Research on Signaling Pathway Reconstruction Based on HMM

Signaling pathway is a fundamental basis to understand the complex life process and the pathogenesis of disease. Developing a computing technology for deducing a signaling pathway is an active research area. NICO is a method of network reconstruction based on the co-occurrence genes. However, this method when applied to signaling pathway reconstruction can not effectively express the regulation directions between the genes. In this article, an improved method based on N-ICO method is proposed, called D-NICO method, where HMM is used as a model for reconstructing the signaling pathway. This method not only is capable of predicting gene regulation relationships, but also is capable of identifying gene regulation directions, which provide necessary information for further understanding the function of the signaling pathway and life process. At last, this article takes a PKA and MAPK signaling pathway reconstruction as an example to verify this method.