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2014-February Volume 7 Issue 2

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Article

Microarray analysis of genes and gene functions in disc degeneration

  • Authors:
    • Yanchun Tang
    • Shaokun Wang
    • Ying Liu
    • Xuyun Wang
  • View Affiliations / Copyright

    Affiliations: Department of Rheumatism and Immunity, Yantai Yuhuangding Hospital, Yantai, Shandong 264000, P.R. China, Department of Health, Yantai Yuhuangding Hospital, Yantai, Shandong 264000, P.R. China
  • Pages: 343-348
    |
    Published online on: November 22, 2013
       https://doi.org/10.3892/etm.2013.1421
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Abstract

The aim of the present study was to screen differentially expressed genes (DEGs) in human degenerative intervertebral discs (IVDs), and to perform functional analysis on these DEGs. The gene expression profile was downloaded from the Gene Expression Omnibus database (GSE34095)and included six human IVD samples: three degenerative and three non‑degenerative. The DEGs between the normal and disease samples were identified using R packages. The online software WebGestalt was used to perform the functional analysis of the DEGs, followed by Osprey software to search for interactions between the DEGs. The Database for Annotation, Visualization and Integrated Discovery was utilized to annotate the DEGs in the interaction network and then the DEGs were uploaded to the Connectivity Map database to search for small molecules. In addition, the active binding sites for the hub genes in the network were obtained, based on the Universal Protein database. By comparing the gene expression profiles of the non‑degenerative and degenerative IVDs, the DEGs between the samples were identified. The DEGs were significantly associated with transforming growth factor β and the extracellular matrix. Matrix metalloproteinase 2 (MMP2) was identified as the hub gene of the interaction network of DEGs. In addition, MMP2 was found to be upregulated in degenerative IVDs. The screened small molecules and the active binding sites of MMP2 may facilitate the development of methods to inhibit overexpression of MMP2.
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1 

Sambrook PN, MacGregor AJ and Spector TD: Genetic influences on cervical and lumbar disc degeneration: a magnetic resonance imaging study in twins. Arthritis Rheum. 42:366–372. 1999. View Article : Google Scholar : PubMed/NCBI

2 

Sobajima S, Kim JS, Gilbertson LG and Kang JD: Gene therapy for degenerative disc disease. Gene Ther. 11:390–401. 2004. View Article : Google Scholar : PubMed/NCBI

3 

Wallach CJ, Kim JS, Sobajima S, et al: Safety assessment of intradiscal gene transfer: a pilot study. Spine J. 6:107–112. 2006. View Article : Google Scholar : PubMed/NCBI

4 

Beltran S, Angulo M, Pignatelli M, Serras F and Corominas M: Functional dissection of the ash2 and ash1 transcriptomes provides insights into the transcriptional basis of wing phenotypes and reveals conserved protein interactions. Genome Biol. 8:R672007. View Article : Google Scholar

5 

Sohn P, Cox M, Chen D and Serra R: Molecular profiling of the developing mouse axial skeleton: a role for Tgfbr2 in the development of the intervertebral disc. BMC Dev Biol. 10:292010. View Article : Google Scholar : PubMed/NCBI

6 

Pache RA, Zanzoni A, Naval J, Mas JM and Aloy P: Towards a molecular characterisation of pathological pathways. FEBS Lett. 582:1259–1265. 2008. View Article : Google Scholar : PubMed/NCBI

7 

Thorn CF, Whirl-Carrillo M, Klein TE and Altman RB: Pathway-based approaches to pharmacogenomics. Current Pharmacogenomics. 5:79–86. 2007. View Article : Google Scholar

8 

Cloyd JM and Elliott DM: Elastin content correlates with human disc degeneration in the anulus fibrosus and nucleus pulposus. Spine (Phila Pa 1976). 32:1826–1831. 2007. View Article : Google Scholar : PubMed/NCBI

