TUTORIAL - COMBINE EXPERIMENTS

Combine experiments to make your own set of experiment and identify the most significant genes and modules altered

Go to www.intogen.org& Click Browser

STEP 1

Select the option ‘create a new experiment set´ from the pull down menu in ‘Experiments’

STEP 2

For this tutorial we are going to create a set of gene expression experiments in breast cancer using the affymetrix platform and published in 2010. Enter a name in the ‘Name’ text-box. You may also add description in the ‘Description’ text-box. Then click ‘Create’.

STEP 3

Here is the new experiment set that for the moment has 0 experiments.

This Table gives a list of all the experiments in IntOGen to chose from.

With these links you can go to the next page to see the rest of experiments

You can also use the search box to select the experiments you are interested.

You can select for a particular tumor type to filter for the experiments of this tumor type

Select tumor type breast

STEP 4

Search for affymetrix in the search box in order to filter for those experiments done in this platform.

STEP 5

Note that now we have breast cancer selected

This table now only shows breast cancer experiments

Select the three experiments published in 2010

STEP 6

Click on ‘submit’.

STEP 7

Note that now your experiment set contains 3 experiments

We are on the page for our new experiment set.

This box give details of the experiment set, if you want to remove the experiment set, then click ‘delete’

Click on the Genes tab

STEP 8

We are on the page for our experiment set, for breast and for Genes.

This table gives information of transcriptomic alterations for each gene given the combination of the selected experiments

you can go to the other pages clicking on page number

These colors indicate significance. Color means that this gene is significantly altered given the combination of experiments.

Gray means that this gene is not significantly altered in these experiments

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

You can also search for a gene of your interest to see how it is altered in this set of experiments. For example type ERBB2 and click search.

STEP 10

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

Click on the Ensembl ID of the ERBB2 gene.

STEP 11

This box shows some gene details and link to ensembl

This box shows the p-value for transcriptomic alteration of ERBB2 given the combination of this set of experiments

This box shows details of mutations of ERBB2 in breast cancer. The number of samples with mutations (5), the number of samples analyzed (504) and the link to COSMIC for this gene.

Note that now we are in the page of ERBB2 for this experiment set

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 12

This Table gives information on the alterations found in ERBB2 in different morphology types for Breast Cancer given this combination of experiments.

Now click on Experiments Tab

STEP 13

This is the list of experiments in the experiment set that have analyzed ERBB2 in breast cancer.

N = number of samples analyzed

The color indicates that this gene is up-regulated in a significant number of samples of the 51 samples that were analyzed.

White cells means no data. In this case means that this experiment has not analyzed copy number alterations.

Click on the Sircoulomb F et al experiment to see the details.

STEP 14

Note that now we are in the page of ERBB2 for this particular experiment of breast cancer.

This box gives details of down-regulation of ERBB2 in this experiment. 51 samples have been analyzed. The expected number of samples with down-regulation by chance is about 2.2. Yet, 15 samples were found to have this gene down-regulated. This is highly significant down-regulation.

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

To go back and continue exploring the results or our gene set, click Breast Affymetrix 2008 in experiments, and all in genes.

STEP 15

You can also explore this set of experiments for alterations at the level of modules.Select KEGG Pathways.

STEP 16

This table gives information transcriptional alterations in pathways combining the three experiments of our set.Note that you can

retrieve the data in a tabulated file by clicking on ‘CSV file’ under ‘Export”

Here, the color indicates that this pathway is enriched down-regulated genes in this set of experiments.Gray means that the

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

Click on the Down title to sort by the pathways that have higher enrichment of down-regulated genes in this experiment set.

STEP 17

THANKS FOR USING INTOGEN

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