Pathway relevance scoring.

<p>Given a subset of the global similarity matrix (S_exp S_cnv, S_mut, S_met, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0133503#pone.0133503.g001" target="_blank">Fig 1</a>) and a set of genes (a,b,d) constituting a pathway <i>P</i>, a score for each input dataset is calculated by first removing genes from S_exp S_cnv, S_mut, S_met that do not belong to the pathway and then taking the average of all remaining values in S_exp S_cnv, S_mut, S_met. This process is repeated for <i>n</i> randomly generated gene sets (with the same number of genes as the pathway <i>P</i>) yielding <i>n</i> scores for each input dataset. The random pathway scores are used to calculate a <i>p</i>-value for obtaining the pathway scores purely by chance. The resulting <i>p</i>-values are multiplied, resulting in a single aggregated pathway score.