Tutorial 2.3. Identifying significantly upregulated genes

Run Oncodrive to identify the genes that are significantly up-regulated taking into account a set of tumour samples

Files needed

gse19188_l2r-cancer-vs-normal.cdm.gz : which contains log2 ratios of tumour samples versus normal controls.

Run Oncodrive analysis

  • Select gse19188_l2r-cancer-vs-normal.cdm.gz as data file
  • In filtering options choose “Transform to 1 (0 otherwise) cells with values greater than 1.297 (this is the optimal cutoff for this dataset obtained as explained in the supplementary material of IntOGen paper ).
  • Do not select anything in the sets of columns window.
  • Leave the default values in the statistical test window (binomial, and Benjamin Hochberg FDR).
  • Give a name to the analysis. Select a directory where to save it and click Finish.
  • In the analysis details tab, click on “heatmap” under “Results” to view the heatmap of the results.

Import annotations for probes using Gitools

  • Import Ensembl gene ids, symbol and description for probes in the Affymetrix HG U133 Plus 2 platform.

  • Go to the Welcome tab and click the Biomart wizard. Choose “Table” and click Next.

  • Select “Ensembl Genes 62” and “Homo Sapiens”, and then the desired attributes. Leave only “Ensembl Gene ID” from the defaults, and add “Description” (under Gene/ENSEMBL), “Associated gene name” (under Gene/ENSEMBL) and “Affy HG U133-PLUS-2” (under microarray).

  • Bring up in the list the Affymetrix attribute and click Next.

  • Do not apply any filters, and skip rows with empty values.

  • Give a meaningful name to the file, select an output folder where to save it and finish.

  • Load the annotations for rows by going to the rows tab under properties and loading the annotation file. Click “Filter”.

  • Add a header in the rows tab and select “Text labels”, then “Ensembl Gene ID” and finish. Do the same for the other two annotations.

  • Bring up the header for “Associated Gene name” and sort by this label.

  • Alternatively, you can download the Affymetrix HG U133 Plus 2 ids from here:

Explore the results

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