A proteogenomics data-driven knowledge base of human cancer.
CPTAC
cancer
data integration
knowledge base
multi-omics
pan-cancer
phosphoproteomics
proteogenomics
proteomics
visualization
Journal
Cell systems
ISSN: 2405-4720
Titre abrégé: Cell Syst
Pays: United States
ID NLM: 101656080
Informations de publication
Date de publication:
20 09 2023
20 09 2023
Historique:
received:
02
03
2023
revised:
11
05
2023
accepted:
25
07
2023
pmc-release:
20
09
2024
medline:
25
9
2023
pubmed:
25
8
2023
entrez:
24
8
2023
Statut:
ppublish
Résumé
By combining mass-spectrometry-based proteomics and phosphoproteomics with genomics, epi-genomics, and transcriptomics, proteogenomics provides comprehensive molecular characterization of cancer. Using this approach, the Clinical Proteomic Tumor Analysis Consortium (CPTAC) has characterized over 1,000 primary tumors spanning 10 cancer types, many with matched normal tissues. Here, we present LinkedOmicsKB, a proteogenomics data-driven knowledge base that makes consistently processed and systematically precomputed CPTAC pan-cancer proteogenomics data available to the public through ∼40,000 gene-, protein-, mutation-, and phenotype-centric web pages. Visualization techniques facilitate efficient exploration and reasoning of complex, interconnected data. Using three case studies, we illustrate the practical utility of LinkedOmicsKB in providing new insights into genes, phosphorylation sites, somatic mutations, and cancer phenotypes. With precomputed results of 19,701 coding genes, 125,969 phosphosites, and 256 genotypes and phenotypes, LinkedOmicsKB provides a comprehensive resource to accelerate proteogenomics data-driven discoveries to improve our understanding and treatment of human cancer. A record of this paper's transparent peer review process is included in the supplemental information.
Identifiants
pubmed: 37619559
pii: S2405-4712(23)00214-4
doi: 10.1016/j.cels.2023.07.007
pmc: PMC10530292
mid: NIHMS1922268
pii:
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
777-787.e5Subventions
Organisme : NCI NIH HHS
ID : R01 CA245903
Pays : United States
Organisme : NCI NIH HHS
ID : U01 CA271247
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA210954
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA271076
Pays : United States
Informations de copyright
Copyright © 2023 Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of interests B.Z. received consulting fees from AstraZeneca.
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