Biological networks are composed of functional related modules, so-called network motifs, which play an essential role in many biological processes. Network motifs, such as, the feed forward loop (FFL), single input module (SIM) and bi-fan are some of the well known modules. It is known that such modules have interesting dynamical properties. In this research project, we aim to achieve the following; (i) perform a large-scale collection of major types of regulatory relations, (ii) develop an algorithm to identify major types of network motifs, (iii) investigate the possible interactions among the motifs, and (iv) study network motif evolution. A large-scale collection of network motifs serve as the building blocks for any further research purpose. Interactions among the motifs allow us to reconstruct the global architecture of the whole network from a bottom-up approach. Given that a network motif can perform specific biological function, one may expect motifs tend to be conserved during evolution. This proposal will examine this issue for higher organisms. Results will be deployed as a web service. This web service will provide the following functionalities, (1) search for biological pathways according to motif types, (2) motif-motif interacting pairs, and (3) conserved motifs in higher organisms.