<<< Full experiment listing


PXD019127 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitlePhosR enables processing and functional analysis of phosphoproteomic data
DescriptionMass spectrometry-based phosphoproteomics has transformed our ability to profile phosphorylation-based signalling in tissues and cells 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 for the comprehensive analysis of phosphoproteomic data. By applying to both published and new phosphoproteomic datasets, we illustrate PhosR in data imputation and normalisation using a novel set of ‘stably phosphorylated sites’ and in functional analysis for inferring kinase activities and signalling pathways. In particular, we introduce a ‘signalome’ construction method for identifying a collection of signalling modules that allow us to summarise and visualise the interaction of kinases and their collective action 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.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterTaiyun Kim
SpeciesList scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116;
ModificationListphosphorylated residue; monohydroxylated residue
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-05-12 05:59:37ID requested
12021-01-12 23:57:09announced
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: phosphoproteomics, preprecessing, imputation, batch correction, kinase-substrate relationship, signalome, mass-spectrometry
Contact List
Pengyi Yang
contact affiliationSchool of Mathematics and Statistics, The University of Sydney
contact emailpengyi.yang@sydney.edu.au
lab head
Taiyun Kim
contact affiliationThe University of Sydney
contact emailtaiyun.kim@sydney.edu.au
dataset submitter
Full Dataset Link List
Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/01/PXD019127
PRIDE project URI
Repository Record List
[ + ]