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Identification of key genes associated with Schmid-type metaphyseal chondrodysplasia based on microarray data

  • Authors:
    • Bing Wang
    • Li He
    • Wusheng Miao
    • Ge Wu
    • Hai Jiang
    • Yongtao Wu
    • Jining Qu
    • Min Li
  • View Affiliations / Copyright

    Affiliations: Department of Pediatric Orthopedics, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710054, P.R. China, Department of Child Health Care, Xi'an Children's Hospital, Xi'an, Shaanxi 710003, P.R. China
    Copyright: © Wang et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Pages: 1428-1436
    |
    Published online on: April 19, 2017
       https://doi.org/10.3892/ijmm.2017.2954
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Abstract

This study aimed to gain a better understanding of the molecular circuitry of Schmid-type metaphyseal chondrodysplasia (SMCD), and to identify more potential genes associated with the pathogenesis of SMCD. Microarray data from GSE72261 were downloaded from the NCBI GEO database, including collagen X p.Asn617Lys knock-in mutation (ColXN617K), ablated XBP1 activity (Xbp1CartΔEx2), compound mutant (C/X), and wild-type (WT) specimens. Differentially expressed genes (DEGs) were screened in Xbp1 vs. WT, Col vs. WT and CX vs. WT, respectively. Pathway enrichment analysis of these DEGs was performed. Transcription factors (TFs) of the overlapping DEGs were identified. Weighted correlation network analysis (WGCNA) was performed to find modules of DEGs with high correlations, followed by gene function analysis and a protein-protein interaction network construction. In total, 481, 1,530 and 1,214 DEGs were identified in Xbp1 vs. WT, Col vs. WT and CX vs. WT, respectively. These DEGs were enriched in different pathways, such as extracellular matrix (ECM)-receptor interaction and metabolism-related pathways. A total of 7 TFs were found to regulate 19 common upregulated genes, and 4 TFs were identified to regulate 21 common downregulated genes. Two significant gene co-expression modules were enriched and DEGs in the 2 modules were mainly enriched in different biological processes, such as ribosome biogenesis. Moreover, Kras (downregulated), Col5a1 (upregulated) and Furin (upregulated) were both identified in the regulatory networks and protein-protein interaction (PPI) network. On the whole, our findings indicate that the Kras, Col5a1 and Furin genes may play essential roles in the molecular mechanisms of SMCD, which warrants further investigation.
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Copy and paste a formatted citation
Spandidos Publications style
Wang B, He L, Miao W, Wu G, Jiang H, Wu Y, Qu J and Li M: Identification of key genes associated with Schmid-type metaphyseal chondrodysplasia based on microarray data. Int J Mol Med 39: 1428-1436, 2017.
APA
Wang, B., He, L., Miao, W., Wu, G., Jiang, H., Wu, Y. ... Li, M. (2017). Identification of key genes associated with Schmid-type metaphyseal chondrodysplasia based on microarray data. International Journal of Molecular Medicine, 39, 1428-1436. https://doi.org/10.3892/ijmm.2017.2954
MLA
Wang, B., He, L., Miao, W., Wu, G., Jiang, H., Wu, Y., Qu, J., Li, M."Identification of key genes associated with Schmid-type metaphyseal chondrodysplasia based on microarray data". International Journal of Molecular Medicine 39.6 (2017): 1428-1436.
Chicago
Wang, B., He, L., Miao, W., Wu, G., Jiang, H., Wu, Y., Qu, J., Li, M."Identification of key genes associated with Schmid-type metaphyseal chondrodysplasia based on microarray data". International Journal of Molecular Medicine 39, no. 6 (2017): 1428-1436. https://doi.org/10.3892/ijmm.2017.2954
Copy and paste a formatted citation
x
Spandidos Publications style
Wang B, He L, Miao W, Wu G, Jiang H, Wu Y, Qu J and Li M: Identification of key genes associated with Schmid-type metaphyseal chondrodysplasia based on microarray data. Int J Mol Med 39: 1428-1436, 2017.
APA
Wang, B., He, L., Miao, W., Wu, G., Jiang, H., Wu, Y. ... Li, M. (2017). Identification of key genes associated with Schmid-type metaphyseal chondrodysplasia based on microarray data. International Journal of Molecular Medicine, 39, 1428-1436. https://doi.org/10.3892/ijmm.2017.2954
MLA
Wang, B., He, L., Miao, W., Wu, G., Jiang, H., Wu, Y., Qu, J., Li, M."Identification of key genes associated with Schmid-type metaphyseal chondrodysplasia based on microarray data". International Journal of Molecular Medicine 39.6 (2017): 1428-1436.
Chicago
Wang, B., He, L., Miao, W., Wu, G., Jiang, H., Wu, Y., Qu, J., Li, M."Identification of key genes associated with Schmid-type metaphyseal chondrodysplasia based on microarray data". International Journal of Molecular Medicine 39, no. 6 (2017): 1428-1436. https://doi.org/10.3892/ijmm.2017.2954
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