ReviewBriefings in bioinformatics2019
Interpretation of differential gene expression results of RNA-seq data: review and integration.
Review in Briefings in bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 162 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
162 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Freely available genomic datasets for atrial fibrillation research: current resources and analytical pipeline.Frontiers in genetics · 2026Pooled it
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- PROFET predicts continuous gene expression dynamics from scRNA-seq data to elucidate heterogeneity of cancer treatment responses.Cell systems · 2026Article
- Benchmarking RNA-seq with the Quartet and MAQC reference materials to establish best practices for accurate alternative splicing analysis.Nature communications · 2026Article
- Seed endophytic bacterium induces a priming-like drought transcriptomic state in an invasive plant prior to stress exposure.BMC plant biology · 2026Article
- Kernel-smoothed permutation for extreme P-value estimation in genetic association studies.Genetics · 2026Article
- Establishment and validation of an ADP-ribosylation-related gene signature for prognostic prediction in lung adenocarcinoma.Discover oncology · 2026Article
- Sex differences in cardiac recovery and ventricular gene expression in a rat model of donation after circulatory death.Biology of sex differences · 2026Article
- Modeling chronic infection withInfection and immunity · 2026Article
- Integrating BSA-Seq, QTL Mapping, and RNA-Seq to Identify Candidate Genes for Hollow Heart in Cucumber Fruits.Plants (Basel, Switzerland) · 2026Article
- Decoding unchanged transcriptome of Alzheimer's disease reveals an NCAM1 mRNA switch as a potential biomarker.iScience · 2026Article
- Hippocampal transcriptome profiling in a 22q11.2 deletion syndrome mouse model: comparison with human schizophrenia.Molecular brain · 2026Article
- Neural Latent Filtering for Gene Discovery in Breast Cancer Subtypes.Biotechnology reports (Amsterdam, Netherlands) · 2026Article
- The Integration of Bioinformatics with Experimental Validation Has Uncovered Shared Molecular Characteristics Between Sarcopenia and Osteoarthritis.Calcified tissue international · 2026Article
- IL-6 signaling orchestrates proteolytic hubs MuRF1 and Atrogin-1 in NSCLC induced sarcopenia.Frontiers in immunology · 2026Article
- Rewiring of auxin and MAPK signaling is associated with contrasting shoestring and fern-like manifestations in ToBRFV-A134T-infected tomato.Frontiers in plant science · 2026Article
- Systems pharmacology approaches decipher the anti-cancer efficacy of ethnopharmacological agents in hepatocellular carcinoma.Scientific reports · 2025Article
- Transcriptomic insights into nerve growth factor-associated appositional bone formation in the reparative zone in osteonecrosis of the femoral head.Journal of orthopaedic surgery and research · 2025Article
- Avelumab induces greater Fc-Fc receptor-dependent natural killer cell activation and dendritic cell crosstalk compared to durvalumab.Oncoimmunology · 2025Article
- Biomaterial-mediated Cell Atlas: an insight from single-cell and spatial transcriptomics.Bioactive materials · 2025Review
102 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
5 authors.
Funding
Abstract
Differential gene expression (DGE) analysis is one of the most common applications of RNA-sequencing (RNA-seq) data. This process allows for the elucidation of differentially expressed genes across two or more conditions and is widely used in many applications of RNA-seq data analysis. Interpretation of the DGE results can be nonintuitive and time consuming due to the variety of formats based on the tool of choice and the numerous pieces of information provided in these results files. Here we reviewed DGE results analysis from a functional point of view for various visualizations. We also provide an R/Bioconductor package, Visualization of Differential Gene Expression Results using R, which generates information-rich visualizations for the interpretation of DGE results from three widely used tools, Cuffdiff, DESeq2 and edgeR. The implemented functions are also tested on five real-world data sets, consisting of one human, one Malus domestica and three Vitis riparia data sets.
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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.