PXD000901

PXD000901 is an original dataset announced via ProteomeXchange.

Title	Phospho-networks in Ovarian Cancer Cell Lines
Description	Cancer cells acquire pathological phenotypes through accumulation of mutations that perturb signaling processes. While thousands of mutations have been identified, mostly by genome-wide sequencing, systematic interpretation of their role in cancer and impact on cellular information processing is presently missing. Here, we propose a computational approach (ReKINect) to identify mutations attacking signaling networks. We demonstrate six types of network-attacking mutations (NAMs) including changes in kinase modulation, network rewiring as well as the genesis and extinction of specific phosphorylation sites. Through global, quantitative analysis of the exomes and (phospho-)proteomes of five ovarian cancer cell lines we identify and validate numerous NAMs. Finally, we explore the entire cancer genome repertoire and predict hundreds of NAMs affecting kinase and SH2 driven signaling. Our approach is scalable with the complexity of cancer genomes and cell signaling, and can be readily applied in personalized precision medicine.
HostingRepository	PRIDE
AnnounceDate	2016-07-09
AnnouncementXML	Submission_2016-07-08_16:40:39.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Pau Creixell
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue; phosphorylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2014-04-14 04:39:59	ID requested
⏵ 1	2016-07-08 16:40:41	announced

Creixell P, Schoof EM, Simpson CD, Longden J, Miller CJ, Lou HJ, Perryman L, Cox TR, Zivanovic N, Palmeri A, Wesolowska-Andersen A, Helmer-Citterich M, Ferkinghoff-Borg J, Itamochi H, Bodenmiller B, Erler JT, Turk BE, Linding R, Kinome-wide decoding of network-attacking mutations rewiring cancer signaling. Cell, 163(1):202-17(2015) [pubmed]

curator keyword: Biomedical

submitter keyword: SILAC, Ovarian, Cancer, TiO2, Proteome, Phospho

Rune Linding
contact affiliation	Technical University of Denmark
contact email	linding@cbs.dtu.dk
lab head
Pau Creixell
contact affiliation	Technical University of Denmark (DTU)
contact email	creixell@cbs.dtu.dk
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/2016/07/PXD000901

PRIDE project URI

• PRIDE
  1. PXD000901
     1. Label: PRIDE project
     2. Name: Phospho-networks in Ovarian Cancer Cell Lines