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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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The top 15 enriched GO terms of differentially expressed genes. A. molecular functions for DEGs (P value ≤ 9.35E-06); B. biological process for DEGs (P value ≤ 1.92E-07); C. cellular component for DEGs (P value ≤ 2.98E-09).
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Figure 2: The top 15 enriched GO terms of differentially expressed genes. A. molecular functions for DEGs (P value ≤ 9.35E-06); B. biological process for DEGs (P value ≤ 1.92E-07); C. cellular component for DEGs (P value ≤ 2.98E-09).

Mentions: To gain insights into the biological roles of the DEGs from OS, we performed a GO categories enrichment analysis. Gene ontology provides a common descriptive framework and functional annotation and classification for analyze the gene sets data. GO categories are organized into three groups: biological process, cellular component, and molecular function. The biological process and molecular functions are thus examined separately in our analysis by web-based software GENECODIS. Genes that showed a nominal significance level of P < 0.01 were selected and were tested against the background set of all genes with GO annotations. 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) (Figure 2).


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 top 15 enriched GO terms of differentially expressed genes. A. molecular functions for DEGs (P value ≤ 9.35E-06); B. biological process for DEGs (P value ≤ 1.92E-07); C. cellular component for DEGs (P value ≤ 2.98E-09).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: The top 15 enriched GO terms of differentially expressed genes. A. molecular functions for DEGs (P value ≤ 9.35E-06); B. biological process for DEGs (P value ≤ 1.92E-07); C. cellular component for DEGs (P value ≤ 2.98E-09).
Mentions: To gain insights into the biological roles of the DEGs from OS, we performed a GO categories enrichment analysis. Gene ontology provides a common descriptive framework and functional annotation and classification for analyze the gene sets data. GO categories are organized into three groups: biological process, cellular component, and molecular function. The biological process and molecular functions are thus examined separately in our analysis by web-based software GENECODIS. Genes that showed a nominal significance level of P < 0.01 were selected and were tested against the background set of all genes with GO annotations. 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) (Figure 2).

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