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  KinasePA: Phosphoproteomics data annotation using hypothesis driven kinase perturbation analysis

Yang, P., Patrick, E., Humphrey, S. J., Ghazanfar, S., James, D. E., Jothi, R., et al. (2016). KinasePA: Phosphoproteomics data annotation using hypothesis driven kinase perturbation analysis. PROTEOMICS, 16(13), 1868-1871. doi:10.1002/pmic.201600068.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-002B-2F50-4 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-002B-2F51-2
Genre: Journal Article

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 Creators:
Yang, Pengyi1, Author
Patrick, Ellis1, Author
Humphrey, Sean J.2, Author              
Ghazanfar, Shila1, Author
James, David E.1, Author
Jothi, Raja1, Author
Yang, Jean Yee Hwa1, Author
Affiliations:
1external, ou_persistent22              
2Mann, Matthias / Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Max Planck Society, ou_1565159              

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Free keywords: ENRICHMENT ANALYSIS; REVEALS; INHIBITION; PROTEOMICS; PATHWAY; CELLSBioinformatics; Hypothesis testing; Kinase; Perturbation; Phosphoproteomics; Signalling;
 Abstract: Mass spectrometry (MS)-based quantitative phosphoproteomics has become a key approach for proteome-wide profiling of phosphorylation in tissues and cells. Traditional experimental design often compares a single treatment with a control, whereas increasingly more experiments are designed to compare multiple treatments with respect to a control. To this end, the development of bioinformatic tools that can integrate multiple treatments and visualise kinases and substrates under combinatorial perturbations is vital for dissecting concordant and/or independent effects of each treatment. Here, we propose a hypothesis driven kinase perturbation analysis (KinasePA) to annotate and visualise kinases and their substrates that are perturbed by various combinatorial effects of treatments in phosphoproteomics experiments. We demonstrate the utility of KinasePA through its application to two large-scale phosphoproteomics datasets and show its effectiveness in dissecting kinases and substrates within signalling pathways driven by unique combinations of cellular stimuli and inhibitors. We implemented and incorporated KinasePA as part of the "directPA" R package available from the comprehensive R archive network (CRAN). Furthermore, KinasePA also has an interactive web interface that can be readily applied to annotate user provided phosphoproteomics data (http://kinasepa.pengyiyang.org).

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Language(s): eng - English
 Dates: 2016
 Publication Status: Published in print
 Pages: 4
 Publishing info: -
 Table of Contents: -
 Rev. Method: Peer
 Identifiers: ISI: 000379925900007
DOI: 10.1002/pmic.201600068
 Degree: -

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Title: PROTEOMICS
Source Genre: Journal
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Publ. Info: 111 RIVER ST, HOBOKEN 07030-5774, NJ USA : WILEY-BLACKWELL
Pages: - Volume / Issue: 16 (13) Sequence Number: - Start / End Page: 1868 - 1871 Identifier: ISSN: 1615-9853