PhosR enables processing and functional analysis of phosphoproteomic data
Journal article
Kim, Hani Jieun, Kim, Taiyun, Hoffman, Nolan J., Xiao, Di, James, David E., Humphrey, Sean J. and Yang, Pengyi. (2021). PhosR enables processing and functional analysis of phosphoproteomic data. Cell Reports. 34, p. 108771. https://doi.org/10.1101/2020.08.31.276329
Authors | Kim, Hani Jieun, Kim, Taiyun, Hoffman, Nolan J., Xiao, Di, James, David E., Humphrey, Sean J. and Yang, Pengyi |
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Abstract | Mass spectrometry (MS)-based phosphoproteomics has revolutionised our ability to profile phosphorylation-based signalling in cells and tissues on a global scale. To infer the action of kinases and signalling pathways in phosphoproteomic experiments, we present PhosR, a set of tools and methodologies implemented in a suite of R packages facilitating comprehensive analysis of phosphoproteomic data. By applying PhosR to both published and new phosphoproteomic datasets, we demonstrate capabilities in data imputation and normalisation using a novel set of ‘stably phosphorylated sites’, and in functional analysis for inferring active kinases and signalling pathways. In particular, we introduce a ‘signalome’ construction method for identifying a collection of signalling modules to summarise and visualise the interaction of kinases and their collective actions on signal transduction. Together, our data and findings demonstrate the utility of PhosR in processing and generating novel biological knowledge from MS-based phosphoproteomic data. |
Year | 2021 |
Journal | Cell Reports |
Journal citation | 34, p. 108771 |
Publisher | Cell Press |
ISSN | 2211-1247 |
Digital Object Identifier (DOI) | https://doi.org/10.1101/2020.08.31.276329 |
Open access | Published as ‘gold’ (paid) open access |
Research or scholarly | Research |
Page range | 1-9 |
Funder | Australian Research Council (ARC) |
National Health and Medical Research Council (NHMRC) | |
Publisher's version | License File Access Level Open |
Output status | Published |
Publication dates | |
Online | 23 Feb 2021 |
Publication process dates | |
Accepted | 28 Jan 2021 |
Deposited | 30 Jun 2021 |
ARC Funded Research | This output has been funded, wholly or partially, under the Australian Research Council Act 2001 |
Grant ID | ARC/DE170100759 |
NHMRC/1173469 |
https://acuresearchbank.acu.edu.au/item/8w4qw/phosr-enables-processing-and-functional-analysis-of-phosphoproteomic-data
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Publisher's version
OA_Kim_2021_PhosR_enables_processing_and_functional_analysis.pdf | |
License: CC BY-NC-ND 4.0 | |
File access level: Open |
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