PXD018024

PXD018024 is an original dataset announced via ProteomeXchange.

Title	Proteogenomic analysis of glioblstoma reveals survival related patterns
Description	In the current work, we present the first proteogenomic dataset of GBM clinical samples to date. We have assembled a cohort of 87 GBM patients of varying survival rates and performed MS-based proteomics analysis as well as RNA-seq in order to identify the molecular differences associated with survival and examine the contribution of each layer to GBM landscape. We show that each layer alone only partially reflects patient survival, but RNA-protein integration identifies clear patterns of layer-specific and layer-common processes specifically contributing to either short-term or long-term survival of patients. Furthermore, we compare our data to published single-cell RNA-seq of GBM tumors and evaluate the RNA-protein variability within single-cell based tumor subpopulations. We found that while all signatures of the four subpopulations tend to have high RNA-protein correlation, each signature is associated differently with survival. Altogether, these results highlight the potential of proteogenomics to further stratify heterogeneity in GBM tumors and identify processes contributing to poorer survival.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:21:08.188.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tamar Geiger
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-03-12 04:10:04	ID requested
1	2021-04-15 22:11:33	announced
⏵ 2	2024-10-22 05:21:09	announced	2024-10-22: Updated project metadata.

10.1016/j.celrep.2021.108787;

Yanovich-Arad G, Ofek P, Yeini E, Mardamshina M, Danilevsky A, Shomron N, Grossman R, Satchi-Fainaro R, Geiger T, Proteogenomics of glioblastoma associates molecular patterns with survival. Cell Rep, 34(9):108787(2021) [pubmed]

submitter keyword: proteogenomics,proteomics, mass spectrometry, glioblstoma, RNA-seq

Tamar Geiger
contact affiliation	Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Isrel
contact email	geiger@tauex.tau.ac.il
lab head
Tamar Geiger
contact affiliation	Weizmann Institute of Science
contact email	geiger@tauex.tau.ac.il
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/2021/04/PXD018024

PRIDE project URI

• PRIDE
  1. PXD018024
     1. Label: PRIDE project
     2. Name: Proteogenomic analysis of glioblstoma reveals survival related patterns