1. TUTORIAL - TUMOR TYPE SEARCH Search for a cancer type of interest and discover the most significant altered genes and modules
2. STEP 1Go towww.intogen.org& Click Browser
3. STEP 2Select the tumortype of yourinterest
4. NOTE Cancer type annotations are based on International Classification of Disease (ICD)ICD-10nomenclature isused to indicatethe topography orsite of the tumor ICD-O nomenclature is used to indicate the tumor morphology or subtype.
5. STEP 3In this case we will selectbreast cancer, and we willleave blank themorphology type.
6. We are in the page for all experiments of Breast Cancer, and all genes/modules This table summarizes the evidence for the involvement of each gene in breast cancerNote that you canget the data in tableformat by clicking on‘CSV file’ under‘Export”
7. 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 typeColor scale of corrected p-values:Gray = no significantlyalteredRed/Yellow = significantlyaltered Gray means that this White means that gene is not there is no data for significantly altered this gene in this in this tumor type. tumor type
8. These values are basedon predictions by CGPriomethod. Genes withhigher probability rank aremore likely to be involvedin cancer.See Furney et al., NAR2008
9. STEP 4You can sort the table byclicking to the title of anycolumn. For example clickDown.
10. Now the genes in the Note that sometop are those genes are bothsignificantly significantly lost anddownregulated in downregulated.breast cancer. With these links you can navigate to the next pages to see the rest of the genes
11. STEP 5Now we will sort thetable to find thegenes with moremutations known inbreast cancer
12. The first number is the number of samples with mutations in this Now the genes in the gene, and the second number is top are those with the number of samples analyzed. higher number of This information is based on mutations known in COSMIC. breast cancer.We are browsing theinformation for genes inBreast cancer. But wecan also browse otherinformation.This column informs whetherthe gene is in the CancerGene Census of the SangerCenter and which type ofmutations are known incancer samples.
13. STEP 6Select GO process fromModules tab todiscover the mostaltered biologicalprocesses in breastcancer.
14. This table givesinformation on alteredGO processes in breastcancer.
15. STEP 7 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. Here, the red color indicates that the module (GO process) is enriched for altered (up-regulated) genes inGray means that the breast cancer.number of genes inthis pathway that arealtered are not higherthan expected bychance
16. STEP 8Click on the Genes Tabto go back to the genestable
17. STEP 9You can also searchfor a gene of yourinterest to see how itis altered in breastcancer. For exampletype CDKN2A andclick search.
18. STEP 10Click on the Ensembl ID forthe CDKN2A gene.
19. Note that now we are in the page of CDKN2A for breast cancer STEP 11 Click on Tumor types Tab This box shows details ofThis box shows the p- mutations of CDKN2A invalue for up-regulation breast cancer: Theand down-regulation of number of samples with This box shows details ofCDKN2A in breast mutations (46), the the annotations of thiscancer. number of samples gene in the Cancer Gene analyzed (1003) and the Census of the Sanger link to COSMIC for this Center. gene.
20. STEP 12 Now click on Experiments TabThis table providesinformation on thealterations found inCDKN2A in differentmorphology types forBreast Cancer.
21. This is the list of experiments STEP 13that have analyzed CDKN2A Click Down to sort thein breast cancer. table for those experiments in which this gene is more significantly down- regulated. N = number White cells means no of samples data. In this case analyzed means that this experiment has not analyzed for transcriptomic alterations Coloured cells indicate that this gene is down- regulated in a significant number of samples of the STEP 14 experiment.Click on Yu K et al tosee the details of theexperiment.
22. Note that now we are in the page of CDKN2A for a particular experiment of breast cancer STEP 15 To see what is the involvement of CDKN2A in other cancer types click “all” in experiments and “all” in tumor types. This box gives details ofThis box shows details down-regulation ofof the experiment, CDKN2A in thisincluding authors, title experiment. 183 samplesand link to the have been analyzed, ofpublication or original which 24 have this genesource of data. down-regulated. The expected number of samples with down- regulation by chance is about 8. This is highly significant down- regulation.
23. Note that now we are in the page of CDKN2A for all tumor typesGo tothe tab“tumortype”. This table gives information of known cancer alterations found in CDKN2A gene
24. THANKS FOR USING INTOGEN You will find more tutorials and documentation in www.intogen.org