title: Screening of differentially expressed genes associated with human glioblastoma and functional analysis using a DNA microarray.
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.
authors.affiliation: Department of Ophthalmology, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China.
authors.forename: Lina
authors.initials: L
authors.lastname: Wang
authors.affiliation: Department of Neurosurgery, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China.
authors.forename: Bo
authors.initials: B
authors.lastname: Wei
authors.affiliation: Department of Emergency Medicine, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China.
authors.forename: Guozhang
authors.initials: G
authors.lastname: Hu
authors.affiliation: Department of Ophthalmology, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China.
authors.forename: Le
authors.initials: L
authors.lastname: Wang
authors.affiliation: Department of Ophthalmology, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China.
authors.forename: Miaomiao
authors.initials: M
authors.lastname: Bi
authors.affiliation: Department of Neurosurgery, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China.
authors.forename: Zhigang
authors.initials: Z
authors.lastname: Sun
authors.affiliation: Department of Neurology, Institute of Jilin Oilfield General Hospital, Changchun, Jilin 131200, P.R. China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Jin
mesh_terms: D001921:Brain / Q000378:metabolism / Q000473:pathology; D001932:Brain Neoplasms / Q000235:genetics* / Q000473:pathology; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D005909:Glioblastoma / Q000235:genetics* / Q000473:pathology; D015235:HLA-B Antigens / Q000235:genetics; D006681:HLA-D Antigens / Q000235:genetics; D059867:HLA-DP alpha-Chains / Q000235:genetics; D059866:HLA-DQ beta-Chains / Q000235:genetics; D059805:HLA-DR alpha-Chains / Q000235:genetics; D059811:HLA-DRB1 Chains / Q000235:genetics; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D014157:Transcription Factors / Q000235:genetics
chemical_list: D015235:HLA-B Antigens; D006681:HLA-D Antigens; C084245:HLA-DM antigens; D059867:HLA-DP alpha-Chains; C071172:HLA-DPA1 antigen; D059866:HLA-DQ beta-Chains; C069051:HLA-DQB1 antigen; D059805:HLA-DR alpha-Chains; D059811:HLA-DRB1 Chains; D014157:Transcription Factors