ABI: Novel Tools for the Analysis & Interpretation of Gene Signaling Pathways

韦恩州立大学获得了一笔拨款，用于开发分析基因信号通路的新算法和方法。使用系统生物学方法，该项目将进行影响分析，其中包括经典的性能统计数据，但也考虑了以前被忽视的其他关键因素，例如每个基因表达变化的幅度，它们的重要性，它们在给定途径中的位置，它们的相互作用以及途径的完整拓扑结构。初步工作表明，经典分析可以产生假阳性和假阴性，而建议的影响分析可以提供生物学上有意义的结果。这些方法将在零假设下的p值分布以及一些实际的生物学问题中进行测试和验证。验证将在内部完成，也将通过一些外部合作完成。通过与道格拉斯学院和文艺复兴高中的合作，弱势群体的成员将参与这个项目的许多方面。道格拉斯学院是罗格斯大学的一所本科女子学院。每年两次访问道格拉斯将向他们的本科生展示这项研究，目的是吸引他们中的一些人在这个领域毕业，解决更多女性在计算机科学领域的需求。文艺复兴高中是密歇根州底特律的一所少数民族高中。该项目将包括为文艺复兴学生提供一系列讲座，以及有竞争力的暑期实习机会，这些学生将参与动手研究，目的是吸引他们从事科学事业。预计该项目将通过提供基于网络的软件实施所开发的新算法和方法，以及通过促进建立国家生物信息学教育材料储存库，加强国家教育和研究基础设施。本项目的成果将通过以下方式广泛传播：i)在此项目期间开发的所有工具的网络界面，以及ii)在期刊和会议上定期进行科学交流。有关该项目的更多信息将通过PI的实验室网站http://vortex.cs.wayne.edu/index.html获得。

Wayne State University is awarded a grant to develop new algorithms and methods for the analysis of gene signaling pathways. Using a systems biology approach, the project will perform an impact analysis that includes classic performance statistics but also considers other crucial factors that have been previously neglected, such as the magnitude of each gene's expression change, their significance, their position in the given pathways, their interactions, and the full topology of the pathway. Preliminary work shows that the classical analysis can produce both false positives and false negatives while the proposed impact analysis can provide biologically meaningful results. The methods will be tested and validated in terms of the distribution of the p-values under the null hypothesis, as well as in a number of real biological problems. The validation will be done both in-house, as well as through a number of external collaborations.Members of under-represented groups will be involved in many aspects of this project through collaborations established with Douglass College and Renaissance High School. Douglass College is a undergraduate women's college at Rutgers University. Two annual visits to Douglass will present this research to their undergraduates with a view towards attracting some of them to graduate careers in this area, addressing the need for more women in computer science. Renaissance High School is a minority high-school in Detroit, MI. This project will include a series of lectures for the Renaissance students, as well as competitive summer internships that will involve these high-school students in hands-on research with the goal of enticing them to pursue careers in science. This project is expected to enhance the national education and research infrastructure by providing web-based software implementations of the new algorithms and methods developed as well as by contributing to the establishment of a national repository of bioinformatics education materials. The results of this project will be broadly disseminated by providing: i) a web interface to all tools developed during this project, and ii) by regular scientific communications in journals and conferences. More information about this project will be available through the PI's lab website at http://vortex.cs.wayne.edu/index.html .