PXD030784

PXD030784 is an original dataset announced via ProteomeXchange.

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

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.

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]

submitter keyword: human, prostate, cancer, network, analysis, proteomics

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

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

• PRIDE
  1. PXD030784
     1. Label: PRIDE project
     2. Name: MetaNetwork Enhances Biological Insights from Quantitative Proteomics Differences by Combining Clustering and Enrichment Analyses