PXD002619

PXD002619 is an original dataset announced via ProteomeXchange.

Title	Proteomic maps of breast cancer subtypes
Description	Systems-wide profiling of breast cancer has so far built on RNA and DNA analysis by microarray and sequencing techniques. Dramatic developments in proteomic technologies now enable very deep profiling of clinical samples, with high identification and quantification accuracy. We analyzed 40 estrogen receptor positive (luminal), Her2 positive and triple negative breast tumors and reached a quantitative depth of more than 10,000 proteins. Comparison to mRNA classifiers revealed multiple discrepancies between proteins and mRNA markers of breast cancer subtypes. These proteomic profiles identified functional differences between breast cancer subtypes, related to energy metabolism, cell growth, mRNA translation and cell-cell communication. Furthermore, we derived a 19-protein predictive signature, which discriminates between the breast cancer subtypes, through Support Vector Machine (SVM)-based classification and feature selection. The deep proteome profiles also revealed novel features of breast cancer subtypes, which may be the basis for future development of subtype specific therapeutics.
HostingRepository	PRIDE
AnnounceDate	2016-01-05
AnnouncementXML	Submission_2016-01-05_06:52:30.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Stefka Tyanova
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2015-07-29 01:53:10	ID requested
⏵ 1	2016-01-05 06:52:31	announced

Tyanova S, Albrechtsen R, Kronqvist P, Cox J, Mann M, Geiger T, Proteomic maps of breast cancer subtypes. Nat Commun, 7():10259(2016) [pubmed]

curator keyword: Biomedical

submitter keyword: breast cancer subtypes, classification, shotgun proteomics

Tamar Geiger
contact affiliation	Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
contact email	geiger@tauex.tau.ac.il
lab head
Stefka Tyanova
contact affiliation	Max Planck Institute of Biochemistry
contact email	tyanova@biochem.mpg.de
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/2016/01/PXD002619

PRIDE project URI

• PRIDE
  1. PXD002619
     1. Label: PRIDE project
     2. Name: Proteomic maps of breast cancer subtypes