ArticleGenome biology2018
Gene-level differential analysis at transcript-level resolution.
Article in Genome biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers, 2 of them syntheses that pooled it.
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
82 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Systematic Review and Meta-analysis of Peripheral Blood DNA Methylation Studies in Inflammatory Bowel Disease.Journal of Crohn's & colitis · 2023Pooled it
- Transcriptomic Landscape of Herbivore Oviposition in Arabidopsis: A Systematic Review.Frontiers in plant science · 2021Pooled it
- AdipocyteCells · 2026Article
- Subcellular localization of human long non-coding RNAs is an isoform-resolved property masked by gene-level analysis.Molecular genetics and genomics : MGG · 2026Article
- Transcriptomic responses to endurance exercise training in rats.BMC genomic data · 2026Article
- Shape-constrained, changepoint additive models for time series omics data with cpam.Nucleic acids research · 2026Article
- Multimodal bioinformatic analyses of genome-scale expression beyond gene-centric differential expression.Briefings in bioinformatics · 2026Review
- Article
- Conserved genetic markers reveal widespread diatom sexual reproduction in the global ocean.Nature communications · 2025Article
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- Chronic arsenic exposure and hsa-miR-186 overexpression causes transcriptome-wide differential alternative splicing contributing to skin carcinogenesis in human HaCaT cell line.Archives of toxicology · 2025Article
- Article
- mRNA Transcript Variants Expressed in Mammalian Cells.International journal of molecular sciences · 2025Review
- A landscape of X-inactivation during human T cell development.Nature communications · 2024Article
- Article
- Gene count estimation with pytximport enables reproducible analysis of bulk RNA sequencing data in Python.Bioinformatics (Oxford, England) · 2024Article
- Article
- Reduced protein-coding transcript diversity in severe dengue emphasises the role of alternative splicing.Life science alliance · 2024Article
- A Novel Approach to Comparative RNA-Seq Does Not Support a Conserved Set of Orthologs Underlying Animal Regeneration.Genome biology and evolution · 2024Article
- Machine learning unveils an immune-related DNA methylation profile in germline DNA from breast cancer patients.Clinical epigenetics · 2024Article
22 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Compared to RNA-sequencing transcript differential analysis, gene-level differential expression analysis is more robust and experimentally actionable. However, the use of gene counts for statistical analysis can mask transcript-level dynamics. We demonstrate that 'analysis first, aggregation second,' where the p values derived from transcript analysis are aggregated to obtain gene-level results, increase sensitivity and accuracy. The method we propose can also be applied to transcript compatibility counts obtained from pseudoalignment of reads, which circumvents the need for quantification and is fast, accurate, and model-free. The method generalizes to various levels of biology and we showcase an application to gene ontologies.
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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.