ArticleBMC genomics2019
Linear models enable powerful differential activity analysis in massively parallel reporter assays.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers, 2 of them syntheses that pooled it.
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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
44 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Liver eQTL meta-analysis illuminates potential molecular mechanisms of cardiometabolic traits.American journal of human genetics · 2024Pooled it
- Common genetic risk variants identified in the SPARK cohort support DDHD2 as a candidate risk gene for autism.Translational psychiatry · 2020Pooled it
- Massively parallel assessment of gene regulatory activity at human cortical-structure-associated variants.Nature neuroscience · 2026Article
- Mapping and rewiring thebioRxiv : the preprint server for biology · 2026Article
- Uniform processing and analysis of IGVF massively parallel reporter assay data with MPRAsnakeflow.Genome research · 2026Article
- Dynamic neuro-immune regulation of psychiatric risk loci in human neurons.Nature communications · 2026Article
- Identifying severe COVID-19 risk variants modulating enhancer reporter activity in lung cells.PLoS genetics · 2026Article
- Mapping the gene regulatory landscape of archaic hominin introgression in modern Papuans.PLoS genetics · 2026Article
- keju: powerful and accurate inference in Massively Parallel Reporter Assays.bioRxiv : the preprint server for biology · 2026Article
- Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.Cell reports · 2026Article
- Designing synthetic regulatory elements using the generative AI framework DNA-Diffusion.Nature genetics · 2026Article
- Applications of high-throughput reporter assays to gene regulation studies.Current opinion in structural biology · 2025Review
- Uniform processing and analysis of IGVF massively parallel reporter assay data with MPRAsnakeflow.bioRxiv : the preprint server for biology · 2025Article
- Analysis of biased allelic enhancer activity of schizophrenia-linked common variants.Communications biology · 2025Article
- Single Antisense Oligonucleotides Correct Diverse Splicing Mutations in Hotspot Exons.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- A generalized and efficient approach for complete mRNA design improves translation, stability and specificity.bioRxiv : the preprint server for biology · 2025Article
- Article
- Precise measurement of molecular phenotypes with barcode-based CRISPRi systems.Genome biology · 2025Article
- Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity.Nature communications · 2025Article
- Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
backgroundMassively parallel reporter assays (MPRAs) have emerged as a popular means for understanding noncoding variation in a variety of conditions. While a large number of experiments have been described in the literature, analysis typically uses ad-hoc methods. There has been little attention to comparing performance of methods across datasets.
resultsWe present the mpralm method which we show is calibrated and powerful, by analyzing its performance on multiple MPRA datasets. We show that it outperforms existing statistical methods for analysis of this data type, in the first comprehensive evaluation of statistical methods on several datasets. We investigate theoretical and real-data properties of barcode summarization methods and show an unappreciated impact of summarization method for some datasets. Finally, we use our model to conduct a power analysis for this assay and show substantial improvements in power by performing up to 6 replicates per condition, whereas sequencing depth has smaller impact; we recommend to always use at least 4 replicates. An R package is available from the Bioconductor project.
conclusionsTogether, these results inform recommendations for differential analysis, general group comparisons, and power analysis and will help improve design and analysis of MPRA experiments.
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Registered trials
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