ArticleNucleic acids research2010
Rank-rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 312 papers, 4 of them syntheses that pooled it.
What it found
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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.
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Who cites it
312 citing papers in PubMed, 4 syntheses or guidelines pooled it, 500 citations in OpenAlex.
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- A systematic review and meta-analysis on the transcriptomic signatures in alcohol use disorder.Molecular psychiatry · 2025Pooled it
- Alzheimer's disease large-scale gene expression portrait identifies exercise as the top theoretical treatment.Scientific reports · 2022Pooled it
- Genetic factors influencing a neurobiological substrate for psychiatric disorders.Translational psychiatry · 2021Pooled it
- Transcriptomic signatures of treatment response to the combination of escitalopram and memantine or placebo in late-life depression.Molecular psychiatry · 2021Trial
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- Neuronal activity-driven 3D chromatin dynamics in cortical pyramidal neurons depend on SATB2.Nucleic acids research · 2026Article
- Differential immune- and apoptosis-related gene signatures in pancreatic alpha and beta cells contribute to their fate in type 1 diabetes.Cell death and differentiation · 2026Article
- Hematopoietic stem cell aging: a review of transcriptional and multi-omics insights and potential paths for AI integration.Experimental & molecular medicine · 2026Review
- Electric Field-Induced Release and Measurement Liquid Biopsy of Urinary Transcriptomics and Key Proteins from Normal and High-risk Pregnant Women.Reproductive sciences (Thousand Oaks, Calif.) · 2026Article
- Sex-Specific Hippocampal Phosphoproteomic Features Associated with Stress-Induced Phenotypes in Mice Exposed to Chronic Restraint Stress.Neurochemical research · 2026Article
- RepurNet: A network medicine framework for systematic drug repurposing and disease vulnerability discovery.iScience · 2026Article
- Impact of sex chromosomes and gonad type in stress susceptibility in corticostriatal brain regions.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Integrating genetically predicted transcriptomic signatures with longitudinal real-world data enables scalable drug repurposing for Alzheimer's disease.Research square · 2026Article
- Slow RNAPII elongation enhances naive pluripotency rewiring while maintaining high replication fork speed.Science advances · 2026Article
252 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
Comparing independent high-throughput gene-expression experiments can generate hypotheses about which gene-expression programs are shared between particular biological processes. Current techniques to compare expression profiles typically involve choosing a fixed differential expression threshold to summarize results, potentially reducing sensitivity to small but concordant changes. We present a threshold-free algorithm called Rank-rank Hypergeometric Overlap (RRHO). This algorithm steps through two gene lists ranked by the degree of differential expression observed in two profiling experiments, successively measuring the statistical significance of the number of overlapping genes. The output is a graphical map that shows the strength, pattern and bounds of correlation between two expression profiles. To demonstrate RRHO sensitivity and dynamic range, we identified shared expression networks in cancer microarray profiles driving tumor progression, stem cell properties and response to targeted kinase inhibition. We demonstrate how RRHO can be used to determine which model system or drug treatment best reflects a particular biological or disease response. The threshold-free and graphical aspects of RRHO complement other rank-based approaches such as Gene Set Enrichment Analysis (GSEA), for which RRHO is a 2D analog. Rank-rank overlap analysis is a sensitive, robust and web-accessible method for detecting and visualizing overlap trends between two complete, continuous gene-expression profiles. A web-based implementation of RRHO can be accessed at http://systems.crump.ucla.edu/rankrank/.
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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.