ArticleBMC bioinformatics2013
Gene set enrichment analysis of RNA-Seq data: integrating differential expression and splicing.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Enhanced RNA-Seq Expression Profiling and Functional Enrichment in Non-model Organisms Using Custom Annotations.Bio-protocol · 2026Article
- An AI Agent for Fully Automated Multi-Omic Analyses.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Genome-scale CRISPR-Cas9 screening in stem cells: theories, applications and challenges.Stem cell research & therapy · 2024Review
- Article
- The hitchhikers' guide to RNA sequencing and functional analysis.Briefings in bioinformatics · 2023Article
- Arid5a Mediates an IL-17-Dependent Pathway That Drives Autoimmunity but Not Antifungal Host Defense.Journal of immunology (Baltimore, Md. : 1950) · 2022Article
- Transcriptome Analysis of Breast Muscle Reveals Pathways Related to Protein Deposition in High Feed Efficiency of Native Turkeys.Animals : an open access journal from MDPI · 2022Article
- NonLoss: a novel analytical method for differential biological module identification from single-cell transcriptome.Annals of translational medicine · 2021Article
- Transcriptome Analysis Identifies Candidate Genes and Signaling Pathways Associated With Feed Efficiency in Xiayan Chicken.Frontiers in genetics · 2021Article
- Fifteen Years of Gene Set Analysis for High-Throughput Genomic Data: A Review of Statistical Approaches and Future Challenges.Entropy (Basel, Switzerland) · 2020Review
- Identification of key genes and pathways associated with feed efficiency of native chickens based on transcriptome data via bioinformatics analysis.BMC genomics · 2020Article
- Article
- Ex vivo screen identifies CDK12 as a metastatic vulnerability in osteosarcoma.The Journal of clinical investigation · 2019Article
- Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline.Briefings in bioinformatics · 2016Article
- Novel BCOR-MAML3 and ZC3H7B-BCOR Gene Fusions in Undifferentiated Small Blue Round Cell Sarcomas.The American journal of surgical pathology · 2016Article
- A survey of best practices for RNA-seq data analysis.Genome biology · 2016Review
- Article
- Integrative enrichment analysis: a new computational method to detect dysregulated pathways in heterogeneous samples.BMC genomics · 2015Article
- Advanced Applications of RNA Sequencing and Challenges.Bioinformatics and biology insights · 2015Review
- Transcriptator: An Automated Computational Pipeline to Annotate Assembled Reads and Identify Non Coding RNA.PloS one · 2015Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRNA-Seq has become a key technology in transcriptome studies because it can quantify overall expression levels and the degree of alternative splicing for each gene simultaneously. To interpret high-throughout transcriptome profiling data, functional enrichment analysis is critical. However, existing functional analysis methods can only account for differential expression, leaving differential splicing out altogether.
resultsIn this work, we present a novel approach to derive biological insight by integrating differential expression and splicing from RNA-Seq data with functional gene set analysis. This approach designated SeqGSEA, uses count data modelling with negative binomial distributions to first score differential expression and splicing in each gene, respectively, followed by two strategies to combine the two scores for integrated gene set enrichment analysis. Method comparison results and biological insight analysis on an artificial data set and three real RNA-Seq data sets indicate that our approach outperforms alternative analysis pipelines and can detect biological meaningful gene sets with high confidence, and that it has the ability to determine if transcription or splicing is their predominant regulatory mechanism.
conclusionsBy integrating differential expression and splicing, the proposed method SeqGSEA is particularly useful for efficiently translating RNA-Seq data to biological discoveries.
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