9 

Yu J, Fairbank JC, Roberts S and Urban JP: The elastic fiber network of the anulus fibrosus of the normal and scoliotic human intervertebral disc. Spine (Phila Pa 1976). 30:1815–1820. 2005. View Article : Google Scholar : PubMed/NCBI

10 

Matsui Y, Wu JJ, Weis MA, Pietka T and Eyre DR: Matrix deposition of tryptophan-containing allelic variants of type IX collagen in developing human cartilage. Matrix Biol. 22:123–129. 2003. View Article : Google Scholar : PubMed/NCBI

11 

Lamb J, Crawford ED, Peck D, et al: The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science. 313:1929–1935. 2006. View Article : Google Scholar

12 

Yeh CT, Wu AT, Chang PM, et al: Trifluoperazine, an antipsychotic agent, inhibits cancer stem cell growth and overcomes drug resistance of lung cancer. Am J Respir Crit Care Med. 186:1180–1188

13 

Zhou Y, Jiang S, Chen J, Wang T, Jiang D, Chen H and Yu H: 32k Da protein improve ovariectomy-induced bone loss in rats. Prion. 7:335–340. 2013. View Article : Google Scholar : PubMed/NCBI

14 

Troyanskaya O, Cantor M, Sherlock G, et al: Missing value estimation methods for DNA microarrays. Bioinformatics. 17:520–525. 2001. View Article : Google Scholar : PubMed/NCBI

15 

Fujita A, Sato JR, de Rodrigues LO, Ferreira CE and Sogayar MC: Evaluating different methods of microarray data normalization. BMC Bioinformatics. 7:4692006. View Article : Google Scholar : PubMed/NCBI

16 

Smyth GK, Michaud J and Scott HS: Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics. 21:2067–2075. 2005. View Article : Google Scholar : PubMed/NCBI

17 

Zhang B, Kirov S and Snoddy J: WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res. 33:W741–W748. 2005. View Article : Google Scholar : PubMed/NCBI

18 

Duncan DT, Prodduturi N and Zhang B: WebGestalt2: an updated and expanded version of the Web-based Gene Set Analysis Toolkit. BMC Bioinformatics. 11:2010. View Article : Google Scholar

19 

Patil A and Nakamura H: Filtering high-throughput protein-protein interaction data using a combination of genomic features. BMC Bioinformatics. 6:1002005. View Article : Google Scholar : PubMed/NCBI

20 

Breitkreutz BJ, Stark C and Tyers M: Osprey: a network visualization system. Genome Biol. 4:R222003. View Article : Google Scholar : PubMed/NCBI

21 

Willis RC and Hogue CW: Searching, viewing, and visualizing data in the Biomolecular Interaction Network Database (BIND). Curr Protoc Bioinformatics. 8.9.1–8.9.30. 2006.PubMed/NCBI

22 

Breitkreutz BJ, Stark C and Tyers M: The GRID: The General Repository for Interaction Datasets. Genome Biol. 4:R232003. View Article : Google Scholar : PubMed/NCBI

23 

Albert R, Jeong H and Barabasi AL: Error and attack tolerance of complex networks. Nature. 406:378–382. 2000. View Article : Google Scholar : PubMed/NCBI

24 

Huang da W, Sherman BT and Lempicki RA: Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37:1–13. 2009.PubMed/NCBI

25 

Huang da W, Sherman BT and Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 4:44–57. 2009.PubMed/NCBI

26 

Wen Z, Wang Z, Wang S, et al: Discovery of molecular mechanisms of traditional Chinese medicinal formula Si-Wu-Tang using gene expression microarray and connectivity map. PLoS One. 6:e182782011. View Article : Google Scholar : PubMed/NCBI

27 

Leland WE, Taqqu MS, Willinger W and Wilson DV: On the self-similar nature of Ethernet traffic. IEEE/ACM Transactions on Networking (TON). 2:1–15. 1994. View Article : Google Scholar

28 

Papagiannaki K, Taft N, Zhang ZL and Diot C: Long-term forecasting of internet backbone traffic. IEEE Trans Neural Netw. 16:1110–1124. 2005. View Article : Google Scholar : PubMed/NCBI

