PAWER: protein array web exploreR
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PAWER: protein array web exploreR Dmytro Fishman1,2 , Ivan Kuzmin1 , Priit Adler1,2 , Jaak Vilo1,2 and Hedi Peterson1,2* *Correspondence: [email protected] 1 Institute of Computer Science, University of Tartu, Narva mnt 18, 51009 Tartu, Estonia 2 Quretec Ltd, Ülikooli 6a, 51003 Tartu, Estonia
Abstract Background: Protein microarray is a well-established approach for characterizing activity levels of thousands of proteins in a parallel manner. Analysis of protein microarray data is complex and time-consuming, while existing solutions are either outdated or challenging to use without programming skills. The typical data analysis pipeline consists of a data preprocessing step, followed by differential expression analysis, which is then put into context via functional enrichment. Normally, biologists would need to assemble their own workflow by combining a set of unrelated tools to analyze experimental data. Provided that most of these tools are developed independently by various bioinformatics groups, making them work together could be a real challenge. Results: Here we present PAWER, the online web tool dedicated solely to protein microarray analysis. PAWER enables biologists to carry out all the necessary analysis steps in one go. PAWER provides access to state-of-the-art computational methods through the user-friendly interface, resulting in publication-ready illustrations. We also provide an R package for more advanced use cases, such as bespoke analysis workflows. Conclusions: PAWER is freely available at https://biit.cs.ut.ee/pawer. Keywords: Protein microarray, Data analysis, Web tool, Normalisation, Visualisation
Background Protein microarray is the leading high-throughput method to study protein interactions [1], antibody specificity or autoimmunity [2]. In functional protein microarrays, fulllength functional protein targets or protein domains are attached to the surface of the slide and then incubated with a biological sample that contains interacting molecules (e.g. autoantibodies) [3]. After molecules bind to their targets, labelling is done via secondary antibody with a fluorescent marker attached. Resulting fluorescent signal of high intensity indicates the reaction, which can be registered by the specialised scanner. The most popular microarray platforms (e.g. Human Proteome Microarray (HuProt), ProtoArray, NAPPA arrays, Human Protein Fragment arrays and Immunome arrays) allow to measure autoantibody reaction to thousands of unique human protein abundances simultaneously [4, 5].
© The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless ind
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