PXD005235-1

PXD005235 is an original dataset announced via ProteomeXchange.

Title	Genomic determinants of protein abundance variation in colorectal cancer cell lines
Description	Understanding the extent to which genomic alterations compromise the integrity of the proteome is fundamental in identifying the mechanisms that shape cancer heterogeneity. We have used quantitative mass spectrometry to characterize the proteomes and phosphoproteomes of 50 colorectal cancer cell lines that serve as a model of variable tumour clonal expansions. We have used the variation in abundance between 12k proteins and 27k phosphosites to classify the cell lines into subgroups that show distinct yet overlapping organisation with other genomic classifiers. Tightly organised protein co-variation networks deconvoluted the complexity of the molecular landscapes, revealed the proteome-wide interdependencies of biological processes and identified collateral effects of mutations on protein complexes. Proteomic analysis of human iPS cells engineered with gene knockouts confirms the transmission of co-variation as a characteristic of protein interactions and exposes that stoichiometry is tightly regulated at the protein level. Proteomics, genomics and gene expression models all appeared to be largely mutually exclusive in predicting drug responses for 265 compounds further highlighting the utility of proteomics. Overall, we provide a deep integrative view of the molecular structure underlying the variation of colorectal cancer cells.
HostingRepository	PRIDE
AnnounceDate	2017-08-09
AnnouncementXML	Submission_2017-08-09_09:31:13.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	James Wright
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2016-10-28 02:20:53	ID requested
⏵ 1	2017-08-09 09:31:14	announced
2	2017-08-10 00:30:40	announced	Updated project metadata.
3	2017-09-01 06:22:39	announced	Updated project metadata.
4	2024-10-22 04:33:51	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

curator keyword: Biomedical

submitter keyword: TMT, Cancer, Cell Lines, IMAC, CRISPR, Colon

Jyoti Choudhary
contact affiliation	Wellcome Trust Sanger Institute
contact email	jc4@sanger.ac.uk
lab head
James Wright
contact affiliation	Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute
contact email	jw13@sanger.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/2017/08/PXD005235

PRIDE project URI

• PRIDE
  1. PXD005235
     1. Label: PRIDE project
     2. Name: Genomic determinants of protein abundance variation in colorectal cancer cell lines