title: Gene-gene interaction network analysis of ovarian cancer using TCGA data.
abstract: BACKGROUND
  The Cancer Genome Atlas (TCGA) Data portal provides a platform for researchers to search, download, and analysis data generated by TCGA. The objective of this study was to explore the molecular mechanism of ovarian cancer pathogenesis.
  
  
  METHODS
  Microarray data of ovarian cancer were downloaded from TCGA database, and Limma package in R language was used to identify the differentially expressed genes (DEGs) between ovarian cancer and normal samples, followed by the function and pathway annotations of the DEGs. Next, NetBox software was used to for the gene-gene interaction (GGI) network construction and the corresponding modules identification, and functions of genes in the modules were screened using DAVID.
  
  
  RESULTS
  Our studies identified 332 DEGs, including 146 up-regulated genes which mainly involved in the cell cycle related functions and cell cycle pathway, and 186 down-regulated genes which were enriched in extracellular region par function, and Ether lipid metabolism pathway. GGI network was constructed by 127 DEGs and their significantly interacted 209 genes (LINKERs). In the top 10 nodes ranked by degrees in the network, 5 were LINKERs. Totally, 7 functional modules in the network were selected, and they were enriched in different functions and pathways, such as mitosis process, DNA replication and DNA double-strand synthesis, lipid synthesis processes and metabolic pathways. AR, BRCA1, TFDP1, FOXM1, CDK2, and DBF4 were identified as the transcript factors of the 7 modules.
  
  
  CONCLUSIONS
  our data provides a comprehensive bioinformatics analysis of genes, functions, and pathways which may be involved in the pathogenesis of ovarian cancer.
authors: Department of Gynecology and Obstetrics, Shengjing Hospital of China Medical University, No,36, Sanhao Street, Heping District, Shenyang, Liaoning Province 110004, China. huanchunyiing@hotmail.com.
authors: Huanchun
authors: H
authors: Ying
authors: Jing
authors: J
authors: Lv
authors: Tianshu
authors: T
authors: Ying
authors: Shanshan
authors: S
authors: Jin
authors: Jingru
authors: J
authors: Shao
authors: Lili
authors: L
authors: Wang
authors: Hongying
authors: H
authors: Xu
authors: Bin
authors: B
authors: Yuan
authors: Qing
authors: Q
authors: Yang