========================================================= 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 :file:`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: - `homo\_sapiens\_affy\_u133\_plus\_2\_annotations.tsv `__ Explore the results ------------------- .. image:: img/tutorial-gitoolscasestudy2.3.png