PXD005235

PXD005235 is an original dataset announced via ProteomeXchange.

Title	Genomic determinants of protein abundance variation in colorectal cancer cell lines
Description	Assessing the impact of genomic alterations on protein networks is fundamental in identifying the mechanisms that shape cancer heterogeneity. We have used isobaric labelling to characterize the proteomic landscapes of 50 colorectal cancer cell lines and to decipher the functional consequences of somatic genomic variants. The robust quantification of over 9,000 proteins and 11,000 phosphopeptides on average, enabled the de novo construction of a functional protein correlation network which ultimately exposed the collateral effects of mutations on protein complexes. CRISPR-cas9 deletion of key chromatin modifiers confirmed that the consequences of genomic alterations can propagate through protein interactions in a transcript-independent manner. Lastly, we leveraged the quantified proteome to perform unsupervised classification of the cell lines and to build predictive models of drug response in colorectal cancer. Overall, we provide a deep integrative view of the functional network and the molecular structure underlying the heterogeneity of colorectal cancer cells.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:33:43.183.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; iodoacetamide derivatized residue; deamidated 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.

10.1016/j.celrep.2017.08.010;

Roumeliotis TI, Williams SP, Gon, ç, alves E, Alsinet C, Del Castillo Velasco-Herrera M, Aben N, Ghavidel FZ, Michaut M, Schubert M, Price S, Wright JC, Yu L, Yang M, Dienstmann R, Guinney J, Beltrao P, Brazma A, Pardo M, Stegle O, Adams DJ, Wessels L, Saez-Rodriguez J, McDermott U, Choudhary JS, Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells. Cell Rep, 20(9):2201-2214(2017) [pubmed]

curator keyword: Biomedical

submitter keyword: networks, TMT,Proteomics, protein complexes, CRISPR/cas9, phosphorylation, cell lines, drug response, mutations, colorectal cancer

Jyoti Choudhary
contact affiliation	Wellcome Trust Sanger Institute
contact email	jc4@sanger.ac.uk
lab head
James Wright
contact affiliation	Functional Proteomics, Institute Cancer Research & 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