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Analyze Your Modules

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Analyze Your Modules

  1. 1. TUTORIAL - ANALYZE YOUR MODULES Use Gitools to analyze your own modules and find out if they are enriched for genes significantly altered in different cancer types
  2. 2. Note, a module set is a group of modules or gene sets. A module set can contain one or several modules. In the example for this tutorial we are going to analyze a module set with six modules. Each module is a list of genes expressed differentially during human cell cycle phases (obtained from Whitfield et al, Mol Biol Cell 2002). We are going to test if the genes in each module are significantly up-regulated in different tumor types. The format of the file must be with two columns tab separated. The second column defines the module and the first the gene in that module
  3. 3. STEP 1 Go to & Click Launch to start using Gitools application
  4. 4. STEP 2 Click here to import data from IntOGen
  5. 5. STEP 3 Select Matrix and click Next
  6. 6. From IntOGen you can download Onco Combinations, results combining several experiments of the same tumor type, or Experiments, results experiment by experiment. Also you can get results from 4 different types of alterations (gain, loss, upreg and downreg). For this tutorial we will use the Onco Combinations for upreg. STEP 4 Select Onco Combinations and upreg
  7. 7. ALL in Morphology means that samples are grouped independently of their morphology type. In IntOGen samples are grouped by Topography and Morphology according to International Classification of Disease Oncology (ICD). All samples with same ICD terms and analyzed together in the same platform form an experiment unit. Experiment units with the same STEP 5 ICD terms are combined to obtain results for Onco Combinations. Select ALL to get IntOGen results per topography and ALL morphologies.
  8. 8. STEP 6 Give a name for the file to be downloaded and indicate a folder where to save it.
  9. 9. Once the download has been completed you will have three new files in the directory that you indicated. The file with extension cdm contains a Continuos Data Matrix with one row per gene and one column per tumor type. The values in each cell are corrected p-values that indicate if the gene is significantly up-regulated in this tumor type.
  10. 10. STEP 7 Click Enrichment Analysis to start analyzing your module
  11. 11. STEP 8 Select the format of the data matrix that you will load. In this case is a Continuous data matrix. And select the file that contains the data matrix. STEP 9 Transform the continous data matrix to a binary matrix by choosing a transformation criteria. In this case, since the data matrix contains p- values, we want that values lower than 0.05 are converted to 1 (significantly up-regulated)
  12. 12. STEP 10 Select the format of the modules file that you will load. In this case is a two columns mappings. And select the file that contains the data matrix and click Next
  13. 13. STEP 11 Select the type of enrichment analysis that you want to run. In this case we will run a binomial test. Click Next
  14. 14. STEP 12 Give a name to the analysis and indicate a Folder where to place it. Click Finish.
  15. 15. Once the calculations are completed you will have a new tab with the This button will open a new tab details of the analysis. for a browsable heatmap with the Results of your Analysis This button will open a new tab for a browsable heatmap depicting your Data STEP 13 Click the Results heatmap button
  16. 16. Every column corresponds This heatmap to a column in the data contains the results matrix. In this case each of your enrichment column is a tumor type analysis Every row corresponds to a module. In this case different phases of the cell cycle Every cell is the result of one enrichment analysis. The color of each cell indicates if the genes in the module are enriched among gene up- regulated in this cancer type.
  17. 17. STEP 14 Select Properties and Columns to change the names of columns and identify the tumor types STEP 15 Open the file that contains annotations for columns, tumor types. STEP 16 Click on ... for Labels and Select Topography as the annotation to show
  18. 18. Now the column label is the name of the tumor type instead of the id. STEP 17 Delete ${id} to not show the id and hit enter.
  19. 19. STEP 18 Select Details and click one cell to see the details of the analysis This panel shows Details of the results for the selected cell.
  20. 20. THANKS FOR USING INTOGEN You will find more tutorials and documentation in

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