ArticleBMC medical genomics2017
N-of-1-pathways MixEnrich: advancing precision medicine via single-subject analysis in discovering dynamic changes of transcriptomes.
Article in BMC medical genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Functional Depth Biomarkers Distinguish Lung Squamous Cell Carcinoma from Lung Adenocarcinoma.Research square · 2026Article
- Enhancing validation of case-control omics signatures through "minimalist" single-subject analysis (N-of-1 trials): proof of concept in sepsis.Journal of the American Medical Informatics Association : JAMIA · 2026Article
- Paired-Sample and Pathway-Anchored MLOps Framework for Robust Transcriptomic Machine Learning in Small Cohorts: Model Classification Study.JMIR bioinformatics and biotechnology · 2025Article
- Multiomics Analysis of Plasma Proteomics and Metabolomics of Steroid Resistance in Childhood Nephrotic Syndrome Using a "Patient-Specific" Approach.Kidney international reports · 2023Article
- Patient-level proteomic network prediction by explainable artificial intelligence.NPJ precision oncology · 2022Article
- 'Single-subject studies'-derived analyses unveil altered biomechanisms between very small cohorts: implications for rare diseases.Bioinformatics (Oxford, England) · 2021Article
- Personalized beyond Precision: Designing Unbiased Gold Standards to Improve Single-Subject Studies of Personal Genome Dynamics from Gene Products.Journal of personalized medicine · 2020Article
- Case report: 16-yr life history and genomic evolution of an ERCold Spring Harbor molecular case studies · 2020Article
- Autologous micrograft accelerates endogenous wound healing response through ERK-induced cell migration.Cell death and differentiation · 2020Article
- Causal network perturbations for instance-specific analysis of single cell and disease samples.Bioinformatics (Oxford, England) · 2020Article
- RNA-seq Profiling Showed Divergent Carbohydrate-Active Enzymes (CAZymes) Expression Patterns inFrontiers in microbiology · 2020Article
- Evaluating single-subject study methods for personal transcriptomic interpretations to advance precision medicine.BMC medical genomics · 2019Article
- Developing a 'personalome' for precision medicine: emerging methods that compute interpretable effect sizes from single-subject transcriptomes.Briefings in bioinformatics · 2019Review
- A Single-Subject Method to Detect Pathways Enriched With Alternatively Spliced Genes.Frontiers in genetics · 2019Article
- Interpretation of 'Omics dynamics in a single subject using local estimates of dispersion between two transcriptomes.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2019Article
- The Emerging Potential for Network Analysis to Inform Precision Cancer Medicine.Journal of molecular biology · 2018Review
- Emergence of pathway-level composite biomarkers from converging gene set signals of heterogeneous transcriptomic responses.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2018Article
- PRECISION MEDICINE: FROM DIPLOTYPES TO DISPARITIES TOWARDS IMPROVED HEALTH AND THERAPIES.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2018Article
- Single subject transcriptome analysis to identify functionally signed gene set or pathway activity.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2018Article
- Evolution of Translational Bioinformatics: lessons learned from TBC 2016.BMC medical genomics · 2017Article
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Authors and funding
9 authors.
Funding
Abstract
backgroundTranscriptome analytic tools are commonly used across patient cohorts to develop drugs and predict clinical outcomes. However, as precision medicine pursues more accurate and individualized treatment decisions, these methods are not designed to address single-patient transcriptome analyses. We previously developed and validated the N-of-1-pathways framework using two methods, Wilcoxon and Mahalanobis Distance (MD), for personal transcriptome analysis derived from a pair of samples of a single patient. Although, both methods uncover concordantly dysregulated pathways, they are not designed to detect dysregulated pathways with up- and down-regulated genes (bidirectional dysregulation) that are ubiquitous in biological systems.
resultsWe developed N-of-1-pathways MixEnrich, a mixture model followed by a gene set enrichment test, to uncover bidirectional and concordantly dysregulated pathways one patient at a time. We assess its accuracy in a comprehensive simulation study and in a RNA-Seq data analysis of head and neck squamous cell carcinomas (HNSCCs). In presence of bidirectionally dysregulated genes in the pathway or in presence of high background noise, MixEnrich substantially outperforms previous single-subject transcriptome analysis methods, both in the simulation study and the HNSCCs data analysis (ROC Curves; higher true positive rates; lower false positive rates). Bidirectional and concordant dysregulated pathways uncovered by MixEnrich in each patient largely overlapped with the quasi-gold standard compared to other single-subject and cohort-based transcriptome analyses.
conclusionThe greater performance of MixEnrich presents an advantage over previous methods to meet the promise of providing accurate personal transcriptome analysis to support precision medicine at point of care.
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