x
M+P

Markers + Patients Visualize genetic relationships. Explore patient cohorts.

x

Overview

Markers and Patients (M+P) allows users to explore the relationship between genetic alterations and patients clusters. Users create and explore data in the M+P window. The M+P window is organized into different areas to help focus on different aspects of research, such as specific genes, various patient cohorts, and different plotting mechanisms. Buttons in the control bars show or hide different areas of the application.

M+P
  • Panel Lock: Lock and unlock the panels for a wider screen view.
  • Selected Cohort: Add, edit or delete cohorts. Click the "+" to save, "x" to delete or click the down arrow to select a cohort for edits.
  • Clinical Histogram: Snapshot of clinical information, per cohort. The histogram will adjust with each cohort selection.   Click the down arrow to view other filters. e.g.   Age At Diagnosis, Gender, Race, Ethnicity, Vital, Tumor.
  • Survival Curve: Snapshot of Kaplan Meier survival curves, per cohort. For more in depth analysis push the saved cohorts to the survival tool.
  • Cohorts: All saved cohorts are listed in this area. Each cohort is clickable and will highlight the selections on the main window, as well as adjust any survival curves or clinical histograms that are associated. The last line will always show your current selection, which will also update in the Selected Cohort box at the top of the cohort panel. To learn more visit Oncoscape
  • Cohort Summary: Every cohort includes a summary of available information based on patients and samples.
  • Patient Nodes: Select nodes by holding down the Shift key and selecting either individual or larger node groupings. The variation in node sizing represents the number of mutations a patient or gene carries, e.g. the larger the node the greater the mutation number. Hovering over an individual patient will provide clinical information on the left side of the tool.
  • Edges: Lines that connect the patient and gene nodes. These lines are color-coded and can be toggled on/off in the Edge Visibility box.
  • Gene Nodes: Chromosomes contain known gene mutations for each disease set.
  • Chromosome Area: Includes the chromosomes that correlate to the patient area. The 23rd chromosome is labeled as either "X" or "Y".
  • Edge Toggles: Toggle box that turn the different mutation edges on or off.
  • Color Option Selector: The ablity to select or deselect cohorts based on clinical factors.
  • Control Bar: Collection of controls that operate over the patient and chromosome areas.
x

Use Cases

Define patient cohorts with multiple genetic alterations

Save and view cohorts with multiple genetic alterations.

  1. Show Edges: Search/Select the IDH1 gene, then click "Show Edges of Selected"
  2. Select patients with IDH1 mutation: Click "Select Connected Nodes"
  3. Link patients to new alteration: First, "Hide Edges of Selected" to remove visible edges
  4. Select New Gene while retaining Patient Selection: Hold down the shift key while clicking on IDH1, then (still holding down shift) click on EGFR
  5. Show Alterations of selected patients and EGFR: With EGFR and patients selected, click "Show Edges of Selected" to see the common alterations
  6. Remove All Selections: Click on any open whitespace to deselect all nodes
  7. Select Patients with EGFR and IDH1 mutations: Reselect EGFR and click "Select Connected Nodes"
  8. Patient Cohort with both IDH1 and EGFR genetic alterations

Find patients with certain genetic alterations

Find patients with certain genetic alterations

  1. Search/Select the gene of choice, example PTEN, then hit "Enter" on the keyboard
  2. Click "Show Edges of Selected"
  3. Click "Select Connected Nodes" to select patients with PTEN mutations
  4. On the Cohorts and Collections control bar click the "+" button and rename the chort to save
x

Navigation

Command Modes

M+P can operate in three different modes. Each mode allows users to view or build cohorts in different ways.

Sequential Mode (Default)

Sequential Mode provides a list of different ways the nodes can be connected via the Edge Visibility box. In this mode utilize the commands below as it relates to the next selection, e.g. selections are made sequentially.

