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Experiment Search


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Experiment Search

  1. 1. TUTORIAL - EXPERIMENT SEARCH Search for an experiment and identify the most significant genes and modules altered
  2. 2. STEP 1Go Click Browser
  3. 3. STEP 2Select an option fromdrop down button in‘Experiments’, orclick on Experimenttab
  4. 4. You can sort the tableYou can search for an by clicking any title. Ifexperiment using you click on ‘Platform’this search box title, the table will be sorted by platform. This table shows the list of With this links you all experiments in IntOGen can go to the next page to see the rest of the experiments
  5. 5. STEP 3 Type TCGA and click Search STEP 4Select theexperiment for mRNAexpression forglioblastoma.
  6. 6. We are on the page for TCGA expression microarray experiment which analyzes glioblastoma samplesThis box give details ofthe experiment,including authors, titleand link to thepublication and originalsource of data
  7. 7. STEP 5 Click on the tab ‘Genes’This table givesthe significanceof alterations ofeach gene in theexperiment.
  8. 8. N = number of samples analyzed The colors indicate significance. Red shades mean that this gene is significantly altered in this experiment.Color scale of corrected p-values:Gray = no significantly alteredRed/Yellow = significantly altered Gray means that this gene is not significantly altered in this experiment.
  9. 9. These values are based on predictions by the CGPrio method. Genes with higher probability rank are more likely to be involved in cancer as oncogenes or tumor suppressors. See Furney et al., NAR 2008Note that you canretrieve the data in atabulated file byclicking on ‘CSV file’under ‘Export” Data in the CGC column indicate if the gene is in the Cancer Gene Census and which type of mutations are annotated there.
  10. 10. STEP 6You can sort the table byclicking the title of any column,to have the most significantlyaltered genes in the top. ClickUp to sort by up-regulation.
  11. 11. STEP 7 you can search any gene (e.g., TP53) in this experiment Note that on top of the list, we now see the genes with most significant up- regulation in this experimentWith these links youcan go to the nextpages to see moregenes.
  12. 12. STEP 8Click the EnsemblID of the gene ofinterest.
  13. 13. Now we are on the page for TP53 gene for this experiment 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., NARThis box gives details on the 2008transcriptomic alterations of TP53in this experiment. 387 sampleshave been analyzed, of which 32 This box indicateshave this gene up-regulated. The that this gene is inexpected number of samples the Cancer Genewith alteration by chance is about Census, and it gives11. This is highly significant up- details about theregulation. type of mutations identified there.
  14. 14. STEP 9Click on Genes to goback to the genestable page
  15. 15. STEP 10Select KEGGpathways from theModules tab toexplore the mostsignificantly alteredpathways of thisexperiment.
  16. 16. This table gives thesignificance of eachpathway in thisexperiment Note that here, N is the number of genes in the pathway
  17. 17. STEP 11 Click Up to sort and to see the most significantly up- regulated pathways on top. STEP 12Click p53 signalingpathway to see thedetails of thispathway.
  18. 18. Now we are on the page for KEGG p53 signaling pathway for this experiment. STEP 13Click Genes inmodule tab to see allthe genes in thispathway. This box contains details on up-regulation of genes in this pathway in this experiment. p53 pathway has 60 genes, 22 of which are significantly up-regulated in this experiment. The expected number by chance is approx. 11. The enrichment is therefore significant.
  19. 19. This table gives the significance of alteration for each gene in this module in this experiment. STEP 14Click the GeneSerpine1 to seedetails of the gene inthis experiment.
  20. 20. Note that now we are on the page of Serpine1 for this experiment. This box contains details on the up-regulation of Serpine1 in this experiment. 387 samples have been analyzed, of which 136 over- expressed this gene. The expected number of samples with alteration by chance is about 11. This is highly significant over-expression.This box shows detailson the gene and thelink to ensembl.
  21. 21. STEP 15To see what is theinvolvement ofSerpine1 in otherglioblastomaexperiments click allin experiments.
  22. 22. N = number of samples analyzed A number of experiments have analyzed genomic alterations in glioblastoma. The region of this gene isSTEP 16 significantly amplified in 3 independent experimentsClick on Sun et many of them. have analyzed transcriptomical. experiment alterations of Serpine1 in glioblastoma and in all of them this gene is significantly up- regulated.
  23. 23. Note that now we are STEP 17 on the page of the Sun et al experimentClick the Tab for Serpine1 gene.Tumor types This box shows details of the experiment and link to publication and original data source. This box gives details of up-regulation of Serpine1 in this experiment. 152 samples have been analyzed, of which 50 have this gene over-expressed. The expected number of samples with over-expression is about 4.6. This is highly significant over-expression. Note that at the same time, there is significant down-regulation observed in other samples of the same experiment.
  24. 24. STEP 18 To see the involvement of this gene in other cancer types click all in experiments and allThis table gives information in tumor type.on the tumor morphologiesanalyzed in thisexperiment. Serpine1expression is found to besignificantly altered (up-ordown-regulated) in allanalyzed morphologies.
  25. 25. STEP 19Go to tumor typetab.
  26. 26. Note that now we are on the page of Serpine1 for all tumor types.This table shows evidence ofalterations found in Serpine1in different tumor types. Wecan see that this geneappears to be up- or down-regulated in several tumortypes and that the region ofthis gene is amplifiedsignificantly in many tumortypes.
  27. 27. THANKS FOR USING INTOGEN You will find more tutorials and documentation in