ArticlePloS one2014
A comparative study of techniques for differential expression analysis on RNA-Seq data.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT05378282 (Identification of Diabetic Nephropathy Biomarkers Through Transcriptomics), which is not on this map. Cited by 148 papers, 1 of them a synthesis that pooled it.
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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.
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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.
Identification of Diabetic Nephropathy Biomarkers Through Transcriptomics
Who cites it
148 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Genomic characterization of Salmonella enterica isolates causing typhoid among Ghanaian patients.PloS one · 2026Article
- Tool choice matters: Evaluating edgeR vs. DESeq2 for sensitivity, robustness, and cross-study performance.PloS one · 2026Article
- An Integrative Genomics Approach for the Discovery of Potential Clinically Actionable Diagnostic and Prognostic Biomarkers in Colorectal Cancer.Biomedicines · 2025Article
- Cesium Accumulation Patterns and Stress Response in Hydroponic Radish (Plants (Basel, Switzerland) · 2025Article
- Integrated multi-sample transcriptomic analysis of COVID-19 patients against controls using a bioinformatics pipeline.Scientific reports · 2025Article
- Assessment of Seed Priming With Melatonin to Improve Morpho-Physiological and Biochemical Aspects of Common Bean (Plant direct · 2025Article
- Hmgb2 improves astrocyte to neuron conversion by increasing the chromatin accessibility of genes associated with neuronal maturation in a proneuronal factor-dependent manner.Genome biology · 2025Article
- VMP1 Constitutive Expression in Mice Dampens Pancreatic and Systemic Histopathological Damage in an Experimental Model of Severe Acute Pancreatitis.International journal of molecular sciences · 2025Article
- Metabolic differentiation of brushtail possum populations resistant and susceptible to plant toxins revealed via differential gene expression.Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology · 2025Article
- Bayesian identification of differentially expressed isoforms using a novel joint model of RNA-seq data.PLoS computational biology · 2025Article
- Effects of Different Stocking Densities on SnailAnimals : an open access journal from MDPI · 2024Article
- Comparative Transcriptome Analysis Reveals the Impact of a High-Fat Diet on Hepatic Metabolic Function in Tilapia (Animals : an open access journal from MDPI · 2024Article
- Transcriptomic analysis of rat prefrontal cortex following chronic stress induced by social isolation - Relevance to psychiatric and neurodevelopmental illness, and implications for treatment.Neurobiology of stress · 2024Article
- Endophytic Bacterial Biofilm-Formers Associated with Antarctic Vascular Plants.Microorganisms · 2024Article
- Transcriptomic response to nitrogen availability reveals signatures of adaptive plasticity during tetraploid wheat domestication.The Plant cell · 2024Article
- A comprehensive workflow for optimizing RNA-seq data analysis.BMC genomics · 2024Article
- Challenges and best practices in omics benchmarking.Nature reviews. Genetics · 2024Review
88 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent advances in next-generation sequencing technology allow high-throughput cDNA sequencing (RNA-Seq) to be widely applied in transcriptomic studies, in particular for detecting differentially expressed genes between groups. Many software packages have been developed for the identification of differentially expressed genes (DEGs) between treatment groups based on RNA-Seq data. However, there is a lack of consensus on how to approach an optimal study design and choice of suitable software for the analysis. In this comparative study we evaluate the performance of three of the most frequently used software tools: Cufflinks-Cuffdiff2, DESeq and edgeR. A number of important parameters of RNA-Seq technology were taken into consideration, including the number of replicates, sequencing depth, and balanced vs. unbalanced sequencing depth within and between groups. We benchmarked results relative to sets of DEGs identified through either quantitative RT-PCR or microarray. We observed that edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives. Overall, DESeq or taking the intersection of DEGs from two or more tools is recommended if the number of false positives is a major concern in the study. In other circumstances, edgeR is slightly preferable for differential expression analysis at the expense of potentially introducing more false positives.
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