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Article

Screening of differentially expressed genes associated with human glioblastoma and functional analysis using a DNA microarray

  • Authors:
    • Lina Wang
    • Bo Wei
    • Guozhang Hu
    • Le Wang
    • Miaomiao Bi
    • Zhigang Sun
    • Ying Jin
  • View Affiliations / Copyright

    Affiliations: Department of Ophthalmology, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China, Department of Neurosurgery, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China, Department of Emergency Medicine, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China, Department of Ophthalmology, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China, Department of Neurology, Institute of Jilin Oilfield General Hospital, Changchun, Jilin 131200, P.R. China
  • Pages: 1991-1996
    |
    Published online on: April 22, 2015
       https://doi.org/10.3892/mmr.2015.3659
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Abstract

Glioblastoma multiforme (GBM) is the most malignant type of human glioma, and has a poor prognosis. Screening differentially expressed genes (DEGs) in brain tumor samples and normal brain samples is of importance for identifying GBM and to design specific‑targeting drugs. The transcriptional profile of GSE30563, containing three genechips of brain tumor samples and three genechips of normal brain samples, was downloaded from Gene Expression Omnibus to identify the DEGs. The differences in the expression of the DEGs in the two different samples were compared through hierarchical biclustering. The co‑expression coefficient of the DEGs was calculated using the information from COXPRESdb, the network of the DEGs was constructed and functional enrichment and pathway analysis were performed. Finally, the transcription factors of important DEGs were predicted. A total of 1,006 DEGs, including 368 upregulated and 638 downregulated DEGs, were identified. A close correlation was demonstrated between six important genes, associated with immune response, HLA‑DQB1, HLA‑DRB1, HLA‑DPA1, HLA‑B, HLA‑DMA and HLA‑DRA, and the immune response. Allograft rejection was selected as the most significant pathway. A total of 17 transcription factors, including nuclear factor (NF)‑κB and NF‑κB1, and their binding sites containing these six DEGs, were also identified. The DEGs, including major histocompatibility complex (MHC) class II, DQβ1, MHC class II, DRβ1, MHC class IB, MHC class II, DMα, MHC class II, DPα1, MHC class II, DRα, may provide novel targets for the diagnosis and treatment of GBM. The transcription factors of these six genes and their binding sites may also provide evidence and direction for identifying target-specific drugs.
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1 

Buckner JC: Factors influencing survival in high-grade gliomas. Seminars in oncology. Elsevier; pp. 10–14. 2003, View Article : Google Scholar

2 

Dubrow R, Darefsky AS, Jacobs DI, et al: Time trends in glioblastoma multiforme survival: the role of temozolomide. Neuro Oncol. 15:1750–1761. 2013. View Article : Google Scholar : PubMed/NCBI

3 

Liu Z, Niu Y, Xie M, Bu Y, Yao Z and Gao C: Gene expression profiling analysis reveals that DLG3 is down-regulated in glioblastoma. J Neurooncol. 116:465–476. 2014. View Article : Google Scholar : PubMed/NCBI

4 

Saggioro FP, Neder L, Stávale JN, et al: Fas, FasL and cleaved caspases 8 and 3 in glioblastomas: a tissue microarray-based study. Pathol Res Pract. 210:267–273. 2014. View Article : Google Scholar : PubMed/NCBI

5 

Aghi M and Chiocca EA: Gene therapy for glioblastoma. Neurosurg Focus. 20:E18. 2006.PubMed/NCBI

6 

Mischel PS, Cloughesy TF and Nelson SF: DNA-microarray analysis of brain cancer: molecular classification for therapy. Nat Rev Neurosci. 5:782–792. 2004. View Article : Google Scholar : PubMed/NCBI

7 

Chen JX, Lu YC, Luo C, et al: Expression and function of differentially expressed genes in glioblastoma by using cDNA microarray. AJSMMU. 25:498–502. 2004.

