FIGURE 1

Gene module analysis can detect subtle changes in gene expression from microarray experiments. Each line within the left-hand box labeled "Array" represents a gene positioned along the y-axis according to fold change in expression relative to a reference in a microarray experiment. "Module 1" and "Module 2" are a priori defined sets of genes that are co-activated in two distinct biological pathways; their respective boxes contain their members arranged according to their relative fold change in expression in the "Array" and labeled with the colors orange and green, respectively. Individual gene approaches would detect the two highly upregulated genes in "Module 1" but would not detect any significant change in any of the genes in "Module 2". Gene module analysis, however, demonstrates that "Module 2" may be more significant than "Module 1" in this experiment because "Module 1" has genes that are both upregulated and downregulated, whereas all of the genes in "Module 2" are upregulated.