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PXD030784

PXD030784 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleMetaNetwork Enhances Biological Insights from Quantitative Proteomics Differences by Combining Clustering and Enrichment Analyses
DescriptionInterpreting 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.
HostingRepositoryPRIDE
AnnounceDate2022-01-27
AnnouncementXMLSubmission_2022-01-27_09:20:07.151.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterAustin Carr
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListNo PTMs are included in the dataset
InstrumentLTQ Orbitrap Velos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-01-06 01:53:05ID requested
12022-01-27 09:11:37announced
22022-01-27 09:20:07announced2022-01-27: 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 affiliationDepartment of Chemistry, University of Wisconsin-Madison
contact emailsmith@chem.wisc.edu
lab head
Austin Carr
contact affiliationUniversity of Wisconsin-Madison
contact emailavcarr2@wisc.edu
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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