title: Construction and analysis of the regulatory network disturbed by the silenced Sp1 transcription factor in HeLa cells.
abstract: BACKGROUND
  The objective of our study was to explore the characteristics of the regulatory network after siRNA-Sp1 (Specificity Protein 1) treatment in HeLa cells through the regulation network construction with bioinformatics methods.
  
  
  METHODS
  Using GSE37935 datasets downloaded from Gene Expression Omnibus data, the differentially expressed genes (DEGs) were screened out by the limma package in R software. Combining the DEGs with the data from the microRNA (miRNA) databases and transcription factor databases, an integrated regulatory network was established with Cytoscape. Then the motifs in the network were examined by FANMOD.
  
  
  RESULTS
  A total of 708 DEGs were screened, and a regulatory network consisting of 585 nodes and 1070 edges was constructed. By analyzing the two modules extracted from the network, we found that the most significant biological processes were cell cycle and apoptosis, some significant DEGs among them were CDKN1A, CUL5, and EGFR. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis discovered that DEGs, including EGFR, CDKN1A, RRM2B, and GADD45B, were significantly enriched in glioma pathway and p53 signaling pathway.
  
  
  CONCLUSIONS
  While Sp1 was silenced by siRNA, the regulatory network in HeLa cells changed a lot. Genes related to cell cycle and apoptosis in the cell nucleus were dysregulated and the p53 signaling pathway was disturbed.
authors.forename: Fengyan
authors.initials: F
authors.lastname: Li
authors.affiliation: Department of Gynaecology, First Hospital of Shanxi Medical University, Yingze, Taiyuan, Shanxi Province, China.
authors.forename: Lijun
authors.initials: L
authors.lastname: Yu
authors.forename: Li
authors.initials: L
authors.lastname: Li
authors.forename: Meiyan
authors.initials: M
authors.lastname: Wei
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D020868:Gene Silencing; D006367:HeLa Cells; D006801:Humans; D034741:RNA, Small Interfering / Q000235:genetics; D015398:Signal Transduction; D016329:Sp1 Transcription Factor / Q000037:antagonists & inhibitors* / Q000235:genetics
chemical_list: D014408:Biomarkers, Tumor; D034741:RNA, Small Interfering; D016329:Sp1 Transcription Factor