Big Regeneration Mechanisms via Systems Biology and Big Database Mining Methods

Regeneration is an intriguing process, but the molecular and cellular basis of this process is not fully understood. Biologists have found that embryonic development, regeneration, and cancer share a number of common regulation pathways. Studies of protein–protein interactions (PPIs) and modulations of the pathways may improve the understanding of embryonic development, cancer, and regeneration. Since stem cells are key factors in development, regeneration, and cancer, misregulation in the differentiation processes of stem cells can lead to pathological conditions, such as cancer. In this chapter, the systems mechanisms of three differentiation processes of stem cells are discussed, first based on the PPI network and functional module. Next, the cerebella regeneration-related pathways and their crosstalk after traumatic brain injury in zebrafish are introduced, to investigate the phenotypes and the responses to the second injury that involves the regeneration mechanisms of the cerebella wound healing PPI network, via dynamic modeling and big database mining. Pathway enrichment and ontological analysis are incorporated into a refined network to highlight the main molecular scheme of cerebella wound healing. Finally, we investigate the carcinogenic mechanisms and regeneration mechanism using genetic and epigenetic cell cycle networks between cancer cells and embryonic stem cells by comparing the mechanisms underlying cell cycle progression in stem cells and cancer cells through next generation sequencing (NGS) data and dynamic models.