PXD037601-2

PXD037601 is an original dataset announced via ProteomeXchange.

Title	Functional annotation of proteins for signaling network inference in non-model species
Description	Molecular biology aims to understand the molecular basis of cellular responses, unravel dynamic regulatory networks, and model complex biological systems. However, these studies remain challenging in non-model species as a result of poor functional annotation of regulatory proteins, like kinases or phosphatases. To overcome this limitation, we developed a multi-layer neural network that annotates proteins by determining functionality directly from the protein sequence. We annotated the kinases and phosphatases in the non-model species, Glycine max (soybean), achieving a prediction sensitivity of up to 97%. To demonstrate the applicability, we used our functional annotations in combination with Bayesian network principles to predict signaling cascades using time series phosphoproteomics. We shed light on phosphorylation cascades in soybean seedlings upon cold treatment and identified Glyma.10G173000 (TOI5) and Glyma.19G007300 (TOT3) as key temperature response regulators in soybean. Importantly, the signaling cascade predictions do not rely upon known upstream kinases, kinase motifs, or protein interaction data, enabling de novo identification of kinase-substrate interactions. In addition to high accuracy and strong generalization, we showed that our functional prediction neural network is scalable to other model and non-model species, including Oryza sativa (rice), Zea mays (maize), Sorghum bicolor (sorghum), and Triticum aestivum (wheat). Overall, we demonstrated a data-driven systems biology approach for non-model species leveraging our predicted upstream kinases and phosphatases.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:47:56.471.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Cassio Flavio Fonseca de Lima
SpeciesList	scientific name: Glycine max; NCBI TaxID: 3847;
ModificationList	phosphorylated residue; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2022-10-20 02:23:48	ID requested
1	2023-06-13 02:15:50	announced
⏵ 2	2024-10-22 05:47:56	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: Phosphoproteomics, Protein family,Soybean, Temperature

Ive De Smet
contact affiliation	(1) Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium; (2) VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium.
contact email	ivsme@psb.ugent.be
lab head
Cassio Flavio Fonseca de Lima
contact affiliation	PhD student
contact email	cafon@psb.ugent.be
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/2023/06/PXD037601

PRIDE project URI

• PRIDE
  1. PXD037601
     1. Label: PRIDE project
     2. Name: Functional annotation of proteins for signaling network inference in non-model species