Scheme of CoGAPS algorithm. In the first step, CoGAPS factorizes the gene expression data matrix (D) into the amplitude (A) and pattern (P) matrices. The pattern matrix summarizes common expression patterns among different experimental conditions. The amplitude matrix summarizes the gene expression activity of all genes in the specified patterns. In the second step, the expression activity from matrix A is analyzed for pattern-specific pathway activation. This is done by testing for enriched activity of gene sets of transcription factor targets.