ArticleMolecular systems biology2020
Predictive features of gene expression variation reveal mechanistic link with differential expression.
Article in Molecular systems biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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
44 citing papers in PubMed.
- Bacterial stress responses lower mRNA-protein level correlations.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Inter-individual gene expression variability implies stable regulation of brain-biased genes across organs in three ray-finned fishes.bioRxiv : the preprint server for biology · 2026Article
- Article
- Multimodal bioinformatic analyses of genome-scale expression beyond gene-centric differential expression.Briefings in bioinformatics · 2026Review
- Environmental perturbation increases gene expression variability and unmasks genetic regulation for transcriptional robustness.bioRxiv : the preprint server for biology · 2026Article
- Endogenous fine-mapping and prioritization of functional regulatory elements in complex genetic loci.Cell genomics · 2025Article
- The Genomic Kaleidoscope: On the Hidden Dimensions of Within-Species Genomic Diversity.Genome biology and evolution · 2025Review
- A transcriptional plasticity-aware framework for RNA-seq differential expression analysis.Briefings in bioinformatics · 2025Article
- Global chromatin reorganization and regulation of genes with specific evolutionary ages during differentiation and cancer.Nucleic acids research · 2025Article
- Optimal solution to the set cover problem with a vicinity constraint for estimating genotype tissue expression profiles.Bioinformatics advances · 2025Article
- Active enhancers: recent research advances and insights into disease.Biology direct · 2024Review
- Life history dynamics of evolving tumors: insights into task specialization, trade-offs, and tumor heterogeneity.Cancer cell international · 2024Review
- Evidence for compensatory evolution within pleiotropic regulatory elements.Genome research · 2024Article
- Global chromatin reorganization and regulation of genes with specific evolutionary ages during differentiation and cancer.bioRxiv : the preprint server for biology · 2024Article
- Robust and consistent biomarker candidates identification by a machine learning approach applied to pancreatic ductal adenocarcinoma metastasis.BMC medical informatics and decision making · 2024Article
- Comprehensive genomic features indicative for Notch responsiveness.Nucleic acids research · 2024Article
- Cis-regulatory control of transcriptional timing and noise in response to estrogen.Cell genomics · 2024Article
- Genetic, Environmental, and Stochastic Components of Lifespan Variability: TheInternational journal of molecular sciences · 2024Review
- Genetically encoded transcriptional plasticity underlies stress adaptation in Mycobacterium tuberculosis.Nature communications · 2024Article
- Article
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.
Funding
No grant is acknowledged in the PubMed record.
Abstract
For most biological processes, organisms must respond to extrinsic cues, while maintaining essential gene expression programmes. Although studied extensively in single cells, it is still unclear how variation is controlled in multicellular organisms. Here, we used a machine-learning approach to identify genomic features that are predictive of genes with high versus low variation in their expression across individuals, using bulk data to remove stochastic cell-to-cell variation. Using embryonic gene expression across 75 Drosophila isogenic lines, we identify features predictive of expression variation (controlling for expression level), many of which are promoter-related. Genes with low variation fall into two classes reflecting different mechanisms to maintain robust expression, while genes with high variation seem to lack both types of stabilizing mechanisms. Applying this framework to humans revealed similar predictive features, indicating that promoter architecture is an ancient mechanism to control expression variation. Remarkably, expression variation features could also partially predict differential expression after diverse perturbations in both Drosophila and humans. Differential gene expression signatures may therefore be partially explained by genetically encoded gene-specific features, unrelated to the studied treatment.
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.