Bioinformatics Tools for Kinome Microarrays

磷酸化是细胞信号传导的基本机制。该反应涉及一个蛋白激酶（一种将磷酸基团添加到某些氨基酸上的酶）和一个靶蛋白（底物）。以高通量方式研究蛋白激酶的一种方法是使用激酶体微阵列，它由数百或数千个贴在玻璃载玻片上的探针组成。暴露于制备的样品后，微阵列上的所有探针同时测量样品中激酶磷酸化的证据，提供（潜在的）细胞磷酸化活性的“快照”。在过去的几年里，我们的团队开发了各种生物信息学工具来支持这项技术。我们设计了软件来帮助确定作为物种特异性或途径特异性阵列探针的肽，以及过滤、调整、可视化和询问结果测量的软件。我们还开发了工具，以协助评估软件的基因组数据分析。与合作者一起，我们已经展示了该技术和软件在从植物到昆虫再到人类等生物中的实用性，其应用范围从确定个体的“基因型”到研究埃博拉感染的致病机制。然而，该领域还远未成熟，还有许多悬而未决的问题。提出的研究计划的重点是解决当前支持基因体微阵列技术的软件的缺点，找到已知问题的解决方案，并开发新的改进算法和软件工具。具体来说，我们将开发改进的数据归一化技术，利用特殊的校准探针从微阵列中提取更多更好的信息，并利用我们独特的，广泛的数据收集来改进kinome微阵列技术，并开发软件，从而发现以前未知的信号通路。******这项研究对从病毒学到作物科学等广泛的生物科学领域的研究人员很重要，因为细胞信号传导是细胞中的一种基本机制。更好的识别和研究信号网络的工具将促进更快速的基础和应用研究，并带来更多的生物学知识。基因组微阵列是一种极有价值的研究工具，因为它们可以用于研究广泛的生物学问题，从人类健康到农业，再到细胞生理学的基础研究。拟议的研究将使基因组阵列在所有这些目的中更加有用。该计划的另一个好处是，它将为本科生和研究生提供一个非常理想的跨学科领域（生物信息学）的培训，该领域的HQP（高素质人才）供应不足。

Phosphorylation is a fundamental mechanism of cellular signalling. The reaction involves a protein kinase (an enzyme that adds a phosphate group to certain amino acids) and a target (substrate) protein. One way to study protein kinases in a high-throughput manner is with kinome microarrays, which consist of hundreds or thousands of probes affixed to a glass slide. After exposure to a prepared sample, all the probes on the microarray are simultaneously measured for evidence of phosphorylation by kinases in the sample, providing a "snapshot" of (potential) cellular phosphorylation activity. Over the past several years, our group has developed various bioinformatics tools to support this technology. We have devised software to help determine the peptides to be used as probes for species-specific or pathway-specific arrays, and software to filter, adjust, visualize, and interrogate the resulting measurements. We have also developed tools for assisting with the evaluation of software for kinome data analysis. With collaborators, we have demonstrated the utility of the technology and software in organisms ranging from plants to insects to humans, with applications ranging from determining an individual's "kinotype" to studying pathogenic mechanisms of Ebola infection. However, the field is still far from mature, with many open questions remaining. The focus of the proposed research program is to address shortcomings of current software supporting kinome microarray technology, to find solutions to known problems, and to develop new, improved algorithms and software tools. Specifically, we will develop improved data normalization techniques, utilize special calibration probes to extract more and better information from the microarrays, and exploit our unique, wide-ranging collection of data to improve kinome microarray technology and to develop software that leads to the discovery of previously unknown signalling pathways. ******This research is important to researchers in a broad range of biological sciences, from virology to crop science since cellular signalling is such a fundamental mechanism in cells. Better tools to identify and study signalling networks will facilitate more rapid basic and applied research, and lead to greater biological knowledge. Kinome microarrays are an extremely valuable research tool because they can be employed to study a wide range of biological problems, from human health to agriculture to basic research into cellular physiology. The proposed research will make kinome arrays even more useful for all of these purposes. Another benefit of the proposed program is that it will provide training for undergraduate and graduate students in a highly desirable, inter-disciplinary field (bioinformatics) in which there is a under-supply of HQP (highly-qualified personnel).