Successfully reported this slideshow.
We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.

The Stanford-Cancer Genome Atlas Portal Tutorial

2,564 views

Published on

The Stanford-Cancer Genome Atlas Portal Tutorial

Published in: Data & Analytics
  • Be the first to comment

The Stanford-Cancer Genome Atlas Portal Tutorial

  1. 1. THE STANFORD-CANCER GENOME ATLAS PORTAL: A WEB/MOBILE NAVIGATION INTERFACE FOR EXPLORING THE CLINICAL ASSOCIATIONS OF CANCER DRIVERS Tutorial: How to navigate the web portal
  2. 2. Three ways of looking TCGA data What are the clinically relevant genes/miRs/proteins? • By name of genes, miRs or proteins • By cancer type • By clinical parameters Profiling by clinical parameters: What is the difference in genetic/proteomic changes between classes in a clinical parameter in a certain cancer? Two hit hypothesis test: Do the two genetic/proteomic changes occur together or not? I II III
  3. 3. I. Checking what clinical parameters are associated with genes/miRs/proteins of your interest Type the name of gene/miR/protein here: Ex) TP53 Click Submit
  4. 4. I. Checking what clinical parameters are associated with genes/miRs/proteins of your interest Type the name of gene/miR/protein here: Ex) TP53 Click Submit Get to the summary page of TP53
  5. 5. I. Check what clinical parameters are associated with genes/miRs/proteins of your interest TP53 is associated with: i) Race in breast cancer ii) Triple marker in breast cancer iii) N-Status in thyroid cancer iv) Histo grade in uterine cancer
  6. 6. The mutation frequency of genes/miRs/proteins of your interest across all cancer types Sort function
  7. 7. The copy number variation frequency of genes/miRs/proteins of your interest across all cancer types
  8. 8. I. What are the clinically relevant genes/miRs/proteins? When you are interested in a certain cancer type, click here and select a cancer type
  9. 9. I. What are the clinically relevant genes/miRs/proteins? If you select COADREAD, webpage shows the summary list with clinical parameters that are available in COADREAD
  10. 10. I. What are the clinically relevant genes/miRs/proteins? If you select genes in ClinicalStage, webpage shows the list of genes associated with a clinical stage in COADREAD
  11. 11. I. What are the clinically relevant genes/miRs/proteins? Clinical parameters with categorical values; click each class in a clinical parameter
  12. 12. I. What are the clinically relevant genes/miRs/proteins? When you are interested in a clinical parameter, click here and select a clinical parameter
  13. 13. I. What are the clinically relevant genes/miRs/proteins? If you select clinical stage, the web page shows the summary list from all the cancer types currently in our data set where clinical stage is available. This is a pan-TCGA summary type page.
  14. 14. I. What are the clinically relevant genes/miRs/proteins? If you select genes in STAD, the web page shows the list of genes associated with a clinical stage in stomach cancers
  15. 15. I. In summary, you can get to the summary page of WRN which is associated with clinical stage in colorectal cancer three different ways
  16. 16. I. In summary, you can get to the summary page of WRN which is associated with clinical stage in colorectal cancer by three different ways
  17. 17. II. Profiling by Clinical Parameter When you want to know the differences of a gene between samples with different clinical parameter types - in terms of genetic/proteomic profiling - use the middle panel How does PIK3CA behave differently between EBV infected and non-infected samples in stomach cancer? 1. Type PIK3CA 2. Select STAD 3. Select EBV present 4. Click Submit
  18. 18. II. Profiling by Clinical Parameter Summary of PIK3CA CNV between EBV infected and non-infected samples in stomach cancer
  19. 19. II. Profiling by Clinical Parameter Difference in PIK3CA mutations between EBV infected and non-infected samples in stomach cancer
  20. 20. II. Profiling by Clinical Parameter Difference in expression level of PIK3CA between EBV infected and non-infected samples in stomach cancer
  21. 21. III. Two hit hypothesis test What is the difference in copy number changes of TP53 between samples with and without TP53 mutation in colorectal cancers? Second level sample group: With this example, it will then split colorectal cancers into two groups – i) samples with TP53 mutation ii) samples without TP53 mutations First level sample group: With this example, what is the distribution of copy number changes of TP53 in each group?
  22. 22. III. Testing two hit hypothesis Summarize the copy number changes of TP53 by samples with/without TP53 mutations in colorectal cancers
  23. 23. III. Testing two hit hypothesis Summarize the copy number changes of TP53 by samples with/without TP53 mutations in colorectal cancers Hemizygous deletion occurred significantly more in samples with TP53 mutations than samples without TP53 mutations

×