ArticleBMC medical genomics2012
Identification and characterization of alternative exon usage linked glioblastoma multiforme survival.
Article in BMC medical genomics, 2012. 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.
- Establishment of a Lymph Node Metastasis-Associated Prognostic Signature for Lung Adenocarcinoma.Genetics research · 2023Article
- Exome sequencing of glioblastoma-derived cancer stem cells reveals rare clinically relevant frameshift deletion in MLLT1 gene.Cancer cell international · 2022Article
- Article
- Genome-wide profiling of alternative splicing in glioblastoma and their clinical value.BMC cancer · 2021Article
- Role of alternative splicing signatures in the prognosis of glioblastoma.Cancer medicine · 2019Article
- Illuminating the Onco-GPCRome: Novel G protein-coupled receptor-driven oncocrine networks and targets for cancer immunotherapy.The Journal of biological chemistry · 2019Review
- Analysis of Expression Pattern of snoRNAs in Different Cancer Types with Machine Learning Algorithms.International journal of molecular sciences · 2019Article
- The aberrant splicing of BAF45d links splicing regulation and transcription in glioblastoma.Neuro-oncology · 2018Article
- iOPTICS-GSO for identifying protein complexes from dynamic PPI networks.BMC medical genomics · 2017Article
- Computer Analysis of Glioma Transcriptome Profiling: Alternative Splicing Events.Journal of integrative bioinformatics · 2017Article
- RNA processing as an alternative route to attack glioblastoma.Human genetics · 2017Review
- Differential Transcriptome Networks between IDO1-Knockout and Wild-Type Mice in Brain Microglia and Macrophages.PloS one · 2016Article
- Microglia Transcriptome Changes in a Model of Depressive Behavior after Immune Challenge.PloS one · 2016Article
- Triple-layer dissection of the lung adenocarcinoma transcriptome: regulation at the gene, transcript, and exon levels.Oncotarget · 2015Article
- New insights into the genetics of glioblastoma multiforme by familial exome sequencing.Oncotarget · 2015Article
- Systematic analysis of new drug indications by drug-gene-disease coherent subnetworks.CPT: pharmacometrics & systems pharmacology · 2014Article
- Bivariate genome-wide association analysis of the growth and intake components of feed efficiency.PloS one · 2013Article
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5 authors.
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Abstract
backgroundAlternative exon usage (AEU) is an important component of gene regulation. Exon expression platforms allow the detection of associations between AEU and phenotypes such as cancer. Numerous studies have identified associations between gene expression and the brain cancer glioblastoma multiforme (GBM). The few consistent gene expression biomarkers of GBM that have been reported may be due to the limited consideration of AEU and the analytical approaches used. The objectives of this study were to develop a model that accounts for the variations in expression present between the exons within a gene and to identify AEU biomarkers of GBM survival.
methodsThe expression of exons corresponding to 25,403 genes was related to the survival of 250 individuals diagnosed with GBM in a training data set. Genes exhibiting AEU in the training data set were confirmed in an independent validation data set of 78 patients. A hierarchical mixed model that allows the consideration of covariation between exons within a gene and of the effect of the epidemiological characteristics of the patients was developed to identify associations between exon expression and patient survival. This general model describes all three possible scenarios: multi-exon genes with and without AEU, and single-exon genes.
resultsAEU associated with GBM survival was identified on 2477 genes (P-value < 5.0E-04 or FDR-adjusted P-value < 0.05). G-protein coupled receptor 98 (Gpr98) and epidermal growth factor (Egf) were among the genes exhibiting AEU with 30 and 9 exons associated with GBM survival, respectively. Pathways enriched among the AEU genes included focal adhesion, ECM-receptor interaction, ABC transporters and pathways in cancer. In addition, 24 multi-exon genes without AEU and 8 single-exon genes were associated with GBM survival (FDR-adjusted P-value < 0.05).
conclusionsThe inferred patterns of AEU were consistent with in silico AS models. The hierarchical model used offered a flexible and simple way to interpret and identify associations between survival that accommodates multi-exon genes with or without AEU and single exon genes. Our results indicate that differential expression of AEU could be used as biomarker for GBM and potentially other cancers.
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