KSEA应用程序：一种基于网络的工具，用于从定量磷酸化蛋白质组学推断激酶活性。
The KSEA App: a web-based tool for kinase activity inference from quantitative phosphoproteomics.
作者信息
Wiredja Danica D, Koyutürk Mehmet, Chance Mark R
机构信息
Center for Proteomics and Bioinformatics, Department of Nutrition, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106.
Department Electrical Engineering and Computer Science, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106.
出版信息
Bioinformatics. 2017 Nov 1;33(21):3489-3491. doi: 10.1093/bioinformatics/btx415. Epub 2017 Jun 26.
SUMMARY
Computational characterization of differential kinase activity from phosphoproteomics datasets is critical for correctly inferring cellular circuitry and how signaling cascades are altered in drug treatment and/or disease. Kinase-Substrate Enrichment Analysis (KSEA) offers a powerful approach to estimating changes in a kinase's activity based on the collective phosphorylation changes of its identified substrates. However, KSEA has been limited to programmers who are able to implement the algorithms. Thus, to make it accessible to the larger scientific community, we present a web-based application of this method: the KSEA App. Overall, we expect that this tool will offer a quick and user-friendly way of generating kinase activity estimates from high-throughput phosphoproteomics datasets.
AVAILABILITY AND IMPLEMENTATION
the KSEA App is a free online tool: casecpb.shinyapps.io/ksea/. The source code is on GitHub: github.com/casecpb/KSEA/. The application is also available as the R package "KSEAapp" on CRAN: CRAN.R-project.org/package=KSEAapp/.
CONTACT
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
从磷酸化蛋白质组学数据集中对差异激酶活性进行计算表征，对于正确推断细胞回路以及药物治疗和/或疾病中信号级联如何改变至关重要。激酶-底物富集分析（KSEA）提供了一种强大的方法，可根据其已鉴定底物的集体磷酸化变化来估计激酶活性的变化。然而，KSEA一直仅限于能够实现这些算法的程序员。因此，为了让更广泛的科学界能够使用它，我们展示了这种方法的基于网络的应用程序：KSEA应用程序。总体而言，我们期望这个工具将提供一种快速且用户友好的方式，从高通量磷酸化蛋白质组学数据集中生成激酶活性估计值。
可用性与实现方式
KSEA应用程序是一个免费的在线工具：casecpb.shinyapps.io/ksea/。源代码位于GitHub上：github.com/casecpb/KSEA/。该应用程序也作为R包“KSEAapp”在CRAN上提供：CRAN.R-project.org/package=KSEAapp/。
联系方式
补充信息
补充数据可在《生物信息学》在线获取。
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