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. .. image:: _images/caseSubtype-1.png :width: 750 px 2. In **Select Attribute** type in **brca** and click on **BRCA Subtype**. Observe that the breast tumors are colored by the molecular subtypes. .. image:: _images/caseSubtype-2.png :width: 750 px 3. In the Short List **BRCA Subtype** entry click on the filter button |shortlistFilterButton| and select **Basal** in the drop down menu. Then click the create attribute button |shortlistCreateAttr|. Name this attribute **Basal_BRCA**. .. image:: _images/caseSubtype-3.png :width: 300 px 4. Select **BRCA Subtype** for display in the Short List by clicking on the **display selector** |primaryButton|. 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. .. image:: _images/caseSubtype-4.png :width: 700 px 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**. .. image:: _images/caseSubtype-5.png :width: 300 px 8. Click on the **Sort Attributes** button in the map header. .. image:: _images/caseSubtype-6.png :width: 700 px 9. In the window, **Sort Attributes by Associative Statistics**, select the values as shown below then click on the **Sort** button. .. image:: _images/caseSubtype-7.png :width: 350 px 10. The message to the right of the **Sort** button will appear as below. .. image:: _images/caseTopDiff-10.png :width: 350 px 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**. .. image:: _images/caseSubtype-8.png :width: 700 px .. |shortlistFilterButton| image:: https://tumormap.ucsc.edu/icons/filter.png :width: 20 px .. |shortlistCreateAttr| image:: https://tumormap.ucsc.edu/icons/file-new.png :width: 20 px .. |primaryButton| image:: https://tumormap.ucsc.edu/icons/primary.png :width: 20 px