ArticleBMC medical genomics2020
Genome-wide analysis reveals the association between alternative splicing and DNA methylation across human solid tumors.
Article in BMC medical genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- The identification of RNA splicing aberrations and their potential regulatory network in Chinese non-small cell lung cancer.Respiratory research · 2026Article
- Intragenic methylation repatterning is associated with alternative splicing and unique epigenetic phenotypes.bioRxiv : the preprint server for biology · 2026Article
- Intragenic methylation repatterning is associated with alternative splicing and unique epigenetic phenotypes.Environmental epigenetics · 2026Article
- Genome-wide analyses reveal the regulatory roles of DNA methylation-regulated alternative promoter transcripts in breast cancer.Human genetics · 2024Article
- Sex-specific DNA methylation and associations withEpigenetics · 2022Article
- Comprehensive analysis of TCGA data reveals correlation between DNA methylation and alternative splicing.BMC genomics · 2022Article
- The Role of ctDNA in Gastric Cancer.Cancers · 2022Review
- Identification of the TSSK4 Alternative Spliceosomes and Analysis of the Function of the TSSK4 Protein in Yak (Animals : an open access journal from MDPI · 2022Article
- Design and experimental validation of OPERA_MET-A panel for deep methylation analysis by next generation sequencing.Frontiers in oncology · 2022Article
- Integrating machine learning to construct aberrant alternative splicing event related classifiers to predict prognosis and immunotherapy response in patients with hepatocellular carcinoma.Frontiers in pharmacology · 2022Article
- Expression characteristic ofBioengineered · 2021Article
- Novel Insights into Epigenetic Regulation of IL6 Pathway: In Silico Perspective on Inflammation and Cancer Relationship.International journal of molecular sciences · 2021Article
- Altered DNA Methylation Profiles inInternational journal of molecular sciences · 2021Article
- Identification of differentially methylated genes as diagnostic and prognostic biomarkers of breast cancer.World journal of surgical oncology · 2021Article
- Strong Expansion of Human Regulatory T Cells for Adoptive Cell Therapy Results in Epigenetic Changes Which May Impact Their Survival and Function.Frontiers in cell and developmental biology · 2021Article
- Application of Random Forest and data integration identifies three dysregulated genes and enrichment of Central Carbon Metabolism pathway in Oral Cancer.BMC cancer · 2020Article
- Identification of an alternative splicing signature as an independent factor in colon cancer.BMC cancer · 2020Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDysregulation of alternative splicing (AS) is a critical signature of cancer. However, the regulatory mechanisms of cancer-specific AS events, especially the impact of DNA methylation, are poorly understood.
methodsBy using The Cancer Genome Atlas (TCGA) SpliceSeq and TCGA data for ten solid tumor types, association analysis was performed to characterize the potential link between cancer-specific AS and DNA methylation. Functional and pathway enrichment analyses were performed, and the protein-protein interaction (PPI) network was constructed with the String website. The prognostic analysis was carried out with multivariate Cox regressions models.
results15,818 AS events in 3955 annotated genes were identified across ten solid tumor types. The different DNA methylation patterns between tumor and normal tissues at the corresponding alternative spliced exon boundaries were shown, and 51.3% of CpG sites (CpGs) revealed hypomethylated in tumors. Notably, 607 CpGs were found to be highly correlated with 369 cancer-specific AS events after permutation tests. Among them, the hypomethylated CpGs account for 52.7%, and the number of down-regulated exons was 173. Furthermore, we found 38 AS events in 35 genes could serve as new molecular biomarkers to predict patient survival.
conclusionsOur study described the relationship between DNA methylation and AS events across ten human solid tumor types and provided new insights into intragenic DNA methylation and exon usage during the AS process.
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