Open Access

Identification of hub genes and regulatory factors of glioblastoma multiforme subgroups by RNA-seq data analysis

  • Authors:
    • Yanan Li
    • Weijie Min
    • Mengmeng Li
    • Guosheng Han
    • Dongwei Dai
    • Lei Zhang
    • Xin Chen
    • Xinglai Wang
    • Yuhui Zhang
    • Zhijian Yue
    • Jianmin Liu
  • View Affiliations

  • Published online on: August 26, 2016     https://doi.org/10.3892/ijmm.2016.2717
  • Pages: 1170-1178
  • Copyright: © Li et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

Glioblastoma multiforme (GBM) is the most common malignant brain tumor. This study aimed to identify the hub genes and regulatory factors of GBM subgroups by RNA sequencing (RNA-seq) data analysis, in order to explore the possible mechanisms responsbile for the progression of GBM. The dataset RNASeqV2 was downloaded by TCGA-Assembler, containing 169 GBM and 5 normal samples. Gene expression was calculated by the reads per kilobase per million reads measurement, and nor malized with tag count comparison. Following subgroup classification by the non-negative matrix factorization, the differentially expressed genes (DEGs) were screened in 4 GBM subgroups using the method of significance analysis of microarrays. Functional enrichment analysis was performed by DAVID, and the protein-protein interaction (PPI) network was constructed based on the HPRD database. The subgroup-related microRNAs (miRNAs or miRs), transcription factors (TFs) and small molecule drugs were predicted with pre-defined criteria. A cohort of 19,515 DEGs between the GBM and control samples was screened, which were predominantly enriched in cell cycle- and immunoreaction-related pathways. In the PPI network, lymphocyte cytosolic protein 2 (LCP2), breast cancer 1 (BRCA1), specificity protein 1 (Sp1) and chromodomain-helicase-DNA-binding protein 3 (CHD3) were the hub nodes in subgroups 1-4, respectively. Paired box 5 (PAX5), adipocyte protein 2 (aP2), E2F transcription factor 1 (E2F1) and cAMP-response element-binding protein-1 (CREB1) were the specific TFs in subgroups 1-4, respectively. miR‑147b, miR‑770-5p, miR‑220a and miR‑1247 were the particular miRNAs in subgroups 1-4, respectively. Natalizumab was the predicted small molecule drug in subgroup 2. In conclusion, the molecular regulatory mechanisms of GBM pathogenesis were distinct in the different subgroups. Several crucial genes, TFs, miRNAs and small molecules in the different GBM subgroups were identified, which may be used as potential markers. However, further experimental validations may be required.

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October-2016
Volume 38 Issue 4

Print ISSN: 1107-3756
Online ISSN:1791-244X

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Copy and paste a formatted citation
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Spandidos Publications style
Li Y, Min W, Li M, Han G, Dai D, Zhang L, Chen X, Wang X, Zhang Y, Yue Z, Yue Z, et al: Identification of hub genes and regulatory factors of glioblastoma multiforme subgroups by RNA-seq data analysis. Int J Mol Med 38: 1170-1178, 2016
APA
Li, Y., Min, W., Li, M., Han, G., Dai, D., Zhang, L. ... Liu, J. (2016). Identification of hub genes and regulatory factors of glioblastoma multiforme subgroups by RNA-seq data analysis. International Journal of Molecular Medicine, 38, 1170-1178. https://doi.org/10.3892/ijmm.2016.2717
MLA
Li, Y., Min, W., Li, M., Han, G., Dai, D., Zhang, L., Chen, X., Wang, X., Zhang, Y., Yue, Z., Liu, J."Identification of hub genes and regulatory factors of glioblastoma multiforme subgroups by RNA-seq data analysis". International Journal of Molecular Medicine 38.4 (2016): 1170-1178.
Chicago
Li, Y., Min, W., Li, M., Han, G., Dai, D., Zhang, L., Chen, X., Wang, X., Zhang, Y., Yue, Z., Liu, J."Identification of hub genes and regulatory factors of glioblastoma multiforme subgroups by RNA-seq data analysis". International Journal of Molecular Medicine 38, no. 4 (2016): 1170-1178. https://doi.org/10.3892/ijmm.2016.2717