8 

Zhao Z, Lu Y, Chen J, Hou L-j, Hu G-h and Luo C: Using Bioinformatics Method to Investigate the Genes Related to Chemosensitivity in Human Glioblastoma. Prog Mod Biomed. 19:0032011.

9 

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

10 

Gentleman R, Carey V, Huber W, Irizarry RA and Dudoit S: Bioinformatics and computational biology solutions using R and Bioconductor. Springe. 2005. View Article : Google Scholar

11 

Szekely GJ and Rizzo ML: Hierarchical clustering via joint between-within distances: Extending Ward’s minimum variance method. J Classif. 22:151–183. 2005. View Article : Google Scholar

12 

Deza MM and Deza E: Encyclopedia of distances. Springer; 2009, View Article : Google Scholar

13 

Obayashi T, Hayashi S, Shibaoka M, Saeki M, Ohta H and Kinoshita K: COXPRESdb: a database of coexpressed gene networks in mammals. Nucleic Acids Res. 36:D77–D82. 2008. View Article : Google Scholar :

14 

Janaki C and Joshi RR: Motif detection in Arabidopsis: Correlation with gene expression data. In Silico Biol. 4:149–161. 2004.PubMed/NCBI

15 

Smoot ME, Ono K, Ruscheinski J, Wang PL and Ideker T: Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 27:431–432. 2011. View Article : Google Scholar :

16 

Huang da W, Sherman BT and Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinfor-matics resources. Nat Protoc. 4:44–57. 2009. View Article : Google Scholar

17 

Dudoit S, Shaffer JP and Boldrick JC: Multiple hypothesis testing in microarray experiments. Stat Sci. 18:71–103. 2003. View Article : Google Scholar

18 

Kanehisa M, Goto S, Hattori M, et al: From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34:D354–D357. 2006. View Article : Google Scholar :

19 

Kanehisa M, Goto S, Kawashima S, Okuno Y and Hattori M: The KEGG resource for deciphering the genome. Nucleic Acids Res. 32:D277–D280. 2004. View Article : Google Scholar :

20 

Stower H: Gene regulation: Resolving transcription factor binding. Nat Rev Genet. 13:71. 2011.PubMed/NCBI

21 

Han L, Suzek TO, Wang Y and Bryant SH: The text-mining based PubChem bioassay neighboring analysis. BMC Bioinformatics. 11:5492010. View Article : Google Scholar : PubMed/NCBI

22 

Ohgaki H and Kleihues P: Epidemiology and etiology of gliomas. Acta Neuropathol. 109:93–108. 2005. View Article : Google Scholar : PubMed/NCBI

23 

Wechsler-Reya R and Scott MP: The developmental biology of brain tumors. Annu Rev Neurosci. 24:385–428. 2001. View Article : Google Scholar : PubMed/NCBI

24 

Shiina T, Inoko H and Kulski J: An update of the HLA genomic region, locus information and disease associations: 2004. Tissue Antigens. 64:631–649. 2004. View Article : Google Scholar : PubMed/NCBI

25 

Jäger E, Chen YT, Drijfhout JW, et al: Simultaneous humoral and cellular immune response against cancer-testis antigen NY-ESO-1: Definition of human histocompatibility leukocyte antigen (HLA)-A2-binding peptide epitopes. J Exp Med. 187:265–270. 1998. View Article : Google Scholar : PubMed/NCBI

26 

Palucka K, Ueno H and Banchereau J: Recent developments in cancer vaccines. J Immunol. 186:1325–1331. 2011. View Article : Google Scholar : PubMed/NCBI

27 

Neefjes J, Jongsma ML, Paul P and Bakke O: Towards a systems understanding of MHC class I and MHC class II antigen presentation. Nat Rev Immunol. 11:823–836. 2011.PubMed/NCBI

