Figure 1

Gene expression signatures. Activation of biological processes, such as cell signaling pathways, results in a cascade of activities that ultimately lead to changes in the expression levels of genes downstream, the gene expression signature of that process. To measure that signature, we create experimental conditions that generate differential activation of the process in in vitro cell cultures. We then extract RNA from those samples for microarray analysis, which produces gene expression measurements from which we can score the signature. We show the gene expression signature in a heatmap where the rows are the genes that are differentially expressed in the process, and the columns are the samples that represent the two cellular states. Typically, multiple replicates are done. The colors indicate the expression levels of the genes, where the warm colors signify high expression and cool, low expression. This heatmap shows that the two states exhibit profoundly different gene expression patterns, allowing us to recognize the activation state of the pathway in a gene expression profile using a supervised machine learning algorithm.