PXD046503

PXD046503 is an original dataset announced via ProteomeXchange.

Title	De Novo multi-omics pathway analysis (DMPA) designed for prior data independent inference of cell signaling pathways
Description	New tools for cell signaling pathway inference from multi-omics data that are independent of previous knowledge are needed. Here we propose a new de novo method, the de novo multi-omics pathway analysis (DMPA), to model and combine omics data into network modules and pathways. DMPA was validated with published omics data and was found accurate in discovering published molecular associations in transcriptome, interactome, phosphoproteome, methylome, and metabolomics data and signaling pathways in multi-omics data. DMPA was benchmarked against module discovery and multi-omics integration methods and outperformed previous methods in module and pathway discovery especially when applied to datasets with low sample sizes. Transcription factor, kinase, subcellular location and function prediction algorithms were devised for transcriptome, phosphoproteome and interactome regulatory complexes and pathways, respectively. To apply DMPA in a biologically relevant context, interactome, phosphoproteome, transcriptome and proteome data were collected from analyses carried out using melanoma cells to address gamma-secretase cleavage-dependent signaling characteristics of the receptor tyrosine kinase TYRO3. The pathways modeled with DMPA reflected the predicted function and its direction in validation experiments.
HostingRepository	PRIDE
AnnounceDate	2024-02-21
AnnouncementXML	Submission_2024-02-21_04:34:48.478.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD046503
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Johannes Merilahti
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-30 07:12:47	ID requested
⏵ 1	2024-02-21 04:34:48	announced

10.6019/PXD046503;

submitter keyword: multiomics, TYRO3, RTK, gamma-secretase,pathway analysis

Klaus Elenius
contact affiliation	Turku Bioscience Center, University of Turku and Åbo Akademi University, 20520 Turku, Finland. Medicity Research Laboratories, University of Turku, 20520 Turku, Finland Institute of Biomedicine, University of Turku, 2520 Turku, Finland
contact email	klaus.elenius@utu.fi
lab head
Johannes Merilahti
contact affiliation	Turku Bioscience University of Turku
contact email	johannes.merilahti@utu.fi
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/2024/02/PXD046503

PRIDE project URI

• PRIDE
  1. PXD046503
     1. Label: PRIDE project
     2. Name: De Novo multi-omics pathway analysis (DMPA) designed for prior data independent inference of cell signaling pathways