ArticleNature methods2015
Pathway and network analysis of cancer genomes.
Article in Nature methods, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 186 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
186 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Role of innate immunity-triggered pathways in the pathogenesis of Sickle Cell Disease: a meta-analysis of gene expression studies.Scientific reports · 2015Pooled it
- Employing a systematic approach to biobanking and analyzing clinical and genetic data for advancing COVID-19 research.European journal of human genetics : EJHG · 2021Trial
- Exploratory Application of Neuropharmacometabolomics in Severe Childhood Traumatic Brain Injury.Critical care medicine · 2018Trial
- Functional Depth Biomarkers Distinguish Lung Squamous Cell Carcinoma from Lung Adenocarcinoma.Research square · 2026Article
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- Advancing target discovery through disease-specific integration of multi-modal target identification models and comprehensive benchmarking system.Scientific reports · 2026Article
- DNV-TC: a developmental network vulnerability-based classification system for precision oncology.Frontiers in cell and developmental biology · 2026Article
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- In Silico Analysis of Squamous Cell Carcinoma.Advances in experimental medicine and biology · 2026Review
- Gene set optimization for cancer transcriptomics using sparse principal component analysis.bioRxiv : the preprint server for biology · 2025Article
- GSNCASCR: An R Package to Identify Differentially Co-Expressed Curated Gene Sets with Single-Cell RNA-Seq Data.International journal of molecular sciences · 2025Article
- Network-based multi-omics integrative analysis methods in drug discovery: a systematic review.BioData mining · 2025Review
- Article
- Multidimensional analyses identify genes of high priority for pancreatic cancer research.JCI insight · 2025Article
- Single-cell omics: experimental workflow, data analyses and applications.Science China. Life sciences · 2025Review
- Proteomics appending a complementary dimension to precision oncotherapy.Computational and structural biotechnology journal · 2024Review
- The network structural entropy for single-cell RNA sequencing data during skin aging.Briefings in bioinformatics · 2024Article
- A Comprehensive Review of Bioinformatics Tools for Genomic Biomarker Discovery Driving Precision Oncology.Genes · 2024Review
- 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
126 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
21 authors.
Funding
Abstract
Genomic information on tumors from 50 cancer types cataloged by the International Cancer Genome Consortium (ICGC) shows that only a few well-studied driver genes are frequently mutated, in contrast to many infrequently mutated genes that may also contribute to tumor biology. Hence there has been large interest in developing pathway and network analysis methods that group genes and illuminate the processes involved. We provide an overview of these analysis techniques and show where they guide mechanistic and translational investigations.
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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.