Meta-analysis of differentially expressed genes in osteosarcoma based on gene expression data.

ABSTRACT: BACKGROUND: To uncover the genes involved in the development of osteosarcoma (OS), we performed a meta-analysis of OS microarray data to identify differentially expressed genes (DEGs) and biological functions associated with gene expression changes between OS and normal control (NC) tissues. METHODS: We used publicly available GEO datasets of OS to perform a meta-analysis. We performed Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and Protein-Protein interaction (PPI) networks analysis. RESULTS: Eight GEO datasets, including 240 samples of OS and 35 samples of controls, were available for the meta-analysis. We identified 979 DEGs across the studies between OS and NC tissues (472 up-regulated and 507 down-regulated). We found GO terms for molecular functions significantly enriched in protein binding (GO: 0005515, P = 3.83E-60) and calcium ion binding (GO: 0005509, P?=?3.79E-13), while for biological processes, the enriched GO terms were cell adhesion (GO:0007155, P?=?2.26E-19) and negative regulation of apoptotic process (GO: 0043066, P?=?3.24E-15), and for cellular component, the enriched GO terms were cytoplasm (GO: 0005737, P?=?9.18E-63) and extracellular region (GO: 0005576, P?=?2.28E-47). The most significant pathway in our KEGG analysis was Focal adhesion (P?=?5.70E-15). Furthermore, ECM-receptor interaction (P?=?1.27E-13) and Cell cycle (P?=?4.53E-11) are found to be highly enriched. PPI network analysis indicated that the significant hub proteins containing PTBP2 (Degree?=?33), RGS4 (Degree?=?15) and FXYD6 (Degree?=?13). CONCLUSIONS: Our meta-analysis detected DEGs and biological functions associated with gene expression changes between OS and NC tissues, guiding further identification and treatment for OS.

SUBMITTER: Yang Z 

PROVIDER: S-EPMC4109777 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature