecule to produce another small molecule.

    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.

    Detailed Process Level (SBGN) View

    When you are interested in process level details of an interaction, you may either right-click on that interaction or click the "Detailed Process (SBGN)" button in the Details tab while inspecting the interaction. This will pop up a detailed process view in SBGN Process Description Language. The shown network corresponds to all paths between source and target genes of that interaction as returned by Pathway Commons' web service. SBGN view allows users to modify the process level view in many ways, including changing its layout and topology through complexity management techniques such as hiding or collapsing. You may also store the current network as a static image or in SBGN-ML format. For further help, please refer to the Help menu of this view.

    Technology

    Network visualization is powered by Cytoscape.js and SBGNViz.js.

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

        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)