TUTORIAL - GENE SEARCH

Search for a gene of interest and have a overview of the implication of this gene in cancer

Go to www.intogen.org& Click Browser

STEP 1

Type the name of the gene of interest and click search

STEP 2

Click the Ensembl ID of the gene of interest

STEP 3

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

This box shows some gene details and link to ensembl

This box indicates that this gene is in the Cancer Gene Census, and it give details about the type of mutations identified.

Click on the tab Tumor type to go to the tumor types table for the gene.

STEP 4

We are in the page for MYC for all experiments and all tumor types.

These columns indicate the number of samples with mutations and the number of samples analyzed for this gene in each tumor type.This data is from COSMIC.

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

These colors indicate significance. Color 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

You can sort the table by clicking to the title of any column.

With this links you can go to the next page to see the rest of the tumor types

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

Click on “breast” to see details of MYC alterations in breast cancer

STEP 6

Sort the table by clicking to the Gain title, to have the tumor types in which this gene has the most significant copy number gain on top.

STEP 5

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

This box shows some gene details and link to ensembl

This box shows the p-value for copy number alterations of MYC in breast cancer.

This box shows details of mutations of MYC in breast cancer from the Cancer Gene Census

Click on Tumor types Tab

STEP 7

This table gives information on the alterations found in MYC in different morphologies of breast cancer.

Now click on Experiments Tab

STEP 8

This is the list of experiments that have analyzed MYC in breast cancer. N = number

of samples analyzed

The color shows that there is copy number gain for this gene in a significant number of samples of the 76 samples that were analyzed.

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

Click on the Gain column to sort by significance of copy number gain.

STEP 9

Click on Chin SF et al to see the details of this experiment.

STEP 9

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

This box gives details of copy number gain of MYC in this experiment. 76 samples have been analyzed, of which 36 have a gain in this gene. The expected number of samples with alteration by chance is about 5.2. This is highly significant copy number alteration.

STEP 10

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

This table give information of the tumor type and morphology type analyzed by this experiment

To explore other genes involved in breast cancer click all in Experiments and all in Genes/Modules

STEP 10

Note that now we are in a page for all experiments for this tumor type, and all genes and modules.

This Table gives the list of experiments analyzed for this tumor topography and morphology.

Change to the Genes tab in the browser.

STEP 11

This table summarizes the evidence for alterations of each gene involved in this tumor type.

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

Note that now we are in a page for all experiments of Breast Cancer/Infiltrating duct carcinoma, and all genes.

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You will find more tutorials and documentation in www.intogen.org