KRSA: An R package and R Shiny web application for an end-to-end upstream kinase analysis of kinome array data.
KRSA: An R package and R Shiny web application for an end-to-end upstream kinase analysis of kinome array data.
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DOI：
10.1371/journal.pone.0260440
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发表时间：
2021
期刊：
影响因子：
3.7
通讯作者：
McCullumsmith RE
中科院分区：
文献类型：
--
作者：
DePasquale EAK;Alganem K;Bentea E;Nawreen N;McGuire JL;Tomar T;Naji F;Hilhorst R;Meller J;McCullumsmith RE
丝氨酸-苏氨酸和酪氨酸激酶的磷酸化是决定蛋白质功能的关键。用于测量报告肽信号水平的阵列平台允许在不同活性激酶的条件下进行差异磷酸化分析。肽阵列技术，如PamGene的PamStation12，可以生成高通量、多维、复杂的功能蛋白质组学数据。随着此类技术采用率的提高，对简化分析此类数据过程的软件工具的需求是迫切的。我们提出了Kinome Random Sampling Analyzer (KRSA)，这是一个R软件包和R Shiny web应用程序，用于分析Kinome阵列数据，以帮助用户更好地了解复杂生物系统中功能蛋白质组学的模式。KRSA是一个读取、格式化、拟合模型、分析和可视化PamStation12基因组数据的一体化工具。虽然基础算法已经在先前的出版物中得到了实验验证，但我们在男性（n = 3）和女性（n = 3）受试者的背外侧前额叶皮层（DLPFC）上展示了KRSA工作流程，以识别不同的磷酸化特征和上游激酶活性。将男性和女性之间的激酶活性差异与先前发表的kinome数据集（11名女性和7名男性受试者）进行比较，结果显示出相似的全球磷酸化信号模式。
Phosphorylation by serine-threonine and tyrosine kinases is critical for determining protein function. Array-based platforms for measuring reporter peptide signal levels allow for differential phosphorylation analysis between conditions for distinct active kinases. Peptide array technologies like the PamStation12 from PamGene allow for generating high-throughput, multi-dimensional, and complex functional proteomics data. As the adoption rate of such technologies increases, there is an imperative need for software tools that streamline the process of analyzing such data. We present Kinome Random Sampling Analyzer (KRSA), an R package and R Shiny web-application for analyzing kinome array data to help users better understand the patterns of functional proteomics in complex biological systems. KRSA is an All-In-One tool that reads, formats, fits models, analyzes, and visualizes PamStation12 kinome data. While the underlying algorithm has been experimentally validated in previous publications, we demonstrate KRSA workflow on dorsolateral prefrontal cortex (DLPFC) in male (n = 3) and female (n = 3) subjects to identify differential phosphorylation signatures and upstream kinase activity. Kinase activity differences between males and females were compared to a previously published kinome dataset (11 female and 7 male subjects) which showed similar global phosphorylation signals patterns.