PXD027329

PXD027329 is an original dataset announced via ProteomeXchange.

Title	Computational analysis of cholangiocarcinoma phosphoproteomes identifies patient-specific drug targets
Description	We used mass-spectrometry based phosphoproteomics and computational methods to identify patient-specific drug targets in primary CCA and CCA-derived cell lines. We analyzed 13 primary CCA with matched background tissue and 8 different cell lines leading to the identification and quantification of >13,000 phosphorylation sites. Application of the Drug Ranking Using Machine Learning (DRUML) algorithm identified inhibitors of HDAC and PI3K pathway members as highly ranking in primary CCA relative to background. The accuracy of drug rankings based on predicted responses was confirmed using cell line models of CCA. Together, our study uncovers frequently overactive biochemical pathways in primary CCA and provides a proof-of-concept of the use of machine learning for ranking drugs based on efficacy within individual patient tumors.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:39:56.270.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD027329
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Vinothini Rajeeve
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-07-15 09:28:43	ID requested
1	2023-03-11 01:13:34	announced
⏵ 2	2023-11-14 08:39:59	announced	2023-11-14: Updated project metadata.

Khorsandi SE, Dokal AD, Rajeeve V, Britton DJ, Illingworth MS, Heaton N, Cutillas PR, Computational Analysis of Cholangiocarcinoma Phosphoproteomes Identifies Patient-Specific Drug Targets. Cancer Res, 81(22):5765-5776(2021) [pubmed]

10.6019/PXD027329;

submitter keyword: Cholangiocarcinoma

Professor Pedro R Cutillas
contact affiliation	Pedro R. Cutillas Professor of Cell Signalling & Proteomics Centre for Genomics and Computational Biology Barts Cancer Institute Queen Mary, University of London John Vane Science Centre, Charterhouse Square, London EC1M 6BQ
contact email	p.cutillas@qmul.ac.uk
lab head
Vinothini Rajeeve
contact affiliation	Centre for Haemato Oncology
contact email	v.rajeeve@qmul.ac.uk
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/2023/03/PXD027329

PRIDE project URI

• PRIDE
  1. PXD027329
     1. Label: PRIDE project
     2. Name: Computational analysis of cholangiocarcinoma phosphoproteomes identifies patient-specific drug targets