  • Show Edges of Selected: Shows all possible edges from the edge visibility box.
  • Hide Edges of Selected: Hides edges of selected nodes.
  • Hide Edges of Unselected: Hides edge of patients or genes that have not been selected.
  • Hide all Edges: Will hide all edges whether selections have been made or not.
  • Invert Node Selection: Will inverse the selection.
  • Select Connected Nodes: Select nodes that have both visible edges and selected counterparts.
  • Hide Unselected Nodes: Hides nodes that are not in current selection.
  • Show all Nodes: If nodes are hidden, this function will reveal them.

Set

Set Mode provides the user the ability to visualize groups over individual selections. While holding the Shift Key users can select a group of patients and then select a chromosome or gene of interest and visualize the correlation between the two selections.

Ad Hoc

Ad Hoc Mode allows the users to make individual rollover selections. It is intended to provide a quick grab of information and not necessarily build working plots.


Edge Visibility

The node connections can be manipulated in the M+P window by selecting or unselecting the various edges. The line colors represent the mutation, gain or loss view in the Edge Visibility box.


Patient Options

Patients areas can be viewed using different clustering techniques and varying layout options, including color-coding by RNA expression, gene selection or clinical factors. To apply these features find the Patient Options header in the command panel. Clicking the Layouts button will expose a list of different clustering techniques and layouts. Select an option to apply it to the patient area. Clicking the Colors button will expose a list of categories that color code the nodes by category type. Select an option to apply it to the patient area.


After a color-coding selection has been made a color key will appear. This key allows patient selections to be made based on a particular option. To select a cohort of patients click the bullseye (right side). To deselect the selection click the open circle (left side). Each selection includes a patient count and the overall percentage of patients who have that option available.


Gender

Diagnosis

Tumor Site



Gene and Patient Search

Specific patients or genes can be selected by using the "Search" box. Enter the patient or gene of interest and hit Enter on the keyboard. The node selection will appear highlighted in either the patient or chromosome area.

Search Box


Zoom Commands

The patient and chromosome area can be zoomed in by clicking the Fit button. The Selected button will zoom on node selections. Alternatively, zooming in on different areas can be achieved by using the scroll wheel or trackpad.


Lock Selections

Locking either set of data will isolate all further commands to operate only over those selections. Locking patient or gene nodes can be done utilizing the lock selections box. To lock a group of patients, select the desired node grouping and click the Patients button. The same can be repeated for genes by clicking the Genes button.

x

Methods

M+P utilizes Multidimensional Scaling (MDS) as means of visualizing the level of similarity of individual patient nodes in a given dataset. M+P can be applied to multiple data types including sequence, expression, DNA methylation. For a deeper analysis please see "Big data visualization identifies the multidimensional molecular landscape of human gliomas" publication by Bolouri H, Zhao L, Holland, E. Links to the genesets used for M+P can be view in the api documentation at Geneset Details.

Oncoscape hosts level 3 public TCGA datasets representing gene and patient data downloaded from UCSC Xena. To review this data in depth visit our data API. User planning to publish on the provided data must adhere to all publishing guideline set by the NIH. Datasets in Oncoscape are classified by disease type according to TCGA studies.

Data was generated using the R-package Classical (Metric) Multidimensional Scaling

x

Frequently Asked Questions

How do I find patients with an alteration in my gene of choice?

Start by entering the gene of choice into the Search box and hit Enter on the keyboard. The gene will highlight in red. Next, make sure Command Mode is set to Sequential then under the Commands Section, click Show Edges of Selected. All patient nodes with the chosen gene node will now be connected.


How do I export or print my graphs?

Currently, the export feature is only available on the Spreadsheet tool. Users can push saved cohorts to the spreadsheet tool by clicking the the Analysis Tool button at the top of the screen. Once there click the Export button. An Excel file will get generated.


How do I save my data for a return visit?

All data for selections and cohorts will be automatically saved for a return visit assuming users are on the same computer to login. User logins that allow stored sessions from any device will be deployed in a future release.


How do I zoom in on my selections?

The patient and chromosome area can be zoomed in by finding the Zoom Command buttons and clicking the Reset button. The Selected button will zoom on node selections. Alternatively, zooming in on different areas can be achieved by using the scroll wheel or trackpad.