ArticleNucleic acids research2013
Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 161 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
161 citing papers in PubMed, 1 synthesis or guideline pooled it, 304 citations in OpenAlex.
- Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE).PLoS computational biology · 2019Pooled it
- A Phase I/II Study of Ibrutinib Plus Trastuzumab in HER2-Positive Metastatic Breast Cancer.Cancer medicine · 2026Trial
- Myeloablation Followed by Hematopoietic Stem Cell Transplantation and Long-Term Normalization of Systemic Sclerosis Molecular Signatures.Arthritis & rheumatology (Hoboken, N.J.) · 2024Trial
- Non-viral, specifically targeted CAR-T cells achieve high safety and efficacy in B-NHL.Nature · 2022Trial
- Molecular determinants of response to PD-L1 blockade across tumor types.Nature communications · 2021Trial
- In vitro responses to platelet-rich-plasma are associated with variable clinical outcomes in patients with knee osteoarthritis.Scientific reports · 2021Trial
- Lithium-responsive genes and gene networks in bipolar disorder patient-derived lymphoblastoid cell lines.The pharmacogenomics journal · 2016Trial
- The administration of intranasal live attenuated influenza vaccine induces changes in the nasal microbiota and nasal epithelium gene expression profiles.Microbiome · 2015Trial
- DLL3 serves as a pivotal hub bridging malignant progression and immunosuppression in NECC with therapeutic implications validated via the organoid-TIL co-culture system.Genes & diseases · 2026Article
- Lactobacillus salivarius potentiates gastrointestinal cancer immunotherapy through its metabolite chenodeoxycholic acid.Cell reports. Medicine · 2026Article
- CD9Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Automated measurement of CD8+ T-cell distribution at the tumor epithelial-stromal interface is associated with NSCLC immunotherapy benefit and transcriptomic pathways.Journal of pathology informatics · 2026Article
- Inflammatory biomarkers of asymptomatic and symptomatic tuberculosis.Nature communications · 2026Article
- Single-cell and spatial transcriptomes reveal oligodendrocyte remodeling fatty acid metabolism microenvironment of lung cancer brain metastases.Journal of translational medicine · 2026Article
- Article
- Therapeutic strategy for cervical gastric-type adenocarcinoma by targeting CLU to relieve CLU-associated stress and sensitize chemotherapy.Precision clinical medicine · 2026Article
- Decoding adipocyte heterogeneity through single-nucleus transcriptomics unveils subtype-specific adipocytes orchestrate immunosuppressive niches in breast cancer.Journal for immunotherapy of cancer · 2026Article
- Distinct diversity of skin cell populations of rhinophyma and hypertrophic scar illustrated by scRNA-seq.Frontiers in immunology · 2026Article
- Single-Cell Sequencing Reveals the Immunosuppressive Trajectory in the Tumor Microenvironment of Human Giant Cell Tumor of Bone.BioMed research international · 2026Article
- Single-cell multi-omic landscape reveals anatomical-specific immune features in adult and pediatric sepsis.Nature immunology · 2026Article
101 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
4 authors at 1 institution in 1 country.
Funding
Abstract
Enrichment analysis of gene sets is a popular approach that provides a functional interpretation of genome-wide expression data. Existing tests are affected by inter-gene correlations, resulting in a high Type I error. The most widely used test, Gene Set Enrichment Analysis, relies on computationally intensive permutations of sample labels to generate a null distribution that preserves gene-gene correlations. A more recent approach, CAMERA, attempts to correct for these correlations by estimating a variance inflation factor directly from the data. Although these methods generate P-values for detecting gene set activity, they are unable to produce confidence intervals or allow for post hoc comparisons. We have developed a new computational framework for Quantitative Set Analysis of Gene Expression (QuSAGE). QuSAGE accounts for inter-gene correlations, improves the estimation of the variance inflation factor and, rather than evaluating the deviation from a null hypothesis with a P-value, it quantifies gene-set activity with a complete probability density function. From this probability density function, P-values and confidence intervals can be extracted and post hoc analysis can be carried out while maintaining statistical traceability. Compared with Gene Set Enrichment Analysis and CAMERA, QuSAGE exhibits better sensitivity and specificity on real data profiling the response to interferon therapy (in chronic Hepatitis C virus patients) and Influenza A virus infection. QuSAGE is available as an R package, which includes the core functions for the method as well as functions to plot and visualize the results.
Indexed as
Identifiers
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.