Figure 1.

Calculating functional coherence scores. Given a hierarchical clustering of genes based on their expression profiles and a set of functional categories (e.g. Gene Ontologies), the CLustering Enrichment ANalysis (CLEAN) score for a gene is calculated as the maximum of -log(Fisher's Exact Test q-value) of enrichment tests across all pairs of clusters containing the gene and functional categories containing the gene (see methods for details). The Cluster-wide CLEAN score (cwCLEAN) is calculated in a similar fashion except that the maximum is taken over all clusters that contain the gene and all functional categories regardless of whether they contain the gene or not.