PXD030784 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | MetaNetwork Enhances Biological Insights from Quantitative Proteomics Differences by Combining Clustering and Enrichment Analyses |
Description | Interpreting proteomics data remains challenging due to the large number of proteins that are quantified by modern mass spectrometry methods. Weighted gene correlation network analysis (WGCNA) can identify groups of biologically related proteins using only protein intensity values by constructing protein correlation networks. However, WGCNA is not widespread in proteomic analyses due to challenges in implementing workflows. To facilitate adoption of WGCNA by the proteomics field, we created MetaNetwork, an open-sourced, R-based application to perform sophisticated WGCNA workflows with no coding skill requirements for the end user. We demonstrate MetaNetwork’s utility by employing it to identify groups of proteins associated with prostate cancer from a proteomics analysis of tumor and adjacent normal tissue samples. We found a decrease in epithelial cell-type specific biomarkers, a known hallmark of prostate tumors. We further identified changes in module eigenproteins indicative of dysregulation in protein translation and trafficking pathways. These results demonstrate the value of using MetaNetwork to improve the biological interpretation of quantitative proteomics experiments for experiments including fifteen or more samples. |
HostingRepository | PRIDE |
AnnounceDate | 2022-01-27 |
AnnouncementXML | Submission_2022-01-27_09:20:07.151.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Austin Carr |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | No PTMs are included in the dataset |
Instrument | LTQ Orbitrap Velos |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2022-01-06 01:53:05 | ID requested | |
1 | 2022-01-27 09:11:37 | announced | |
⏵ 2 | 2022-01-27 09:20:07 | announced | 2022-01-27: Updated publication reference for PubMed record(s): 35073098. |
Publication List
Carr AV, Frey BL, Scalf M, Cesnik AJ, Rolfs Z, Pike KA, Yang B, Keller MP, Jarrard DF, Shortreed MR, Smith LM, MetaNetwork Enhances Biological Insights from Quantitative Proteomics Differences by Combining Clustering and Enrichment Analyses. J Proteome Res, 21(2):410-419(2022) [pubmed] |
Keyword List
submitter keyword: human, prostate, cancer, network, analysis, proteomics |
Contact List
Lloyd M. Smith |
contact affiliation | Department of Chemistry, University of Wisconsin-Madison |
contact email | smith@chem.wisc.edu |
lab head | |
Austin Carr |
contact affiliation | University of Wisconsin-Madison |
contact email | avcarr2@wisc.edu |
dataset submitter | |
Full Dataset Link List
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/2022/01/PXD030784 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD030784
- Label: PRIDE project
- Name: MetaNetwork Enhances Biological Insights from Quantitative Proteomics Differences by Combining Clustering and Enrichment Analyses