ArticleNature2014
Proteogenomic characterization of human colon and rectal cancer.
Article in Nature, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 854 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
854 citing papers in PubMed, 2 syntheses or guidelines pooled it, 1,530 citations in OpenAlex.
- Prognostic significance of p27 in colorectal cancer: a meta-analysis and bioinformatics analysis.Frontiers in oncology · 2024Pooled it
- Integrated meta-analysis of colorectal cancer public proteomic datasets for biomarker discovery and validation.PLoS computational biology · 2024Pooled it
- Trial
- A Multi-Omic Mosaic Model of Acetaminophen Induced Alanine Aminotransferase Elevation.Journal of medical toxicology : official journal of the American College of Medical Toxicology · 2023Trial
- Pan-Cancer Quantification of Driver Alteration Transmission Across Molecular Layers Reveals Limited Propagation to Protein Abundance.International journal of cancer · 2026Article
- Integrating multi-omics data for next-generation cancer research and precision medicine.Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico · 2026Review
- Article
- Inhibitory receptor profiles for joint prediction of benefit and toxicity in immune checkpoint blockade.iScience · 2026Review
- Relating transcriptomics to protein abundance reveals self-driven versus interactor-driven proteins.Protein science : a publication of the Protein Society · 2026Article
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- Proteogenomics in human populations.Nature reviews. Genetics · 2026Review
- Article
- Protein Enrichment from Ascites Fluid Using Nanotrap Hydrogel Particle Technology.Journal of proteome research · 2026Article
- Development and validation of a stromal myeloid-fibrotic index and a tumor-intrinsic immune evasion index for molecular stratification in colorectal cancer.Functional & integrative genomics · 2026Article
- Bimodality in pan-cancer proteomics reveals new opportunities for biomarker discovery.Genome biology · 2026Article
- A Selective History of Protein Sequencing and the Impact of Donald F. Hunt on Protein Sequencing by Tandem Mass Spectrometry.Journal of proteome research · 2026Review
- Multi-Omics Biomarkers From Variant to Clinic: A Systematic Review and Meta-Analysis of Evidence, AI/ML, Governance, Equity, and Real-World Implementation Across Global Health Systems.Health science reports · 2026Review
- Proteogenomic features define subtypes of mantle cell lymphoma.Blood advances · 2026Article
- Multi Omics Integration in Colorectal Cancer: From Molecular Insights to Precision Oncology.Cancers · 2026Review
- Rethinking bioinformatics in liquid-liquid phase separation: data resources, predictive models, and an event-centric perspective.Briefings in bioinformatics · 2026Review
794 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
24 authors at 7 institutions in 2 countries.
Funding
Abstract
Extensive genomic characterization of human cancers presents the problem of inference from genomic abnormalities to cancer phenotypes. To address this problem, we analysed proteomes of colon and rectal tumours characterized previously by The Cancer Genome Atlas (TCGA) and perform integrated proteogenomic analyses. Somatic variants displayed reduced protein abundance compared to germline variants. Messenger RNA transcript abundance did not reliably predict protein abundance differences between tumours. Proteomics identified five proteomic subtypes in the TCGA cohort, two of which overlapped with the TCGA 'microsatellite instability/CpG island methylation phenotype' transcriptomic subtype, but had distinct mutation, methylation and protein expression patterns associated with different clinical outcomes. Although copy number alterations showed strong cis- and trans-effects on mRNA abundance, relatively few of these extend to the protein level. Thus, proteomics data enabled prioritization of candidate driver genes. The chromosome 20q amplicon was associated with the largest global changes at both mRNA and protein levels; proteomics data highlighted potential 20q candidates, including HNF4A (hepatocyte nuclear factor 4, alpha), TOMM34 (translocase of outer mitochondrial membrane 34) and SRC (SRC proto-oncogene, non-receptor tyrosine kinase). Integrated proteogenomic analysis provides functional context to interpret genomic abnormalities and affords a new paradigm for understanding cancer biology.
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What OpenQuestion holds
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.