28 

Boudjema A, Petit-Teixeira E, Cornelis F and Benhamamouch S: HLA-DMA and DMB genes in rheumatoid arthritis. Tissue Antigens. 79:155–156. 2012. View Article : Google Scholar : PubMed/NCBI

29 

Kiepiela P, Leslie AJ, Honeyborne I, et al: Dominant influence of HLA-B in mediating the potential co-evolution of HIV and HLA. Nature. 432:769–775. 2004. View Article : Google Scholar : PubMed/NCBI

30 

Wei J, Barr J, Kong LY, et al: Glioma-associated cancer-initiating cells induce immunosuppression. Clin Cancer Res. 16:461–473. 2010. View Article : Google Scholar : PubMed/NCBI

31 

Machulla HK, Steinborn F, Schaaf A, Heidecke V and Rainov NG: Brain glioma and human leukocyte antigens (HLA)-is there an association. J Neurooncol. 52:253–261. 2001. View Article : Google Scholar : PubMed/NCBI

32 

Moreau A, Varey E, Anegon I and Cuturi MC: Effector mechanisms of rejection. Cold Spring Harb Perspect Med. 3:a0154612013. View Article : Google Scholar : PubMed/NCBI

33 

Le Moine A, Goldman M and Abramowicz D: Multiple pathways to allograft rejection. Transplantation. 73:1373–1381. 2002. View Article : Google Scholar : PubMed/NCBI

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Copy and paste a formatted citation
Spandidos Publications style
Wang L, Wei B, Hu G, Wang L, Bi M, Sun Z and Jin Y: Screening of differentially expressed genes associated with human glioblastoma and functional analysis using a DNA microarray. Mol Med Rep 12: 1991-1996, 2015.
APA
Wang, L., Wei, B., Hu, G., Wang, L., Bi, M., Sun, Z., & Jin, Y. (2015). Screening of differentially expressed genes associated with human glioblastoma and functional analysis using a DNA microarray. Molecular Medicine Reports, 12, 1991-1996. https://doi.org/10.3892/mmr.2015.3659
MLA
Wang, L., Wei, B., Hu, G., Wang, L., Bi, M., Sun, Z., Jin, Y."Screening of differentially expressed genes associated with human glioblastoma and functional analysis using a DNA microarray". Molecular Medicine Reports 12.2 (2015): 1991-1996.
Chicago
Wang, L., Wei, B., Hu, G., Wang, L., Bi, M., Sun, Z., Jin, Y."Screening of differentially expressed genes associated with human glioblastoma and functional analysis using a DNA microarray". Molecular Medicine Reports 12, no. 2 (2015): 1991-1996. https://doi.org/10.3892/mmr.2015.3659
Copy and paste a formatted citation
x
Spandidos Publications style
Wang L, Wei B, Hu G, Wang L, Bi M, Sun Z and Jin Y: Screening of differentially expressed genes associated with human glioblastoma and functional analysis using a DNA microarray. Mol Med Rep 12: 1991-1996, 2015.
APA
Wang, L., Wei, B., Hu, G., Wang, L., Bi, M., Sun, Z., & Jin, Y. (2015). Screening of differentially expressed genes associated with human glioblastoma and functional analysis using a DNA microarray. Molecular Medicine Reports, 12, 1991-1996. https://doi.org/10.3892/mmr.2015.3659
MLA
Wang, L., Wei, B., Hu, G., Wang, L., Bi, M., Sun, Z., Jin, Y."Screening of differentially expressed genes associated with human glioblastoma and functional analysis using a DNA microarray". Molecular Medicine Reports 12.2 (2015): 1991-1996.
Chicago
Wang, L., Wei, B., Hu, G., Wang, L., Bi, M., Sun, Z., Jin, Y."Screening of differentially expressed genes associated with human glioblastoma and functional analysis using a DNA microarray". Molecular Medicine Reports 12, no. 2 (2015): 1991-1996. https://doi.org/10.3892/mmr.2015.3659
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