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Revealing the Potential Pathogenesis of Glioma by Utilizing a Glioma Associated Protein-Protein Interaction Network

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Pathology & Oncology Research

Abstract

This study aims to explore the potential mechanism of glioma through bioinformatic approaches. The gene expression profile (GSE4290) of glioma tumor and non-tumor samples was downloaded from Gene Expression Omnibus database. A total of 180 samples were available, including 23 non-tumor and 157 tumor samples. Then the raw data were preprocessed using robust multiarray analysis, and 8,890 differentially expressed genes (DEGs) were identified by using t-test (false discovery rate < 0.0005). Furthermore, 16 known glioma related genes were abstracted from Genetic Association Database. After mapping 8,890 DEGs and 16 known glioma related genes to Human Protein Reference Database, a glioma associated protein-protein interaction network (GAPN) was constructed. In addition, 51 sub-networks in GAPN were screened out through Molecular Complex Detection (score ≥ 1), and sub-network 1 was found to have the closest interaction (score = 3). What’ more, for the top 10 sub-networks, Gene Ontology (GO) enrichment analysis (p value < 0.05) was performed, and DEGs involved in sub-network 1 and 2, such as BRMS1L and CCNA1, were predicted to regulate cell growth, cell cycle, and DNA replication via interacting with known glioma related genes. Finally, the overlaps of DEGs and human essential, housekeeping, tissue-specific genes were calculated (p value = 1.0, 1.0, and 0.00014, respectively) and visualized by Venn Diagram package in R. About 61 % of human tissue-specific genes were DEGs as well. This research shed new light on the pathogenesis of glioma based on DEGs and GAPN, and our findings might provide potential targets for clinical glioma treatment.

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Abbreviations

DEGs:

Differentially expressed genes

GAPN:

Glioma associated protein-protein interaction network

GO:

Gene Ontology

NCBI:

National Center for Biotechnology Information

GEO:

Gene Expression Omnibus

RMA:

Robust multiarray analysis

Gene ID:

Gene identifier

FDR:

False discovery rate

GAD:

Genetic Association Database

HPRD:

Human Protein Reference Database

PPIs:

Protein-protein interactions

MCODE:

Molecular Complex Detection

BINGO:

Biological Networks Gene Ontology tool

BRMS1L:

Breast cancer metastasis suppressor 1-like proteins

BRMS1:

Breast cancer metastasis suppressor 1

CCNA1:

Cyclin A1

MCM4:

Minichromosome maintenance complex component 4

MCM6:

Minichromosome maintenance complex component 6

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Conflict of interest

The authors have declared that no competing interests exist.

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Authors and Affiliations

  1. Department of Neurosurgery, Shengjing Hospital of China Medical University, NO. 36 Sanhaojie Street, Heping District, Shenyang, 110004, China

    Weiran Pan, Gang Li, Xiaoxiao Yang & Jinming Miao

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  1. Weiran Pan
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  2. Gang Li
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  3. Xiaoxiao Yang
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  4. Jinming Miao
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Correspondence to Weiran Pan.

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Pan, W., Li, G., Yang, X. et al. Revealing the Potential Pathogenesis of Glioma by Utilizing a Glioma Associated Protein-Protein Interaction Network. Pathol. Oncol. Res. 21, 455–462 (2015). https://doi.org/10.1007/s12253-014-9848-9

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  • DOI: https://doi.org/10.1007/s12253-014-9848-9

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