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

Yang Z, Chen Y, Fu Y, Yang Y, Zhang Y, Chen Y, Li D - BMC Med. Genet. (2014)

Bottom Line: 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).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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan 650118, PR China. yangzuozhangpre@163.com.

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.

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Related in: MedlinePlus

The constructed protein-protein interaction networks of the top 10 up- and down-regulated DEGs. The edges numbered mean which connect the top 10 up- and down-regulated DEGs directly or indirectly.
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Figure 3: The constructed protein-protein interaction networks of the top 10 up- and down-regulated DEGs. The edges numbered mean which connect the top 10 up- and down-regulated DEGs directly or indirectly.

Mentions: Nodes represent proteins, edges represent interactions between two proteins. The higher the node shape, the greater deagree of connection. The PPI networks we established for the top 10 up-regulated and down-regulated DEGs by Cytoscape software included 129 nodes and 182 edges. The significant hub proteins containing PTBP2 (polypyrimidine tract binding protein 2, Degree = 33), RGS4 (regulator of G-protein signaling 4, Degree = 15) and FXYD6 (FXYD domain containing ion transport regulator 6, Degree = 13) (Figure 3), we also annotated the edges connecting the top 10 up-regulated and down-regulated DEGs directly or indirectly in Additional file 3: Table S2, and numbered in Figure 3.


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

Yang Z, Chen Y, Fu Y, Yang Y, Zhang Y, Chen Y, Li D - BMC Med. Genet. (2014)

The constructed protein-protein interaction networks of the top 10 up- and down-regulated DEGs. The edges numbered mean which connect the top 10 up- and down-regulated DEGs directly or indirectly.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4109777&req=5

Figure 3: The constructed protein-protein interaction networks of the top 10 up- and down-regulated DEGs. The edges numbered mean which connect the top 10 up- and down-regulated DEGs directly or indirectly.
Mentions: Nodes represent proteins, edges represent interactions between two proteins. The higher the node shape, the greater deagree of connection. The PPI networks we established for the top 10 up-regulated and down-regulated DEGs by Cytoscape software included 129 nodes and 182 edges. The significant hub proteins containing PTBP2 (polypyrimidine tract binding protein 2, Degree = 33), RGS4 (regulator of G-protein signaling 4, Degree = 15) and FXYD6 (FXYD domain containing ion transport regulator 6, Degree = 13) (Figure 3), we also annotated the edges connecting the top 10 up-regulated and down-regulated DEGs directly or indirectly in Additional file 3: Table S2, and numbered in Figure 3.

Bottom Line: 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).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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan 650118, PR China. yangzuozhangpre@163.com.

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.

Show MeSH
Related in: MedlinePlus