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Gene expression profiling via bioinformatics analysis reveals biomarkers in laryngeal squamous cell carcinoma
- Source :
- Molecular Medicine Reports
- Publication Year :
- 2014
-
Abstract
- The present study aimed to identify key genes and relevant microRNAs (miRNAs) involved in laryngeal squamous cell carcinoma (LSCC). The gene expression profiles of LSCC tissue samples were analyzed with various bioinformatics tools. A gene expression data set (GSE51985), including ten laryngeal squamous cell carcinoma (LSCC) tissue samples and ten adjacent non-neoplastic tissue samples, was downloaded from the Gene Expression Omnibus. Differential analysis was performed using software package limma of R. Functional enrichment analysis was applied to the differentially expressed genes (DEGs) using the Database for Annotation, Visualization and Integrated Discovery. Protein-protein interaction (PPI) networks were constructed for the protein products using information from the Search Tool for the Retrieval of Interacting Genes/Proteins. Module analysis was performed using ClusterONE (a software plugin from Cytoscape). MicroRNAs (miRNAs) regulating the DEGs were predicted using WebGestalt. A total of 461 DEGs were identified in LSCC, 297 of which were upregulated and 164 of which were downregulated. Cell cycle, proteasome and DNA replication were significantly over-represented in the upregulated genes, while the ribosome was significantly over-represented in the downregulated genes. Two PPI networks were constructed for the up- and downregulated genes. One module from the upregulated gene network was associated with protein kinase. Numerous miRNAs associated with LSCC were predicted, including miRNA (miR)-25, miR-32, miR-92 and miR-29. In conclusion, numerous key genes and pathways involved in LSCC were revealed, which may aid the advancement of current knowledge regarding the pathogenesis of LSCC. In addition, relevant miRNAs were also identified, which may represent potential biomarkers for use in the diagnosis or treatment of the disease.
- Subjects :
- DNA Replication
Cancer Research
Proteasome Endopeptidase Complex
differentially expressed genes
Cell
Gene regulatory network
Computational biology
Biology
Biochemistry
microRNA
Gene expression
Databases, Genetic
Protein Interaction Mapping
Genetics
medicine
Biomarkers, Tumor
Humans
Gene Regulatory Networks
Molecular Biology
Gene
Laryngeal Neoplasms
Oncogene
Gene Expression Profiling
Cell Cycle
Computational Biology
Molecular Sequence Annotation
Articles
functional enrichment analysis
Cell cycle
Gene expression profiling
Gene Expression Regulation, Neoplastic
MicroRNAs
medicine.anatomical_structure
laryngeal squamous cell carcinoma
Oncology
Carcinoma, Squamous Cell
Molecular Medicine
protein-protein interaction network
Protein Kinases
Ribosomes
Software
Subjects
Details
- ISSN :
- 17913004
- Volume :
- 12
- Issue :
- 2
- Database :
- OpenAIRE
- Journal :
- Molecular medicine reports
- Accession number :
- edsair.doi.dedup.....3cc75b3eabad827b1901920684dfb4f8