Computational Identification of RNA-Seq Based miRNA-Mediated Prognostic Modules in Cancer
Autor: | Jiawei Luo, Jiao Zhang, Chu Pan |
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Rok vydání: | 2020 |
Předmět: |
0301 basic medicine
RNA-Seq Computational biology Biology 03 medical and health sciences 0302 clinical medicine Breast cancer Health Information Management Neoplasms microRNA Biomarkers Tumor medicine Humans Electrical and Electronic Engineering Bladder cancer Sequence Analysis RNA Mechanism (biology) Gene Expression Profiling Cancer Prognosis medicine.disease Computer Science Applications MicroRNAs 030104 developmental biology 030220 oncology & carcinogenesis Informatics DECIPHER Biotechnology |
Zdroj: | IEEE Journal of Biomedical and Health Informatics. 24:626-633 |
ISSN: | 2168-2208 2168-2194 |
Popis: | Systematic identification of miRNA prognostic signature can help decipher the effects of biomarkers in cancer treatment. A number of previous studies have only characterized a single miRNA as a promising prognostic biomarker. There is currently a trend toward combining several miRNAs as a panel of prognostic signatures, but few attempts to explain the mechanism of miRNA combination. Throughout this paper, we refer to “miRNA-mediated prognostic modules” and propose a novel computational approach called ProModule to analyze prognostic biomarkers from the module perspective. ProModule works in two main stages: it first uses univariate and multivariable Cox proportional hazard regressions to find individual miRNA biomarkers and then employs a clustering method to systematically detect miRNA-mediated modules with statistical prognostic significance. We applied ProModule to three data sets in bladder cancer, breast cancer, and liver cancer, and identified several miRNA prognostic modules for each data set. We found that miRNA prognostic modules have more powerful prognostic value than individuals while presenting coherent miRNA–miRNA expression as well as significant functional enrichment, and thus are likely to be biologically meaningful. Availability: ProModule is implemented in R and available at https://github.com/chupan1218/ProModule . |
Databáze: | OpenAIRE |
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