ArticleBriefings in bioinformatics2019
Comparative analysis of differential gene expression tools for RNA sequencing time course data.
Article 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 58 papers.
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Who cites it
58 citing papers in PubMed.
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- The Role of Nucleotide Sequencing in Natural Product Drug Discovery.Journal of natural products · 2025Review
- Cluefish: mining the dark matter of transcriptional data series with over-representation analysis enhanced by aggregated biological prior knowledge.NAR genomics and bioinformatics · 2025Article
- Mutual suppression between mutations in the Dictyostelium Greenbeard pathway restores wild-type development.BMC genomics · 2025Article
- Longitudinal host-microbiome dynamics of metatranscription identify hallmarks of progression in periodontitis.Microbiome · 2025Article
- Model-to-crop conserved NUE Regulons enhance machine learning predictions of nitrogen use efficiency.The Plant cell · 2025Article
- Systems analysis of miR-199a/b-5p and multiple miR-199a/b-5p targets during chondrogenesis.eLife · 2024Article
- An integrative epigenome-based strategy for unbiased functional profiling of clinical kinase inhibitors.Molecular systems biology · 2024Article
- The ctenophore Mnemiopsis leidyi deploys a rapid injury response dating back to the last common animal ancestor.Communications biology · 2024Article
- Effect of Repeated Greater Occipital Nerve Block in Patients with Ocular Neuropathic Pain: A Retrospective Observational Study.Journal of clinical medicine · 2023Article
- Sex-biased gene expression across mammalian organ development and evolution.Science (New York, N.Y.) · 2023Article
- Transcriptome software results show significant variation among different commercial pipelines.BMC genomics · 2023Article
- Reconstructing disease dynamics for mechanistic insights and clinical benefit.Nature communications · 2023Article
- Transcriptomic Insight into the Pollen Tube Growth ofPlants (Basel, Switzerland) · 2023Article
- Gene Functional Networks from Time Expression Profiles: A Constructive Approach Demonstrated in Chili Pepper (Plants (Basel, Switzerland) · 2023Article
- Parallelized multidimensional analytic framework applied to mammary epithelial cells uncovers regulatory principles in EMT.Nature communications · 2023Article
- Article
- Identifying novel regulators of placental development using time-series transcriptome data.Life science alliance · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA sequencing (RNA-seq) has become a standard procedure to investigate transcriptional changes between conditions and is routinely used in research and clinics. While standard differential expression (DE) analysis between two conditions has been extensively studied, and improved over the past decades, RNA-seq time course (TC) DE analysis algorithms are still in their early stages. In this study, we compare, for the first time, existing TC RNA-seq tools on an extensive simulation data set and validated the best performing tools on published data. Surprisingly, TC tools were outperformed by the classical pairwise comparison approach on short time series (<8 time points) in terms of overall performance and robustness to noise, mostly because of high number of false positives, with the exception of ImpulseDE2. Overlapping of candidate lists between tools improved this shortcoming, as the majority of false-positive, but not true-positive, candidates were unique for each method. On longer time series, pairwise approach was less efficient on the overall performance compared with splineTC and maSigPro, which did not identify any false-positive candidate.
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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 Socratic graph.