Expression of viral early genes is central to viral growth and replication in acute reproductive infections or reactivation from latency. However, innate immune cytokines are also activated rapidly in respond to invading pathogens. This observation suggests that the expression of viral and innate immune genes are parallel. Although the mechanism is not clearly defined, it is known that viral early gene expression is extensively regulated by cellular transcriptional factors. Here we hypothesize that viral and innate immune genes may share a common regulatory mechanism for the co-expression phenomenon. A total of 7 viral genes and 6 innate immune genes were enrolled in this group project. Our aim was to depict and then compare transcriptional factors of these genes by using pathway diagram. Results showed extensively overlapped transcriptional factors in the regulation of both viral and innate immune genes. Multiple sequence alignment, using either entire promoter sequences or synthetic functional sequence with only transcriptional binding elements, demonstrated a random distribution of viral and innate immune gene clusters. These findings suggest the presence of a functional homology between viral and innate immune genes in our project. Positive and negative controls genes will be added in future work to investigate the extent of similarity between viral and innate immune genes.