Improved intra-array and interarray normalization of peptide microarray phosphorylation for phosphorylome and kinome profiling by rational selection of relevant spots
| Autor: | Marcel J. T. Reinders, Jos Joore, Alan F. List, Maikel P. Peppelenbosch, Jetse Scholma, Marc Hulsman, Janine N. Post, Stefano Schivo, Gwenny M. Fuhler |
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| Přispěvatelé: | Human genetics, General practice, Other Research, Developmental BioEngineering, Gastroenterology & Hepatology |
| Jazyk: | angličtina |
| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Male Microarrays In silico Image Processing Regulator Protein Array Analysis Proteomic analysis Computational biology Biology Article 03 medical and health sciences 0302 clinical medicine Humans Kinome Kinase activity Phosphorylation Genetics Multidisciplinary Phosphoproteins 030104 developmental biology 030220 oncology & carcinogenesis Female Peptide microarray DNA microarray |
| Zdroj: | Scientific Reports, 6:26695. Nature Publishing Group Scientific Reports Scientific reports, 6:26695. Nature Publishing Group Scholma, J, Fuhler, G M, Joore, J, Hulsman, M, Schivo, S, List, A F, Reinders, M J T, Peppelenbosch, M P & Post, J N 2016, ' Improved intra-array and interarray normalization of peptide microarray phosphorylation for phosphorylome and kinome profiling by rational selection of relevant spots ', Scientific Reports, vol. 6, 26695 . https://doi.org/10.1038/srep26695 Scientific Reports, 6. Nature Publishing Group |
| ISSN: | 2045-2322 |
| Popis: | Massive parallel analysis using array technology has become the mainstay for analysis of genomes and transcriptomes. Analogously, the predominance of phosphorylation as a regulator of cellular metabolism has fostered the development of peptide arrays of kinase consensus substrates that allow the charting of cellular phosphorylation events (often called kinome profiling). However, whereas the bioinformatical framework for expression array analysis is well-developed, no advanced analysis tools are yet available for kinome profiling. Especially intra-array and interarray normalization of peptide array phosphorylation remain problematic, due to the absence of “housekeeping” kinases and the obvious fallacy of the assumption that different experimental conditions should exhibit equal amounts of kinase activity. Here we describe the development of analysis tools that reliably quantify phosphorylation of peptide arrays and that allow normalization of the signals obtained. We provide a method for intraslide gradient correction and spot quality control. We describe a novel interarray normalization procedure, named repetitive signal enhancement, RSE, which provides a mathematical approach to limit the false negative results occuring with the use of other normalization procedures. Using in silico and biological experiments we show that employing such protocols yields superior insight into cellular physiology as compared to classical analysis tools for kinome profiling. |
| Databáze: | OpenAIRE |
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