Run Oncodrive to identify the genes that are significantly up-regulated taking into account a set of tumour samples
gse19188_l2r-cancer-vs-normal.cdm.gz : which contains log2 ratios of tumour samples versus normal controls.
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.