title: Key genes and pathways predicted in papillary thyroid carcinoma based on bioinformatics analysis.
abstract: OBJECTIVE
  The aim of this study was to predict the key genes and pathways associated with papillary thyroid carcinoma (PTC).
  
  
  METHODS
  Based on the microarray data of GSE3467 from Gene Expression Omnibus database, we identified the differentially expressed genes (DEGs) between 9 PTC samples and 9 normal controls. With the identified DEGs, functional enrichment analyses were performed. Additionally, a protein-protein interaction network was constructed to screened out some key gene nodes. These key nodes were then performed clustering analysis and pathway enrichment analysis. Furthermore, human PTC-associated network was constructed based on these key genes to investigate the potential relationships between genes and PTC.
  
  
  RESULTS
  A total of 651 up-regulated and 692 down-regulated DEGs were identified in PTC samples compared with controls. The up-regulated DEGs, such as complement component 3 (C3), were mainly enriched in hsa04610:Complement and coagulation cascades. The down-regulated DEGs, including paired box 8 (PAX8), peroxisome proliferator-activated receptor gamma (PPARG), and cadherin 1, type 1 were found enriched in hsa05216:Thyroid cancer. Total 33 DEGs were considered as key genes, such as PAX8, PPARG and Jun proto-oncogene (JUN). Disease-associated network analysis found that 15 key genes such as JUN, PPARG and matrix metallopeptidase 9 (MMP9) were involved in this network.
  
  
  CONCLUSIONS
  DEGs of C3, PPARG, PAX8, JUN and MMP9 were differentially expressed in PTC samples and may be used as potential biomarkers in the diagnosis and treatment of PTC. Additionally, pathways of complement and coagulation cascades and thyroid cancer may also play important roles in the development of PTC.
authors.affiliation: Department of Head and Neck Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, 150081, China.
authors.forename: J
authors.initials: J
authors.lastname: Yu
authors.affiliation: Department of Orthopedics, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, 150081, China.
authors.forename: W
authors.initials: W
authors.lastname: Mai
authors.affiliation: Department of Radiation Oncology, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, 150081, China.
authors.forename: Y
authors.initials: Y
authors.lastname: Cui
authors.affiliation: Department of Head and Neck Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, 150081, China. lingykongl@sina.com.
authors.forename: L
authors.initials: L
authors.lastname: Kong
mesh_terms: D002291:Carcinoma, Papillary / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D006801:Humans; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D046228:Microarray Analysis; D054730:Protein Interaction Domains and Motifs; D000090063:Proto-Oncogene Mas; D013964:Thyroid Neoplasms / Q000235:genetics*
keywords: Differentially expressed gene; Disease-associated network; Papillary thyroid carcinoma; Pathway