ArticleNature communications2020
Pathway and network analysis of more than 2500 whole cancer genomes.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 62 papers, 1 of them a synthesis 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
62 citing papers in PubMed, 1 synthesis or guideline pooled it, 113 citations in OpenAlex.
- Gene expression signatures of response to fluoxetine treatment: systematic review and meta-analyses.Molecular psychiatry · 2025Pooled it
- The molecular heterogeneity and clinical impact of genomic driver alterations in prostate cancer.Nature communications · 2026Article
- Identifying multigenic modules under selection in the tumor genome.Bioinformatics (Oxford, England) · 2026Article
- Review
- Hemizygous loss of helicases promotes genomic instability and cancer development.Science advances · 2026Article
- Multimodal artificial intelligence and machine learning in oncology: from data integration to precision cancer care.Frontiers in digital health · 2026Review
- Distinct cerebrospinal fluid proteomic signatures define clinicopathological subtypes of sporadic Creutzfeldt-Jakob disease and predict patient survival.Acta neuropathologica communications · 2025Article
- Clinical Implementation of Matched Tumor/Germline Sequencing Improves Accuracy of Tumor Genomic Profiling and Therapeutic Recommendations.The Journal of molecular diagnostics : JMD · 2025Article
- DGHNN: a deep graph and hypergraph neural network for pan-cancer related gene prediction.Bioinformatics (Oxford, England) · 2025Article
- Elucidating the role of artificial intelligence in drug development from the perspective of drug-target interactions.Journal of pharmaceutical analysis · 2025Review
- ctDNA-based liquid biopsy reveals wider mutational profile with therapy resistance and metastasis susceptibility signatures in early-stage breast cancer patients.The journal of liquid biopsy · 2025Article
- Decoding the functional impact of the cancer genome through protein-protein interactions.Nature reviews. Cancer · 2025Review
- Reproducible processing of TCGA regulatory networks.GigaScience · 2025Article
- A comprehensive benchmark study of methods for identifying significantly perturbed subnetworks in cancer.Briefings in bioinformatics · 2024Article
- Anticancer Target Combinations: Network-Informed Signaling-Based Approach to Discovery.bioRxiv : the preprint server for biology · 2024Article
- Death-associated protein kinase 3 modulates migration and invasion of triple-negative breast cancer cells.PNAS nexus · 2024Article
- Mapping the Multiscale Proteomic Organization of Cellular and Disease Phenotypes.Annual review of biomedical data science · 2024Review
- Identifying new cancer genes based on the integration of annotated gene sets via hypergraph neural networks.Bioinformatics (Oxford, England) · 2024Article
- All paths lead to hubs in the spectroscopic networks of water isotopologues HCommunications chemistry · 2024Article
- Network analysis of driver genes in human cancers.Frontiers in bioinformatics · 2024Article
2 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
28 authors at 20 institutions in 36 countries.
Funding
Abstract
The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancer across 38 tumor types, we perform multi-faceted pathway and network analyses of non-coding mutations across 2583 whole cancer genomes from 27 tumor types compiled by the ICGC/TCGA PCAWG project that was motivated by the success of pathway and network analyses in prioritizing rare mutations in protein-coding genes. While few non-coding genomic elements are recurrently mutated in this cohort, we identify 93 genes harboring non-coding mutations that cluster into several modules of interacting proteins. Among these are promoter mutations associated with reduced mRNA expression in TP53, TLE4, and TCF4. We find that biological processes had variable proportions of coding and non-coding mutations, with chromatin remodeling and proliferation pathways altered primarily by coding mutations, while developmental pathways, including Wnt and Notch, altered by both coding and non-coding mutations. RNA splicing is primarily altered by non-coding mutations in this cohort, and samples containing non-coding mutations in well-known RNA splicing factors exhibit similar gene expression signatures as samples with coding mutations in these genes. These analyses contribute a new repertoire of possible cancer genes and mechanisms that are altered by non-coding mutations and offer insights into additional cancer vulnerabilities that can be investigated for potential therapeutic treatments.
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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.