ArticleGenome biology2015
Errors in RNA-Seq quantification affect genes of relevance to human disease.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 papers.
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Who cites it
100 citing papers in PubMed, 183 citations in OpenAlex.
- The promise of long-read RNA-seq: reducing bias in analyses of allele imbalance.NAR genomics and bioinformatics · 2026Article
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- A novel H2A-A127 variant is associated with human cancer and enhances tumor-related phenotypes inFrontiers in oncology · 2026Article
- A Human-specific Protein Regulated by Alternative Polyadenylation Shapes Uniqueness of Human Brain Development.Genomics, proteomics & bioinformatics · 2025Article
- Tree-based differential testing using inferential uncertainty for RNA-seq.Genome research · 2025Article
- Current Bioinformatics Tools in Precision Oncology.MedComm · 2025Review
- MapID-based quantitative mapping of chemical modifications and expression of human transfer RNA.Cell chemical biology · 2025Article
- All the sites we cannot see: Sources and mitigation of false negatives in RNA modification studies.Nature reviews. Molecular cell biology · 2025Review
- Tree-based differential testing using inferential uncertainty for RNA-Seq.bioRxiv : the preprint server for biology · 2025Article
- Batch correcting single-cell spatial transcriptomics count data with Crescendo improves visualization and detection of spatial gene patterns.Genome biology · 2025Article
- Molecular profiles of blood from numerous species that differ in sensitivity to acute inflammation.Molecular medicine (Cambridge, Mass.) · 2024Article
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- Comprehensive analysis identifies ubiquitin ligase FBXO42 as a tumor-promoting factor in neuroblastoma.Scientific reports · 2024Article
- Exploring the impact of primer length on efficient gene detection via high-throughput sequencing.Nature communications · 2024Article
- Spatially Exploring RNA Biology in Archival Formalin-Fixed Paraffin-Embedded Tissues.bioRxiv : the preprint server for biology · 2024Article
- Voltage-gated ion channels are expressed in the Malpighian tubules and anal papillae of the yellow fever mosquito (Aedes aegypti), and may regulate ion transport during salt and water imbalance.The Journal of experimental biology · 2024Article
- sRNAflow: A Tool for the Analysis of Small RNA-Seq Data.Non-coding RNA · 2024Article
- SAILoR: Structure-Aware Inference of Logic Rules.PloS one · 2024Article
40 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
backgroundRNA-Seq has emerged as the standard for measuring gene expression and is an important technique often used in studies of human disease. Gene expression quantification involves comparison of the sequenced reads to a known genomic or transcriptomic reference. The accuracy of that quantification relies on there being enough unique information in the reads to enable bioinformatics tools to accurately assign the reads to the correct gene.
resultsWe apply 12 common methods to estimate gene expression from RNA-Seq data and show that there are hundreds of genes whose expression is underestimated by one or more of those methods. Many of these genes have been implicated in human disease, and we describe their roles. We go on to propose a two-stage analysis of RNA-Seq data in which multi-mapped or ambiguous reads can instead be uniquely assigned to groups of genes. We apply this method to a recently published mouse cancer study, and demonstrate that we can extract relevant biological signal from data that would otherwise have been discarded.
conclusionsFor hundreds of genes in the human genome, RNA-Seq is unable to measure expression accurately. These genes are enriched for gene families, and many of them have been implicated in human disease. We show that it is possible to use data that may otherwise have been discarded to measure group-level expression, and that such data contains biologically relevant information.
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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.