PXD015744-2

PXD015744 is an original dataset announced via ProteomeXchange.

Title	Co-expression analysis of label-free proteomics data reveals prognostic biomarkers in pancreatic ductal adenocarcinoma
Description	Despite extensive biological and clinical studies, including comprehensive genomics and transcriptomics analysis, pancreatic ductal adenocarcinoma (PDAC) remains a devastating disease, with poor survival and no effective therapies to date. Correlation networks are emerging as a powerful approach to infer tumor biology and to prioritize candidate genes as biomarkers or drug targets. In this study we applied a weighted co-expression analysis to the functionally relevant proteome of 20 surgically resected patients with PDAC. We obtained twelve modules with overlapping yet distinct biology, which implicated metabolism and ECM complexes in several modules. Notably, one module enriched for metabolic processes and epithelial-mesenchymal-transition (EMT) was significantly associated with overall survival (p=0.01) and was validated in public RNA data (p=0.02). The prognostic value of three proteins (SPTBN1, KHSRP and PYGL) belonging to this module was confirmed using immunohistochemistry in a cohort of 82 radically resected patients.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:11:39.623.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sander Piersma
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-10-08 09:01:55	ID requested
1	2020-09-01 04:55:23	announced
⏵ 2	2024-10-22 05:11:40	announced	2024-10-22: Updated project metadata.

Mantini G, Vall, é, s AM, Le Large TYS, Capula M, Funel N, Pham TV, Piersma SR, Kazemier G, Bijlsma MF, Giovannetti E, Jimenez CR, Co-expression analysis of pancreatic cancer proteome reveals biology and prognostic biomarkers. Cell Oncol (Dordr), 43(6):1147-1159(2020) [pubmed]

10.1007/s13402-020-00548-y;

submitter keyword: co-expression, pancreatic ductal adenocarcinoma, fresh-frozen tissue,Label-free, prognosis

Connie Ramona Jimenez
contact affiliation	Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, Netherlands
contact email	c.jimenez@amsterdamumc.nl
lab head
Sander Piersma
contact affiliation	OncoProteomics Laboratory, dept of Medical Oncology, VUmc Medical Center, Amsterdam, The Netherlands
contact email	s.piersma@vumc.nl
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/2020/09/PXD015744

PRIDE project URI

• PRIDE
  1. PXD015744
     1. Label: PRIDE project
     2. Name: Co-expression analysis of label-free proteomics data reveals prognostic biomarkers in pancreatic ductal adenocarcinoma