Characterization of protein-protein interaction has become a key step in understanding the cellular mechanism because most biological processes cannot be carried out without protein protein interaction. This dissertation focuses on a set of well-validated protein complex data from MIPS. It is commonly believed that functionally related genes tend to have similar expression patterns. However, we found notable contradictory evidence. Indeed, except for a few large protein complexes such as cytoplasmic or mitochondrial ribosomal proteins, the co-expression level of genes from the same complex is on the average not much higher than that from a pair of randomly selected genes. We then demonstrate the impact of these six protein complexes on other genes.