Enormous amount of biological data have been and are continue to be generated, including genomic sequences, gene expression profiles, protein interactions, gene regulation networks, and genetic polymorphisms. An important problem is the integration of different data sources to solve biological problems of interest. Our philosophy is that different data will give us some but not all the information about the biological problems. By combining different data sources intelligently, we are able to obtain a more complete picture of the problems of interest. We will use the following three examples to show our points: a). Predicting protein function, b) prioritizing RNAi hits from RNAi experiments, and  c) inferring pathways or complexes related to phenotypes.