PXD046188-2

PXD046188 is an original dataset announced via ProteomeXchange.

Title	A meta-analysis of rice phosphoproteomics data to understand variation in cell signalling across the rice pan-genome
Description	Abstract We have re-analysed publicly available mass spectrometry (MS) data sets enriched for phosphopeptides from Asian rice (Oryza sativa). In total we have identified, 15522 phosphosites on Serine, Threonine and Tyrosine residues on rice proteins. The data has been loaded into UniProtKB, enabling researchers to visualise the sites alongside other stored data on rice proteins, including structural models from AlphaFold2, and into PeptideAtlas, enabling visualisation of the source evidence for each site, including scores and source mass spectra. We identified sequence motifs for phosphosites, and link motifs to enrichment of different biological processes, indicating different downstream regulation caused by different kinase groups. We cross-referenced phosphosites against single amino acid variation (SAAV) data sourced from the rice 3000 genomes data, to identify SAAVs within or proximal to phosphosites that could cause loss of a particular site in a given rice variety. The data was further clustered to identify groups of sites with similar patterns across rice family groups, allowing us to identify sites highly conserved in Japonica, but mostly absent in, for example, Aus type rice varieties - known to have different responses to drought. These resources can assist rice researchers to discover alleles with significantly different functional effects across rice varieties.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:13:49.348.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD046188
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Yasset Perez-Riverol
SpeciesList	scientific name: Oryza sativa (Rice); NCBI TaxID: 4530;
ModificationList	phosphorylated residue
Instrument	TripleTOF 5600; Q Exactive; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-17 07:56:00	ID requested
1	2023-11-08 02:29:09	announced
⏵ 2	2024-10-22 06:13:49	announced	2024-10-22: Updated project metadata.

10.6019/PXD046188;

submitter keyword: Phosphoproteomics, PTMeXchange, FLR, public data,Reanalysis

Andrew R Jones
contact affiliation	Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3BX, United Kingdom
contact email	jonesar@liverpool.ac.uk
lab head
Yasset Perez-Riverol
contact affiliation	EBI
contact email	yperez@ebi.ac.uk
dataset submitter

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/2023/11/PXD046188

PRIDE project URI

• PRIDE
  1. PXD046188
     1. Label: PRIDE project
     2. Name: A meta-analysis of rice phosphoproteomics data to understand variation in cell signalling across the rice pan-genome