ArticleBiostatistics (Oxford, England)2014
Differential expression analysis of RNA-seq data at single-base resolution.
Article in Biostatistics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 36 papers.
What it found
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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.
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Who cites it
36 citing papers in PubMed.
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- A viral movement protein mediates host volatile biosynthesis to co-attract vectors and non-vectors and enhances viral infection.Frontiers in plant science · 2025Article
- Comparison of baseline global gene expression profiles of prostate cancer cell lines LNCaP and DU145.BMC research notes · 2024Article
- DiffSegR: an RNA-seq data driven method for differential expression analysis using changepoint detection.NAR genomics and bioinformatics · 2023Article
- Co-localization of clusters of TCR-regulated genes with TAD rearrangements.BMC genomics · 2023Article
- High throughput sequencing revealed enhanced cell cycle signaling in SLE patients.Scientific reports · 2023Article
- Exon-intron split analysis reveals posttranscriptional regulatory signals induced by high and low n-6/n-3 polyunsaturated fatty acid ratio diets in piglets.Journal of animal science · 2023Article
- CRISPR/Cas9-mediated gene editing ofFrontiers in plant science · 2023Article
- Transcriptome analysis of fasudil treatment in the APPswe/PSEN1dE9 transgenic (APP/PS1) mice model of Alzheimer's disease.Scientific reports · 2022Article
- An alternative splicing hypothesis for neuropathology of schizophrenia: evidence from studies on historical candidate genes and multi-omics data.Molecular psychiatry · 2022Review
- A Competitive Endogenous RNA Network Based on Differentially Expressed lncRNA in Lipopolysaccharide-Induced Acute Lung Injury in Mice.Frontiers in genetics · 2021Article
- Repeat RNAs associate with replication forks and post-replicative DNA.RNA (New York, N.Y.) · 2020Article
- Feasibility of primary human cell cultures as a model for adamantinomatous craniopharyngioma research: Evidence from RNA-Seq analysis.Oncology letters · 2020Article
- An NMF-based approach to discover overlooked differentially expressed gene regions from single-cell RNA-seq data.NAR genomics and bioinformatics · 2020Article
- How well do RNA-Seq differential gene expression tools perform in a complex eukaryote? A case study in Arabidopsis thaliana.Bioinformatics (Oxford, England) · 2019Article
- Article
- Improving the value of public RNA-seq expression data by phenotype prediction.Nucleic acids research · 2018Article
- DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition.Genome biology · 2017Article
Corrections and comments
- Erratum issued
Authors and funding
5 authors.
Funding
Abstract
RNA-sequencing (RNA-seq) is a flexible technology for measuring genome-wide expression that is rapidly replacing microarrays as costs become comparable. Current differential expression analysis methods for RNA-seq data fall into two broad classes: (1) methods that quantify expression within the boundaries of genes previously published in databases and (2) methods that attempt to reconstruct full length RNA transcripts. The first class cannot discover differential expression outside of previously known genes. While the second approach does possess discovery capabilities, statistical analysis of differential expression is complicated by the ambiguity and variability incurred while assembling transcripts and estimating their abundances. Here, we propose a novel method that first identifies differentially expressed regions (DERs) of interest by assessing differential expression at each base of the genome. The method then segments the genome into regions comprised of bases showing similar differential expression signal, and then assigns a measure of statistical significance to each region. Optionally, DERs can be annotated using a reference database of genomic features. We compare our approach with leading competitors from both current classes of differential expression methods and highlight the strengths and weaknesses of each. A software implementation of our method is available on github (https://github.com/alyssafrazee/derfinder).
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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.