ArticleNature communications2016
SURVIV for survival analysis of mRNA isoform variation.
Article in Nature communications, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed.
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- Epigenetic Regulation and Therapeutic Targeting of Alternative Splicing Dysregulation in Cancer.Pharmaceuticals (Basel, Switzerland) · 2025Review
- A comprehensive review of cancer survival prediction using multi-omics integration and clinical variables.Briefings in bioinformatics · 2025Review
- Steering research on mRNA splicing in cancer towards clinical translation.Nature reviews. Cancer · 2024Review
- Pan-Cancer Profiling of Intron Retention and Its Clinical Significance in Diagnosis and Prognosis.Cancers · 2023Article
- Extensive Alternative Splicing Patterns in Systemic Lupus Erythematosus Highlight Sexual Differences.Cells · 2023Article
- Identification of a comprehensive alternative splicing function during epithelial-mesenchymal transition.iScience · 2023Article
- Sources of Cancer Neoantigens beyond Single-Nucleotide Variants.International journal of molecular sciences · 2022Review
- A widespread length-dependent splicing dysregulation in cancer.Science advances · 2022Article
- Comprehensive characterization of 11 prognostic alternative splicing events in ovarian cancer interacted with the immune microenvironment.Scientific reports · 2022Article
- Computational Biology Predicts the Efficacy of Tumor Immune Checkpoint Blockade.BioMed research international · 2022Article
- Differential Splicing of Skipped Exons Predicts Drug Response in Cancer Cell Lines.Genomics, proteomics & bioinformatics · 2021Article
- Transcript-targeted analysis reveals isoform alterations and double-hop fusions in breast cancer.Communications biology · 2021Article
- Systematic analysis of the relationship between ovarian cancer prognosis and alternative splicing.Journal of ovarian research · 2021Article
- Genome-Wide Profiling of Alternative Splicing Signatures Associated with Prognosis and Immune Microenvironment of Hepatocellular Carcinoma.Medical science monitor : international medical journal of experimental and clinical research · 2021Article
- RBFOX2/GOLIM4 Splicing Axis Activates Vesicular Transport Pathway to Promote Nasopharyngeal Carcinogenesis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2021Article
- Article
- Isoginkgetin derivative IP2 enhances the adaptive immune response against tumor antigens.Communications biology · 2021Article
- Alternative splicing of ceramide synthase 2 alters levels of specific ceramides and modulates cancer cell proliferation and migration in Luminal B breast cancer subtype.Cell death & disease · 2021Article
- Overexpressed P75CUX1 promotes EMT in glioma infiltration by activating β-catenin.Cell death & disease · 2021Article
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Authors and funding
5 authors.
Funding
Abstract
The rapid accumulation of clinical RNA-seq data sets has provided the opportunity to associate mRNA isoform variations to clinical outcomes. Here we report a statistical method SURVIV (Survival analysis of mRNA Isoform Variation), designed for identifying mRNA isoform variation associated with patient survival time. A unique feature and major strength of SURVIV is that it models the measurement uncertainty of mRNA isoform ratio in RNA-seq data. Simulation studies suggest that SURVIV outperforms the conventional Cox regression survival analysis, especially for data sets with modest sequencing depth. We applied SURVIV to TCGA RNA-seq data of invasive ductal carcinoma as well as five additional cancer types. Alternative splicing-based survival predictors consistently outperform gene expression-based survival predictors, and the integration of clinical, gene expression and alternative splicing profiles leads to the best survival prediction. We anticipate that SURVIV will have broad utilities for analysing diverse types of mRNA isoform variation in large-scale clinical RNA-seq projects.
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