PXD006449

PXD006449 is an original dataset announced via ProteomeXchange.

Title	A systematic multi-omics investigation of breast cancer metabolism mapping its tiered regulation
Description	Altered metabolism is a hallmark of cancer, but little is still known about its regulation. Here we measure transcriptomic, proteomic, phospho-proteomic and fluxomics data in a breast cancer cell-line across three different conditions. Integrating these multiomics data within a genome scale human metabolic model in combination with machine learning we systematically chart the different layers of metabolic regulation in breast cancer, predicting which enzymes and pathways are regulated at which level. We distinguish between two types of reactions, directly or indirectly regulated. Directly-regulated reactions include those whose flux is regulated by transcriptomic alterations (~890) or via proteomic or phospho-proteomics alterations (~140) in the enzymes catalyzing them. Indirectly regulated reactions are those that currently lack evidence for direct regulation in our measurements or predictions (~930). Remarkably, we find that the flux of indirectly regulated reactions is strongly coupled to the flux of the directly regulated ones, uncovering a hierarchical organization of breast cancer metabolism. Furthermore, the predicted indirectly regulated reactions are predominantly bi-directional. Taken together, this architecture may facilitate the formation of stochiometrically consistent flux distributions in response to the varying environmental conditions incurred by the tumor cells. The approach presented lays a conceptual and computational basis for a more complete mapping of metabolic regulation in different cancers with incoming additional data.
HostingRepository	PRIDE
AnnounceDate	2020-05-26
AnnouncementXML	Submission_2020-05-26_11:14:58.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	phosphorylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-05-04 02:36:37	ID requested
⏵ 1	2020-05-26 11:15:00	announced

Katzir R, Polat IH, Harel M, Katz S, Foguet C, Selivanov VA, Sabatier P, Cascante M, Geiger T, Ruppin E, The landscape of tiered regulation of breast cancer cell metabolism. Sci Rep, 9(1):17760(2019) [pubmed]

curator keyword: Biomedical

submitter keyword: phosphoproteomics, proteomics, breast cancer, metabolomics, metabolic modeling

Tamar Geiger
contact affiliation	Sackler Faculty of Medicine, Tel Aviv University
contact email	geiger@tauex.tau.ac.il
lab head
Tamar Geiger
contact affiliation	Tel Aviv University
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/2020/05/PXD006449

PRIDE project URI

• PRIDE
  1. PXD006449
     1. Label: PRIDE project
     2. Name: A systematic multi-omics investigation of breast cancer metabolism mapping its tiered regulation