Advances in transcriptional analysis offer great opportunities to delineate the structure and hierarchy of regulatory networks in biochemical systems. We present an approach based on Boolean analysis to reconstruct a set of parsimonious networks from gene disruption and over expression data. Our algorithms, Causal Predictor (CP) and Relaxed Causal Predictor (RCP) distinguish the direct and indirect causality relations from the non-causal interactions, thus significantly reducing the number of miss-predicted edges. The algorithms also yield substantially fewer plausible networks. This greatly reduces the number of experiments required to deduce a unique network from the plausible network structures. Computational simulations are presented to substantiate these results. The algorithms are also applied to reconstruct the entire network of galactose utilization pathway in Saccharomyces cerevisiae. These algorithms will greatly facilitate the elucidation of regulatory networks using large scale gene expression profile data.