Figure 2: Systems biology. [A] Systems Biology is a conceptual framework for the analysis of complex biological systems from genomic information to the organismic level. Such systems derive from interactions among many distinct components (DNA, RNA, microRNA and proteins, in varying contexts (at the cellular, organ and organism level). These systems exhibit properties, such as nonlinear dynamics and emergent behavior that cannot easily be inferred from studies using reductionism. Systems biology relies on mathematical methods and computational models to generate hypotheses and to design new experiments that are driven from bioinformatics analysis. The quantity and quality of data required for these approaches often challenge current technologies, and development of new technologies, and cross-disciplinary collaborations, may be required. When applied to CSCs, systems biology can be a powerful tool to test hypotheses relevant to their development, role in cancer and provide avenues to novel therapeutic interventions. [B] Ingenuity analysis identifies novel gene networks involved in the maintenance of pluripotency. Genes over-expressed in non-human primate embryonic stem cells compared to fibroblasts are depicted in red. Genes shaded in green are over-expressed in fibroblasts. [C] Non-coding RNAs can be identified as members of pluripotent pathways using Ingenuity. Ingenuity analysis shows that genes known to be involved in stemness (Nanog and Sox-2) are overexpressed (red) in non-human primate embryonic stem cells (nhpESCs) compared to fibroblasts. In addition, we could identify non-coding RNAs that were over-expressed in nhpESCs and associated with Nanog. (figures 2B and 2C have been adopted from the Open Access article by Ahmi Ben- Yehudah Stem Cell research and therapy).