ArticleProceedings of the National Academy of Sciences of the United States of America2019
Predictability of human differential gene expression.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers, 3 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.
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.
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Who cites it
70 citing papers in PubMed, 3 syntheses or guidelines pooled it, 136 citations in OpenAlex.
- A Cross-Species and Sex-Specific Meta-Analysis of Transcriptomic Studies of Pulmonary Hypertension.American journal of respiratory cell and molecular biology · 2025Pooled it
- Differential and spatial expression meta-analysis of genes identified in genome-wide association studies of depression.Translational psychiatry · 2021Pooled it
- Pooled it
- Large-scale analysis of temporal gene expression variation in peripheral blood.Nature communications · 2026Article
- Biopsy and Blood Gene Expression Distinguish Injury, Subclinical and Clinical Rejection in Kidney Transplant Recipients.Transplantation direct · 2026Article
- Novel insights into post-myocardial infarction cardiac remodeling through algorithmic detection of cell-type composition shifts.PLoS genetics · 2025Article
- Differential gene expression study in whole blood identifies candidate genes for psychosis in African American individuals.Schizophrenia research · 2025Article
- Transcriptome-wide analysis of differential expression in perturbation atlases.Nature genetics · 2025Article
- From Endoscopic Inspection to Gene-Expression: A Thorough Assessment of the Duodenal Mucosa After Resurfacing-A Prospective Study.Digestive diseases and sciences · 2025Article
- Latent spaces for tumour transcriptomes.Nature biomedical engineering · 2025Article
- Resistance signatures manifested in early drug response across cancer types and species.Cancer drug resistance (Alhambra, Calif.) · 2025Article
- Protocol for identifying key genes using network-based approach as an alternative to differential expression analysis.STAR protocols · 2024Article
- Article
- Gene signatures for cancer research: A 25-year retrospective and future avenues.PLoS computational biology · 2024Article
- Transcriptome-wide characterization of genetic perturbations.bioRxiv : the preprint server for biology · 2024Article
- Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling.Nature biotechnology · 2024Article
- Clover: An unbiased method for prioritizing differentially expressed genes using a data-driven approach.Genes to cells : devoted to molecular & cellular mechanisms · 2024Article
- A protein sequence-based deep transfer learning framework for identifying human proteome-wide deubiquitinase-substrate interactions.Nature communications · 2024Article
- Network-based approach elucidates critical genes in BRCA subtypes and chemotherapy response in triple negative breast cancer.iScience · 2024Article
- Resource: A Curated Database of Brain-Related Functional Gene Sets (Brain.GMT).bioRxiv : the preprint server for biology · 2024Article
10 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
5 authors at 2 institutions in 2 countries.
Funding
Abstract
Differential expression (DE) is commonly used to explore molecular mechanisms of biological conditions. While many studies report significant results between their groups of interest, the degree to which results are specific to the question at hand is not generally assessed, potentially leading to inaccurate interpretation. This could be particularly problematic for metaanalysis where replicability across datasets is taken as strong evidence for the existence of a specific, biologically relevant signal, but which instead may arise from recurrence of generic processes. To address this, we developed an approach to predict DE based on an analysis of over 600 studies. A predictor based on empirical prior probability of DE performs very well at this task (mean area under the receiver operating characteristic curve, ∼0.8), indicating that a large fraction of DE hit lists are nonspecific. In contrast, predictors based on attributes such as gene function, mutation rates, or network features perform poorly. Genes associated with sex, the extracellular matrix, the immune system, and stress responses are prominent within the "DE prior." In a series of control studies, we show that these patterns reflect shared biology rather than technical artifacts or ascertainment biases. Finally, we demonstrate the application of the DE prior to data interpretation in three use cases: (
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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.