PXD046503 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2023-10-30 07:12:47 | ID requested | |
⏵ 1 | 2024-02-21 04:34:48 | announced | |
Publication List
Keyword List
submitter keyword: multiomics, TYRO3, RTK, gamma-secretase,pathway analysis |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD046503
- Label: PRIDE project
- Name: De Novo multi-omics pathway analysis (DMPA) designed for prior data independent inference of cell signaling pathways