TUTORIAL - TUMOR TYPE SEARCH

Search for a cancer type of interest and discover the most significant altered genes and modules

Go to www.intogen.org& Click Browser

STEP 1

Select the tumor type of your interest

STEP 2

Cancer type annotations are based on International Classification of Disease (ICD)

NOTE

ICD-10 nomenclature is used to indicate the topography or site of the tumor

ICD-O nomenclature is used to indicate the tumor morphology or subtype.

In this case we will select breast cancer, and we will leave blank the morphology type.

STEP 3

This table summarizes the evidence for the involvement of each gene in breast cancer

We are in the page for all experiments of Breast Cancer, and all genes/modules

Note that you can get the data in table format by clicking on ‘CSV file’ under ‘Export”

This part gives summary information of the alterations found in each gene in the cancer type selected given a number of experiments combined

These colors indicate significance. Colors toward red means that this gene is significantly altered in this tumor type

Gray means that this gene is not significantly altered in this tumor type.

White means that there is no data for this gene in this tumor type

Color scale of corrected p-values:Gray = no significantly alteredRed/Yellow = significantly altered

These values are based on predictions by CGPrio method. Genes with higher probability rank are more likely to be involved in cancer.See Furney et al., NAR 2008

You can sort the table by clicking to the title of any column. For example click Down.

STEP 4

Now the genes in the top are those significantly downregulated in breast cancer.

Note that some genes are both significantly lost and downregulated.

With these links you can navigate to the next pages to see the rest of the genes

Now we will sort the table to find the genes with more mutations known in breast cancer

STEP 5

Now the genes in the top are those with higher number of mutations known in breast cancer.

The first number is the number of samples with mutations in this gene, and the second number is the number of samples analyzed.This information is based on COSMIC.

We are browsing the information for genes in Breast cancer. But we can also browse other information.

This column informs whether the gene is in the Cancer Gene Census of the Sanger Center and which type of mutations are known in cancer samples.

STEP 6

Select GO process from Modules tab to discover the most altered biological processes in breast cancer.

This table gives information on altered GO processes in breast cancer.

If we click to the Up title, we will sort by the pathways that have the highest enrichment of genes up-regulated in breast cancer.

STEP 7

Here, the red color indicates that the module (GO process) is enriched for altered (up-regulated) genes in breast cancer.Gray means that the

number of genes in this pathway that are altered are not higher than expected by chance

Click on the Genes Tab to go back to the genes table

STEP 8

You can also search for a gene of your interest to see how it is altered in breast cancer. For example type CDKN2A and click search.

STEP 9

Click on the Ensembl ID for the CDKN2A gene.

STEP 10

This box shows the p-value for up-regulation and down-regulation of CDKN2A in breast cancer.

This box shows details of mutations of CDKN2A in breast cancer: The number of samples with mutations (46), the number of samples analyzed (1003) and the link to COSMIC for this gene.

Note that now we are in the page of CDKN2A for breast cancer

This box shows details of the annotations of this gene in the Cancer Gene Census of the Sanger Center.

Click on Tumor types Tab

STEP 11

This table provides information on the alterations found in CDKN2A in different morphology types for Breast Cancer.

Now click on Experiments Tab

STEP 12

Click on Yu K et al to see the details of the experiment.

STEP 14

This is the list of experiments that have analyzed CDKN2A in breast cancer.

N = number of samples analyzed

Coloured cells indicate that this gene is down-regulated in a significant number of samples of the experiment.

White cells means no data. In this case means that this experiment has not analyzed for transcriptomic alterations

Click Down to sort the table for those experiments in which this gene is more significantly down-regulated.

STEP 13

Note that now we are in the page of CDKN2A for a particular experiment of breast cancer

This box gives details of down-regulation of CDKN2A in this experiment. 183 samples have been analyzed, of which 24 have this gene down-regulated. The expected number of samples with down-regulation by chance is about 8. This is highly significant down-regulation.

This box shows details of the experiment, including authors, title and link to the publication or original source of data.

To see what is the involvement of CDKN2A in other cancer types click “all” in experiments and “all” in tumor types.

STEP 15

Note that now we are in the page of CDKN2A for all tumor types

This table gives information of known cancer alterations found in CDKN2A gene

Go to the tab “tumor type”.

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