Modeling the Evolution of Gene Regulatory Modules for Complex Traits

伊利诺伊大学厄巴纳-香槟分校获得了一笔赠款，以促进对复杂性状进化的理解，例如多细胞身体计划或生物体社会行为的发展。PI将使用大脑可塑性和社会行为的分析作为测试问题，以建立和测试复杂性状进化的定量基因组模型。大脑可塑性是指大脑通过形成新的神经连接来重组自己的能力。该项目将通过开发新的分析模型和计算工具来模拟基因调控模块的进化，来验证介导大脑可塑性的遗传途径在不同物种的脑组织中富含保守的基因调控模块的假设。第一个模型是一个进化模型的遗传模块，它可以应用于确定保守的，以及物种特异性的遗传模块使用和基因表达数据在多个物种和系统发育距离。第二个模型可以应用于分析在具有保守表型的相关物种中实现的转录网络。一个正交集的TF和靶基因之间的调控关系将同时建模，并确定在所有考虑的物种。序列数据和基因表达数据（如果可用）都将被建模。该项目将提供两个软件工具，用于基因组和转录组数据的综合比较分析。 这些软件工具将放在一个专用服务器上（http：//sysbio.bioen.uiuc.edu/grn.htm），并通过方便用户的网络应用程序提供给整个研究界。该项目将包括本科生，研究生和博士后学生的参与，该软件将用于由研究人员在年轻女性生物信息学夏令营教授的实践课程。

The University of Illinois at Urbana-Champaign is awarded a grant to advance the understanding of the evolution of complex traits, such as the development of multi-cellular body plans or an organism's social behavior. The PI will use the analysis of brain plasticity and social behavior as test-bed questions to build and test quantitative genomic models for the evolution of complex traits. Brain plasticity refers to the brain's ability to reorganize itself by forming new neural connections as a result of experience. The project will test the hypothesis that genetic pathways that mediate brain plasticity are enriched in conserved gene regulatory modules in brain tissues across species, by developing novel analytical models and computational tools for modeling the evolution of gene regulatory modules. The first model is an evolutionary model for genetic modules, which can be applied to identify conserved as well as species-specific genetic modules using and gene expression data in multiple species and phylogenetic distances. The second model can be applied to analyze the transcription networks implemented in related species with a conserved phenotype. The regulatory relationships between an orthologous set of TFs and target genes will be simultaneously modeled and identified in all the species under consideration. Both sequence data and gene expression data, when available, will be modeled. This project will deliver two software tools for integrated comparative analysis of genome and transcriptome data. by These software tools will be hosted on a dedicated server (http://sysbio.bioen.uiuc.edu/grn.htm) and made available to the entire research community through user-friendly web applications. The project will include the participation of undergraduate, graduate, and postdoctoral students, and the software will be used in a hands-on course taught by the investigator at a bioinformatics camp for young women.