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Bioinformatics and machine learning methodologies to identify the effects of central nervous system disorders on glioblastoma progression
- Source :
- Briefings in bioinformatics. 22(5)
- Publication Year :
- 2020
-
Abstract
- Glioblastoma (GBM) is a common malignant brain tumor which often presents as a comorbidity with central nervous system (CNS) disorders. Both CNS disorders and GBM cells release glutamate and show an abnormality, but differ in cellular behavior. So, their etiology is not well understood, nor is it clear how CNS disorders influence GBM behavior or growth. This led us to employ a quantitative analytical framework to unravel shared differentially expressed genes (DEGs) and cell signaling pathways that could link CNS disorders and GBM using datasets acquired from the Gene Expression Omnibus database (GEO) and The Cancer Genome Atlas (TCGA) datasets where normal tissue and disease-affected tissue were examined. After identifying DEGs, we identified disease-gene association networks and signaling pathways and performed gene ontology (GO) analyses as well as hub protein identifications to predict the roles of these DEGs. We expanded our study to determine the significant genes that may play a role in GBM progression and the survival of the GBM patients by exploiting clinical and genetic factors using the Cox Proportional Hazard Model and the Kaplan–Meier estimator. In this study, 177 DEGs with 129 upregulated and 48 downregulated genes were identified. Our findings indicate new ways that CNS disorders may influence the incidence of GBM progression, growth or establishment and may also function as biomarkers for GBM prognosis and potential targets for therapies. Our comparison with gold standard databases also provides further proof to support the connection of our identified biomarkers in the pathology underlying the GBM progression.
- Subjects :
- Central Nervous System
Central nervous system
Datasets as Topic
Glutamic Acid
Kaplan-Meier Estimate
Biology
Bioinformatics
Machine Learning
03 medical and health sciences
0302 clinical medicine
Atlases as Topic
Downregulation and upregulation
medicine
Humans
Gene Regulatory Networks
Molecular Biology
Gene
Survival analysis
030304 developmental biology
Proportional Hazards Models
0303 health sciences
Proportional hazards model
Brain Neoplasms
Gene Expression Profiling
Computational Biology
Molecular Sequence Annotation
medicine.disease
Comorbidity
Neoplasm Proteins
Gene Expression Regulation, Neoplastic
medicine.anatomical_structure
Gene Ontology
Signal transduction
Glioblastoma
030217 neurology & neurosurgery
Function (biology)
Information Systems
Signal Transduction
Subjects
Details
- ISSN :
- 14774054
- Volume :
- 22
- Issue :
- 5
- Database :
- OpenAIRE
- Journal :
- Briefings in bioinformatics
- Accession number :
- edsair.doi.dedup.....a2d0ef62cc4d365f21b9ccd920c541a4