Figure 1
From: Dissecting complex transcriptional responses using pathway-level scores based on prior information
Scoring pathway activity: gene sets versus regression. Two types of prior information, categorical and quantitative, may be combined with non-thresholded genome-wide expression data to derive a statistical measure of pathway-level activity. In (A) a pre-defined gene set (gray), such as those annotated by the Gene Ontology project, is scored using a t-test for its expression response (red = positive, green = negative) compared to all other genes. In (B) estimated interaction strengths (shades of gray), such as those derived from regulatory sequence analysis or ChIP-chip experiments, are correlated with the expression response of all genes. In both instances the result is a t-value (yellow = positive, blue = negative) that measures the change in mRNA expression associated with a category (A) or interaction (B).