ArticleBioinformatics (Oxford, England)2018
Hierarchical analysis of RNA-seq reads improves the accuracy of allele-specific expression.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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Who cites it
67 citing papers in PubMed.
- A panel of Diversity Outbred mouse embryonic stem cells: enabling the functional characterization of natural genetic variationbioRxiv : the preprint server for biology · 2026Article
- CellMAGE: cell-type deconvolution for multi-parent population analysis of gene expression.bioRxiv : the preprint server for biology · 2026Article
- The promise of long-read RNA-seq: reducing bias in analyses of allele imbalance.NAR genomics and bioinformatics · 2026Article
- Genomic diversification between aposematic and cryptic phenotypes of Oophaga granulifera (Anura: Dendrobatidae).Scientific reports · 2026Article
- Trans-regulation of heterochromatin underlies genetic variation in 3D genome contacts in mouse embryonic stem cells.Genome biology · 2026Article
- Multimodal analysis of molecular remodeling in aging spleen identified global and cell type specific changes.bioRxiv : the preprint server for biology · 2026Article
- Identification of blood-brain barrier injury-related biomarkers in cerebral infarction using transcriptomic analysis.Scientific reports · 2026Article
- scRepli-RamDA-seq: a multi-omics technology enabling the analysis of gene expression dynamics during S-phase.Nature communications · 2025Article
- Low-coverage whole-genome sequencing facilitates accurate and cost-effective haplotype reconstruction in complex mouse crosses.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- Gain of Alternative Allele Expression of LINC02449 at rs149707223 in Schizophrenia and Bipolar Disorder: Inducing Synaptic Transmission and Behavioral Deficits in Mice.Nature communications · 2025Article
- Genotype by Environment Interactions in Gene Regulation Underlie the Response to Soil Drying in the Model Grass Brachypodium distachyon.Molecular biology and evolution · 2025Article
- kMermaid: Ultrafast metagenomic read assignment to protein clusters by hashing of amino acid k-mer frequencies.PLoS computational biology · 2025Article
- The regulatory architecture of gene expression variation in Caenorhabditis elegans revealed by multi-strain allele-specific analysis.Genetics · 2025Article
- Systems genetics reveals the influence of expression QTLs in mouse embryonic stem cells on transcriptional variation later in differentiated neural progenitor cells.G3 (Bethesda, Md.) · 2025Article
- Anapc5 and Anapc7 as genetic modifiers of KIF18A function in fertility and mitotic progression.Scientific reports · 2025Article
- Transcripts with high distal heritability mediate genetic effects on complex metabolic traits.Nature communications · 2025Article
- The regulatory architecture of gene expression variation inbioRxiv : the preprint server for biology · 2025Article
- Mapping the genetic landscape establishing a tumor immune microenvironment favorable for anti-PD-1 response.Cell reports · 2025Article
- Cross cell-type systems genetics reveals the influence of eQTL at multiple points in the developmental trajectory of mouse neural progenitor cells.bioRxiv : the preprint server for biology · 2025Article
- CompMap: an allele-specific expression read counter based on competitive mapping.microPublication biology · 2025Article
7 more citing papers are in PubMed but not listed here.
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9 authors.
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Abstract
Motivation: Allele-specific expression (ASE) refers to the differential abundance of the allelic copies of a transcript. RNA sequencing (RNA-seq) can provide quantitative estimates of ASE for genes with transcribed polymorphisms. When short-read sequences are aligned to a diploid transcriptome, read-mapping ambiguities confound our ability to directly count reads. Multi-mapping reads aligning equally well to multiple genomic locations, isoforms or alleles can comprise the majority (>85%) of reads. Discarding them can result in biases and substantial loss of information. Methods have been developed that use weighted allocation of read counts but these methods treat the different types of multi-reads equivalently. We propose a hierarchical approach to allocation of read counts that first resolves ambiguities among genes, then among isoforms, and lastly between alleles. We have implemented our model in EMASE software (Expectation-Maximization for Allele Specific Expression) to estimate total gene expression, isoform usage and ASE based on this hierarchical allocation. Results: Methods that align RNA-seq reads to a diploid transcriptome incorporating known genetic variants improve estimates of ASE and total gene expression compared to methods that use reference genome alignments. Weighted allocation methods outperform methods that discard multi-reads. Hierarchical allocation of reads improves estimation of ASE even when data are simulated from a non-hierarchical model. Analysis of RNA-seq data from F1 hybrid mice using EMASE reveals widespread ASE associated with cis-acting polymorphisms and a small number of parent-of-origin effects. Availability and implementation: EMASE software is available at https://github.com/churchill-lab/emase. Supplementary information: Supplementary data are available at Bioinformatics online.
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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.