29 

Suzek BE, Huang H, McGarvey P, Mazumder R and Wu CH: UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics. 23:1282–1288. 2007. View Article : Google Scholar : PubMed/NCBI

30 

Ding F, Shao ZW and Xiong LM: Cell death in intervertebral disc degeneration. Apoptosis. 18:777–785. 2013. View Article : Google Scholar : PubMed/NCBI

31 

Vadalà G, Russo F, Di Martino A and Denaro V: Intervertebral disc regeneration: from the degenerative cascade to molecular therapy and tissue engineering. J Tissue Eng Regen Med. Mar 20–2013.(Epub ahead of print).

32 

Haro H, Crawford HC, Fingleton B, et al: Matrix metalloproteinase-3-dependent generation of a macrophage chemoattractant in a model of herniated disc resorption. J Clin Invest. 105:133–141. 2000. View Article : Google Scholar : PubMed/NCBI

33 

Roberts S, Caterson B, Menage J, Evans EH, Jaffray DC and Eisenstein SM: Matrix metalloproteinases and aggrecanase: their role in disorders of the human intervertebral disc. Spine (Phila Pa 1976). 25:3005–3013. 2000. View Article : Google Scholar : PubMed/NCBI

34 

Meijenhorst GC and de Bruin JN: Hexabrix (ioxaglate), a new low osmolality contrast agent for lumbar epidural double-catheter venography. Neuroradiology. 20:29–32. 1980. View Article : Google Scholar : PubMed/NCBI

35 

Grang L, Gaudin P, Trocme C, Phelip X, Morel F and Juvin R: Intervertebral disk degeneration and herniation: the role of metalloproteinases and cytokines. Joint Bone Spine. 68:547–553. 2001. View Article : Google Scholar : PubMed/NCBI

36 

Hristova GI, Jarzem P, Ouellet JA, et al: Calcification in human intervertebral disc degeneration and scoliosis. J Orthop Res. 29:1888–1895. 2011. View Article : Google Scholar : PubMed/NCBI

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Copy and paste a formatted citation
Spandidos Publications style
Tang Y, Wang S, Liu Y and Wang X: Microarray analysis of genes and gene functions in disc degeneration. Exp Ther Med 7: 343-348, 2014.
APA
Tang, Y., Wang, S., Liu, Y., & Wang, X. (2014). Microarray analysis of genes and gene functions in disc degeneration. Experimental and Therapeutic Medicine, 7, 343-348. https://doi.org/10.3892/etm.2013.1421
MLA
Tang, Y., Wang, S., Liu, Y., Wang, X."Microarray analysis of genes and gene functions in disc degeneration". Experimental and Therapeutic Medicine 7.2 (2014): 343-348.
Chicago
Tang, Y., Wang, S., Liu, Y., Wang, X."Microarray analysis of genes and gene functions in disc degeneration". Experimental and Therapeutic Medicine 7, no. 2 (2014): 343-348. https://doi.org/10.3892/etm.2013.1421
Copy and paste a formatted citation
x
Spandidos Publications style
Tang Y, Wang S, Liu Y and Wang X: Microarray analysis of genes and gene functions in disc degeneration. Exp Ther Med 7: 343-348, 2014.
APA
Tang, Y., Wang, S., Liu, Y., & Wang, X. (2014). Microarray analysis of genes and gene functions in disc degeneration. Experimental and Therapeutic Medicine, 7, 343-348. https://doi.org/10.3892/etm.2013.1421
MLA
Tang, Y., Wang, S., Liu, Y., Wang, X."Microarray analysis of genes and gene functions in disc degeneration". Experimental and Therapeutic Medicine 7.2 (2014): 343-348.
Chicago
Tang, Y., Wang, S., Liu, Y., Wang, X."Microarray analysis of genes and gene functions in disc degeneration". Experimental and Therapeutic Medicine 7, no. 2 (2014): 343-348. https://doi.org/10.3892/etm.2013.1421
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