PXD019127 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | PhosR enables processing and functional analysis of phosphoproteomic data |
Description | Mass 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. |
HostingRepository | PRIDE |
AnnounceDate | 2021-01-13 |
AnnouncementXML | Submission_2021-01-12_23:57:09.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Taiyun Kim |
SpeciesList | scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116; |
ModificationList | phosphorylated residue; monohydroxylated residue |
Instrument | Q Exactive |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2020-05-12 05:59:37 | ID requested | |
⏵ 1 | 2021-01-12 23:57:09 | announced | |
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 affiliation | School of Mathematics and Statistics, The University of Sydney |
contact email | pengyi.yang@sydney.edu.au |
lab head | |
Taiyun Kim |
contact affiliation | The University of Sydney |
contact email | taiyun.kim@sydney.edu.au |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD019127
- Label: PRIDE project
- Name: PhosR enables processing and functional analysis of phosphoproteomic data