Network inference of AP pattern formation system in D.melanogaster by structural equation modeling

2nd International Conference on Mathematical Modeling in Physical Sciences 2013

物理学;数学

Aburatani, S.^1 ; Toh, H.^1

Computational Biology Research Center, AIST, AIST Tokyo Waterfront Bio-IT Research Building, 2-4-7 Aomi, Koto-ku, 135-0064, Tokyo, Japan^1

关键词: Cross correlations;    Direct interactions;    Gene expression profiles;    Partial correlation;    Regulatory mechanism;    Regulatory network;    Structural equation modeling;    Temporal information;   

Others  :  https://iopscience.iop.org/article/10.1088/1742-6596/490/1/012145/pdf
DOI  :  10.1088/1742-6596/490/1/012145

来源: IOP

【 摘 要 】

Within the field of systems biology, revealing the control systems functioning during embryogenesis is an important task. To clarify the mechanisms controlling sequential events, the relationships between various factors and the expression of specific genes should be determined. In this study, we applied a method based on Structural Equation Modeling (SEM), combined with factor analysis. SEM can include the latent variables within the constructed model and infer the relationships among the latent and observed variables, as a network model. We improved a method for the construction of initial models for the SEM calculation, and applied our approach to estimate the regulatory network for Antero-Posterior (AP) pattern formation in D. melanogaster embryogenesis. In this new approach, we combined cross-correlation and partial correlation to summarize the temporal information and to extract the direct interactions from the gene expression profiles. In the inferred model, 18 transcription factor genes were regulated by not only the expression of other genes, but also the estimated factors. Since each factor regulated the same type of genes, these factors were considered to be involved in maternal effects or spatial morphogen distributions. The interpretation of the inferred network model allowed us to reveal the regulatory mechanism for the patterning along the head to tail axis in D. melanogaster.