TUTORIAL - COMBINE EXPERIMENTS Combine experiments to make your own set of experiment and identify the most significant genes and modules altered
STEP 1Go towww.intogen.org& Click Browser
STEP 2Select the option‘create a newexperiment set´ fromthe pull down menuin ‘Experiments’
STEP 3For this tutorial we are goingto create a set of geneexpression experiments inbreast cancer using theaffymetrix platform andpublished in 2010. Enter aname in the ‘Name’ text-box.You may also add descriptionin the ‘Description’ text-box.Then click ‘Create’.
You can select for a particular tumor type to filter for the experiments of this tumor type You can also use the search box to select the experiments you are interested. Here is the new experiment set that for the moment has 0 experiments.This Table gives a list of allthe experiments in IntOGen With these links youto chose from. can go to the next page to see the rest of experiments
STEP 4Select tumor typebreast
Note that now we have breast cancer selected STEP 5 Search for affymetrix in the search box in order to filter for those experiments done in this platform.This table now onlyshows breast cancerexperiments
STEP 6 Select the three experiments published in 2010 STEP 7Note that now Click on ‘submit’.your experimentset contains 3experiments
We are on the page for our new experiment set. STEP 8 Click on the Genes tabThis box give details ofthe experiment set, ifyou want to remove theexperiment set, thenclick ‘delete’
We are on the page for our experiment set, for breast and for Genes.This table givesinformation oftranscriptomicalterations for each you can go to thegene given the other pagescombination of the clicking on pageselected experiments number
These colors indicate significance. Color means that this gene is significantly altered given the combination of experiments.Color scale of corrected p-values: Gray means that thisGray = no significantly altered gene is notRed/Yellow = significantly altered significantly altered in these experiments
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 STEP 10You can also search for agene of your interest tosee how it is altered inthis set of experiments.For example type ERBB2and click search.
STEP 11Click on the Ensembl IDof the ERBB2 gene.
Note that now we are in the page of ERBB2 for this experiment set This box shows details of mutations of ERBB2 in breast cancer. The number of samples with STEP 12 mutations (5), the Click on Tumor types number of samples Tab analyzed (504) and the link to COSMIC for this gene.This box shows the p-value for transcriptomicalteration of ERBB2 This box shows somegiven the combination This box shows details of gene details and linkof this set of the annotations of this to ensemblexperiments gene in the Cancer Gene Census of the Sanger Center.
STEP 13 Now click on Experiments TabThis Table gives informationon the alterations found inERBB2 in differentmorphology types for BreastCancer given thiscombination of experiments.
This is the list of experiments in the experiment set that have analyzed ERBB2 in breast cancer. N = number of samples analyzed White cells means no data. In this case STEP 14 means that thisClick on the Sircoulomb F experiment has notet al experiment to see analyzed copy numberthe details. alterations. The color indicates that this gene is up- regulated in a significant number of samples of the 51 samples that were analyzed.
STEP 15 Note that now we areTo go back and continue in the page of ERBB2exploring the results or our for this particulargene set, click Breast experiment of breastAffymetrix 2008 in experiments, cancer.and all in genes. This box give details of the experiment, including authors, title and link to the publication or original source of data. 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.
STEP 16You can also explore thisset of experiments foralterations at the level ofmodules.Select KEGG Pathways.
This table gives information transcriptional alterations in pathways combining the three experiments of ourNote that you can set.retrieve the data in atabulated file byclicking on ‘CSV file’under ‘Export”
STEP 17 Click on the Down title to sort by the pathways that have higher enrichment of down- regulated genes in this experiment set. Here, the color indicates that this pathway is enriched down- regulated genes in this set ofGray means that the experiments.number of genes inthis pathway that arealtered are not higherthan expected bychance
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