The Stanford-Cancer Genome Atlas Portal Tutorial

THE STANFORD-CANCER GENOME ATLAS PORTAL:

A WEB/MOBILE NAVIGATION INTERFACE FOR

EXPLORING THE CLINICAL ASSOCIATIONS OF CANCER

DRIVERSTutorial: How to navigate the web portal

Three ways of looking TCGA dataWhat 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?

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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

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

I. Check what clinical parameters are associated with genes/miRs/proteins of your interest

TP53 is associated with:i) Race in breast cancerii) Triple marker in breast canceriii) N-Status in thyroid canceriv) Histo grade in uterine cancer

The mutation frequency of genes/miRs/proteins of your interest across all cancer types

Sort function

The copy number variation frequency of genes/miRs/proteins of your interest across all cancer types

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

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

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

I. What are the clinically relevant genes/miRs/proteins?Clinical parameters with categorical values; click each class in a clinical parameter

I. What are the clinically relevant genes/miRs/proteins?When you are interested in a clinical parameter, click here and select a clinical parameter

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.

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

I. In summary, you can get to the summary page of WRN which is associated with clinical stage in colorectal cancer three different ways

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

II. Profiling by Clinical ParameterWhen 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 PIK3CA2. Select STAD3. Select EBV present4. Click Submit

II. Profiling by Clinical Parameter

Summary of PIK3CA CNV between EBV infected and non-infected samples in stomach cancer

II. Profiling by Clinical Parameter

Difference in PIK3CA mutations between EBV infected and non-infected samples in stomach cancer

II. Profiling by Clinical Parameter

Difference in expression level of PIK3CA between EBV infected and non-infected samples in stomach cancer

III. Two hit hypothesis testWhat 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 mutationii) samples without TP53 mutations

First level sample group:With this example, what is the distribution of copy number changes of TP53 in each group?

III. Testing two hit hypothesis Summarize the copy number changes of TP53 by samples with/without TP53 mutations in colorectal cancers

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