ArticleCell systems2023
A proteogenomics data-driven knowledge base of human cancer.
Article in Cell systems, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
41 citing papers in PubMed.
- Biomarker discovery and patient stratification in pancreatic cancer using incomplete multi-omics data.PLoS computational biology · 2026Article
- Mutant TP53 hijacks RNA-splicing factor RBM28 to suppress double-stranded RNA triggered antitumor immunity.Nature communications · 2026Article
- Insulin receptor substrate 2 (IRS2) confers resistance to PI3K pathway inhibition in PIK3CA mutant breast cancer.The Journal of biological chemistry · 2026Article
- Bimodality in pan-cancer proteomics reveals new opportunities for biomarker discovery.Genome biology · 2026Article
- New biological insights into osteosarcoma-lessons from single cell sequencing studies.Cancer metastasis reviews · 2026Review
- Tumor Electric Field Therapy Inhibits Epithelial-Mesenchymal Transition, Invasion, and Migration of Glioblastoma by Targeting the c-FOS/CXCL14 Axis.CNS neuroscience & therapeutics · 2026Article
- Targeting Prolyl 3-hydroxylase 1 inhibits pancreatic cancer progression and macrophage immunity.Nature communications · 2026Article
- Comprehensive bioinformatic analysis reveals TRPM4 as a biomarker for pan-cancer progression and macrophage infiltration.Discover oncology · 2026Article
- NetG2P: Network-based genotype-to-phenotype transformation identifies key signaling crosstalk for prognosis in pan-cancer study.BMC biology · 2026Article
- Aberrant methylation limits antitumoral inflammation in lung adenocarcinoma by restricting RIPK3 expression.Science advances · 2026Article
- A data-driven pan-cancer proteogenomic analysis reveals the characteristics of human cancer protein expression.iScience · 2026Article
- Surface Marker Identification to Capture Live Circulating Tumor Cells in Metastatic Triple-Negative Breast Cancer.Cancer research communications · 2026Article
- Targeting IL-1α Sensitizes HNSCC to PDT by Reversing Hypoxia and NF-κB-Driven Oxidative Stress Resistance.International journal of biological sciences · 2026Article
- Integrative proteomics reveals MSH6 to modulate PARP inhibitor sensitivity in BRCA1/2-proficient ovarian cancer.PloS one · 2026Article
- KDM6A phosphorylation suppresses PER2 to confer a glycolytic vulnerability in HNSCC.Cell death & disease · 2025Article
- Glycoprotein-Notebook: A Pan-Cancer Glycoproteomic Database and Toolkit for Analysis of Protein Glycosylation Changes Associated With Cancer Phenotypes.Molecular & cellular proteomics : MCP · 2025Article
- Characterization of WAC interactions with R2TP and TTT chaperone complexes linking glucose and glutamine availability to mTORC1 activity.FEBS open bio · 2025Article
- RANBP9 and RANBP10 cooperate in regulating non-small cell lung cancer proliferation.Journal of experimental & clinical cancer research : CR · 2025Article
- SCAN-ACT: adoptive T cell therapy target discovery through single-cell transcriptomics.Genome medicine · 2025Article
- Mesothelin-Associated Anti-Senescence Through P53 in Pancreatic Ductal Adenocarcinoma.Cancers · 2025Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.