Cultured glioma cells are motile and invasive. The phenotype of tumor cell motility is likely created by a complex system of molecular interactions because it requires the orchestration of molecular and physical events that modify the cytoskeleton, cell membrane, extracellular matrix, and signaling. Recent reports have described an algorithm for microarray data analysis that generates highly specific genome-scale discovery; these methods identify states of differential gene expression that are true to a high degree of certainty. Here, highly specific discovery of transcriptionally regulated genes combined with logical networks inferred from the functions of known genes predicts states of protein activation, which are validated in cultured glioma cells by independent laboratories. Highly specific discovery of transcriptionally regulated genes facilitates functional genomics of complex molecular systems. © 2005 Elsevier Inc. All rights reserved.