Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne CH-1015, Switzerland.
Center for Integrative Genomics, University of Lausanne, Lausanne CH-1015, Switzerland.
Bioinformatics. 2020 Dec 22;36(20):5117-5119. doi: 10.1093/bioinformatics/btz858.
Protein phosphorylation--catalyzed by protein kinases-is the most common post-translational modification. It increases the functional diversity of the proteome and influences various aspects of normal physiology and can be altered in disease states. High throughput profiling of kinases is becoming an essential experimental approach to investigate their activity and this can be achieved using technologies such as PamChip® arrays provided by PamGene for kinase activity measurement. Here, we present 'pamgeneAnalyzeR', an R package developed as an alternative to the manual steps necessary to extract the data from PamChip® peptide microarrays images in a reproducible and robust manner. The extracted data can be directly used for downstream analysis.
PamgeneAnalyzeR is implemented in R and can be obtained from https://github.com/amelbek/pamgeneAnalyzeR.
蛋白质磷酸化——由蛋白激酶催化——是最常见的翻译后修饰。它增加了蛋白质组的功能多样性，并影响正常生理的各个方面，并且在疾病状态下可能会发生改变。高通量激酶分析正成为研究其活性的必要实验方法，这可以使用 PamGene 提供的 PamChip®阵列等技术来实现，用于激酶活性测量。在这里，我们介绍了 'pamgeneAnalyzeR'，这是一个 R 包，作为从 PamChip®肽微阵列图像中以可重复和稳健的方式手动提取数据的必要步骤的替代方案。提取的数据可以直接用于下游分析。
pamgeneAnalyzeR 是用 R 实现的，可以从 https://github.com/amelbek/pamgeneAnalyzeR 获得。
