Tutorial 2.4: Compare and combine experiments

Compare and combine the significantly up-regulated genes in our experiment and in other lung experiments imported from IntOGen

Files needed

Import p-value matrix from IntOGen for up-regulation in various independent lung cancer experiments.

  • For this tutorial, we provide the matrix file containing p-values for these lung experiments plus the result of the oncodrive analysis in tutorial 2.3, after mapping probes to genes, see files above.
  • See this chapter of the user guide to learn how to import data from IntOGen.

Open heatmap and change scale and labels

  • File>Open>Heatmap… and select the file intogen_lung_upreg_plus_gse19188.cdm.gz.
  • Change the color scale to p-value scale (in Settings).
  • Change the labels of columns: In Settings, select the file file:intogen_lung_upreg-columns.tsv.gz and choose “authors” and “year” as label to show in the columns instead of the id of the experiment.
  • Change the labels of rows: In properties/rows, select the file file:intogen_lung_upreg-rows.tsv.gz and choose “symbol” as label to show in the rows instead of the ensembl id of the gene.
  • Select all the rows and sort to have the most significantly up-regulated genes in the various lung cancer experiments on top.
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Combine

  • To combine the p-values of all the lung cancer experiments, select Analysis>Combinations.
  • See this chapter for further details on how to combine experiments.
  • Apply to columns, with all columns with the same weight.
  • Do not select any file for sets of columns or rows to combine, this way we will combine all columns of the heatmap.
  • Click Next and Finish.

Explore the results

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