ArticleBMC bioinformatics2006
Profiling alternatively spliced mRNA isoforms for prostate cancer classification.
Article in BMC bioinformatics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers, 1 of them a synthesis that pooled it.
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Who cites it
39 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Bimodal gene expression patterns in breast cancer.BMC genomics · 2010Pooled it
- Alternative splicing discriminates molecular subtypes and has prognostic impact in diffuse large B-cell lymphoma.Blood cancer journal · 2017Trial
- Identified γ-glutamyl cyclotransferase (GGCT) as a novel regulator in the progression and immunotherapy of pancreatic ductal adenocarcinoma through multi-omics analysis and experiments.Journal of cancer research and clinical oncology · 2024Article
- Review
- A semi-supervised approach for the integration of multi-omics data based on transformer multi-head self-attention mechanism and graph convolutional networks.BMC genomics · 2024Article
- Interaction of MRPL9 and GGCT Promotes Cell Proliferation and Migration by Activating the MAPK/ERK Pathway in Papillary Thyroid Cancer.International journal of molecular sciences · 2022Article
- Identification of potential diagnostic and prognostic biomarkers for LUAD based on TCGA and GEO databases.Bioscience reports · 2021Article
- Pathway-guided analysis identifies Myc-dependent alternative pre-mRNA splicing in aggressive prostate cancers.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Isoform-specific promotion of breast cancer tumorigenicity by TBX3 involves induction of angiogenesis.Laboratory investigation; a journal of technical methods and pathology · 2020Article
- Dysregulation of the splicing machinery is directly associated to aggressiveness of prostate cancer.EBioMedicine · 2020Article
- Function, clinical application, and strategies of Pre-mRNA splicing in cancer.Cell death and differentiation · 2019Review
- Hub genes and key pathways of non-small lung cancer identified using bioinformatics.Oncology letters · 2018Article
- hnRNPM guides an alternative splicing program in response to inhibition of the PI3K/AKT/mTOR pathway in Ewing sarcoma cells.Nucleic acids research · 2017Article
- Knockdown of GGCT inhibits cell proliferation and induces late apoptosis in human gastric cancer.BMC biochemistry · 2016Article
- A gene expression microarray for Nicotiana benthamiana based on de novo transcriptome sequence assembly.Plant methods · 2016Article
- Isoform level expression profiles provide better cancer signatures than gene level expression profiles.Genome medicine · 2013Article
- Alternative splicing programs in prostate cancer.International journal of cell biology · 2013Article
- Prevention of tumor growth by needle-free jet injection of anti-C7orf24 siRNA.Cancer gene therapy · 2012Article
- MicroRNAs in cerebrospinal fluid identify glioblastoma and metastatic brain cancers and reflect disease activity.Neuro-oncology · 2012Article
- Subgroup-specific alternative splicing in medulloblastoma.Acta neuropathologica · 2012Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundProstate cancer is one of the leading causes of cancer illness and death among men in the United States and world wide. There is an urgent need to discover good biomarkers for early clinical diagnosis and treatment. Previously, we developed an exon-junction microarray-based assay and profiled 1532 mRNA splice isoforms from 364 potential prostate cancer related genes in 38 prostate tissues. Here, we investigate the advantage of using splice isoforms, which couple transcriptional and splicing regulation, for cancer classification.
resultsAs many as 464 splice isoforms from more than 200 genes are differentially regulated in tumors at a false discovery rate (FDR) of 0.05. Remarkably, about 30% of genes have isoforms that are called significant but do not exhibit differential expression at the overall mRNA level. A support vector machine (SVM) classifier trained on 128 signature isoforms can correctly predict 92% of the cases, which outperforms the classifier using overall mRNA abundance by about 5%. It is also observed that the classification performance can be improved using multivariate variable selection methods, which take correlation among variables into account.
conclusionThese results demonstrate that profiling of splice isoforms is able to provide unique and important information which cannot be detected by conventional microarrays.
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