Which genomic events distinguish one subtype of cancer from another?

Objective

Identify genomic events that distinguish one subtype of cancer (e.g. basal breast cancer) from another (e.g. luminal breast cancer).

Skills Covered

• Creating a new group from an existing categorical (multi-valued) attribute.
• Using set operations to combine existing groups.
• Running statistical test to order attributes based on their differential presence/absence in one group versus another.

Steps

1. With the map, Pancan12/SampleMap, make sure the mRNA layout is selected and only Tissue is selected in the Short List. Observe that breast tumors are in blue on the bottom right of the map.

2. In Select Attribute type in brca and click on BRCA Subtype. Observe that the breast tumors are colored by the molecular subtypes.

3. In the Short List BRCA Subtype entry click on the filter button and select Basal in the drop down menu. Then click the create attribute button . Name this attribute Basal_BRCA.

4. Select BRCA Subtype for display in the Short List by clicking on the display selector . Create another attribute like you did above except select LumA and save it as LumA_BRCA.
5. Create one more attribute like above except select LumB and save it as LumB_BRCA.
6. Click on the Set Operation button in the map header.

7. In the window, Perform Set Operation, select the values as shown in the picture below to join the two luminal subtypes. Click on Compute Set Operation and name this Lum_BRCA.

8. Click on the Sort Attributes button in the map header.

9. In the window, Sort Attributes by Associative Statistics, select the values as shown below then click on the Sort button.

10. The message to the right of the Sort button will appear as below.

11. After a few seconds to a few minutes when the computations complete, the sort message will change to the below. Observe that the top differentiating attributes in the Select Attribute list are GP7_Basal gene program and GP7_Estrogen gene program.