title: Microarray data analysis to identify crucial genes regulated by CEBPB in human SNB19 glioma cells.
abstract: BACKGROUND
  Glioma is one of the most common primary malignancies in the brain or spine. The transcription factor (TF) CCAAT/enhancer binding protein beta (CEBPB) is important for maintaining the tumor initiating capacity and invasion ability. To investigate the regulation mechanism of CEBPB in glioma, microarray data GSE47352 was analyzed.
  
  
  METHODS
  GSE47352 was downloaded from Gene Expression Omnibus, including three samples of SNB19 human glioma cells transduced with non-target control small hairpin RNA (shRNA) lentiviral vectors for 72 h (normal glioma cells) and three samples of SNB19 human glioma cells transduced with CEBPB shRNA lentiviral vectors for 72 h (CEBPB-silenced glioma cells). The differentially expressed genes (DEGs) were screened using limma package and then annotated. Afterwards, the Database for Annotation, Visualization, and Integrated Discovery (DAVID) software was applied to perform enrichment analysis for the DEGs. Furthermore, the protein-protein interaction (PPI) network and transcriptional regulatory network were constructed using Cytoscape software.
  
  
  RESULTS
  Total 529 DEGs were identified in the normal glioma cells compared with the CEBPB-silenced glioma cells, including 336 up-regulated and 193 down-regulated genes. The significantly enriched pathways included chemokine signaling pathway (which involved CCL2), focal adhesion (which involved THBS1 and THBS2), TGF-beta signaling pathway (which involved THBS1, THBS2, SMAD5, and SMAD6) and chronic myeloid leukemia (which involved TGFBR2 and CCND1). In the PPI network, CCND1 (degree = 29) and CCL2 (degree = 12) were hub nodes. Additionally, CEBPB and TCF12 might function in glioma through targeting others (CEBPB → TCF12, CEBPB → TGFBR2, and TCF12 → TGFBR2).
  
  
  CONCLUSIONS
  CEBPB might act in glioma by regulating CCL2, CCND1, THBS1, THBS2, SMAD5, SMAD6, TGFBR2, and TCF12.
authors.affiliation: Department of Neurosurgery, The Affiliated Hospital of Inner Mongolia University for the Nationalities, Huolinhe Street No.1742, Tongliao, Inner Mongolia, 028007, China. ChenghuaDuchd@163.com.
authors.forename: Chenghua
authors.initials: C
authors.lastname: Du
authors.affiliation: Department of Hepatology, Tongliao City Hospital for Infectious Diseases, Tongliao, Inner Mongolia, 028007, China.
authors.forename: Pan
authors.initials: P
authors.lastname: Pan
authors.affiliation: Department of Neurosurgery, The Affiliated Hospital of Inner Mongolia University for the Nationalities, Huolinhe Street No.1742, Tongliao, Inner Mongolia, 028007, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Jiang
authors.affiliation: Department of Neurosurgery, The Affiliated Hospital of Inner Mongolia University for the Nationalities, Huolinhe Street No.1742, Tongliao, Inner Mongolia, 028007, China.
authors.forename: Qiuli
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Department of Neurosurgery, The Affiliated Hospital of Inner Mongolia University for the Nationalities, Huolinhe Street No.1742, Tongliao, Inner Mongolia, 028007, China.
authors.forename: Jinsuo
authors.initials: J
authors.lastname: Bao
authors.affiliation: Department of Neurosurgery, The Affiliated Hospital of Inner Mongolia University for the Nationalities, Huolinhe Street No.1742, Tongliao, Inner Mongolia, 028007, China.
authors.forename: Chang
authors.initials: C
authors.lastname: Liu
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics*; D001932:Brain Neoplasms / Q000235:genetics*; D022782:CCAAT-Enhancer-Binding Protein-beta / Q000235:genetics*; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D005910:Glioma / Q000235:genetics*; D006801:Humans; D060066:Protein Interaction Maps; D015398:Signal Transduction; D014407:Tumor Cells, Cultured
chemical_list: D014408:Biomarkers, Tumor; D022782:CCAAT-Enhancer-Binding Protein-beta; C545012:CEBPB protein, human
keywords: CCAAT/enhancer binding protein beta; Differentially expressed genes; Glioma; Protein-protein interaction network; Transcriptional regulatory network