ArticleGenome research2021
Effects of transcriptional noise on estimates of gene and transcript expression in RNA sequencing experiments.
Article in Genome research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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Who cites it
21 citing papers in PubMed, 48 citations in OpenAlex.
- Bramble: projection of spliced genomic alignments into transcriptomic space for improved transcript quantification.bioRxiv : the preprint server for biology · 2026Article
- The minor spliceosome component U4atac regulates JAK/STAT signaling to modulate hematopoiesis and immune responses in Drosophila melanogaster.Nature communications · 2026Article
- Uncovering the isoform-resolution kinetic landscape of nonsense-mediated mRNA decay with EZbakR.Genome biology · 2026Article
- Disease-associated genetic variants can cause missense effects in tissue-specific protein isoforms.Nature communications · 2026Article
- Harnessing transcriptomics for discovery of natural products to overcome acquired cancer resistance.Archives of pharmacal research · 2026Review
- MemorySeq identifies heritable epigenetic phenotypes that initiate cell culture stress tolerance in CHO cells.iScience · 2025Article
- Comprehensive Transcriptome Annotation of Thousands of HIV-1 Genomes.bioRxiv : the preprint server for biology · 2025Article
- Large-scale transcriptomic analyses of major depressive disorder reveal convergent dysregulation of synaptic pathways in excitatory neurons.Nature communications · 2025Article
- Sex-biased gene expression precedes sexual dimorphism in the agonadal annelid Platynereis dumerilii.Development (Cambridge, England) · 2025Article
- Splam: a deep-learning-based splice site predictor that improves spliced alignments.Genome biology · 2024Article
- Sex-biased gene expression precedes sexual dimorphism in the agonadal annelidbioRxiv : the preprint server for biology · 2024Article
- The impact of package selection and versioning on single-cell RNA-seq analysis.bioRxiv : the preprint server for biology · 2024Article
- Detecting differential transcript usage in complex diseases with SPIT.Cell reports methods · 2024Article
- Critical Differential Expression Assessment for Individual Bulk RNA-Seq Projects.bioRxiv : the preprint server for biology · 2024Article
- Transcriptomics analysis reveals potential mechanisms underlying mitochondrial dysfunction and T cell exhaustion in astronauts' blood cells in space.Frontiers in immunology · 2024Article
- CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure.Genome biology · 2023Article
- Investigating Open Reading Frames in Known and Novel Transcripts using ORFanage.Nature computational science · 2023Article
- Splam: a deep-learning-based splice site predictor that improves spliced alignments.bioRxiv : the preprint server for biology · 2023Article
- Detecting differential transcript usage in complex diseases with SPIT.bioRxiv : the preprint server for biology · 2023Article
- Investigating Open Reading Frames in Known and Novel Transcripts using ORFanage.bioRxiv : the preprint server for biology · 2023Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
RNA sequencing is widely used to measure gene expression across a vast range of animal and plant tissues and conditions. Most studies of computational methods for gene expression analysis use simulated data to evaluate the accuracy of these methods. These simulations typically include reads generated from known genes at varying levels of expression. Until now, simulations did not include reads from noisy transcripts, which might include erroneous transcription, erroneous splicing, and other processes that affect transcription in living cells. Here we examine the effects of realistic amounts of transcriptional noise on the ability of leading computational methods to assemble and quantify the genes and transcripts in an RNA sequencing experiment. We show that the inclusion of noise leads to systematic errors in the ability of these programs to measure expression, including systematic underestimates of transcript abundance levels and large increases in the number of false-positive genes and transcripts. Our results also suggest that alignment-free computational methods sometimes fail to detect transcripts expressed at relatively low levels.
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.