Co-expression network analysis identified six hub genes in association with progression and prognosis in human clear cell renal cell carcinoma (ccRCC)

Lushun Yuan; Liang Chen; Kaiyu Qian; Guofeng Qian; Chin-Lee Wu; Xinghuan Wang; Yu Xiao

doi:10.1016/j.gdata.2017.10.006

Co-expression network analysis identified six hub genes in association with progression and prognosis in human clear cell renal cell carcinoma (ccRCC)

Genom Data. 2017 Nov 4:14:132-140. doi: 10.1016/j.gdata.2017.10.006. eCollection 2017 Dec.

Authors

Lushun Yuan¹, Liang Chen¹, Kaiyu Qian^{1

2}, Guofeng Qian³, Chin-Lee Wu⁴, Xinghuan Wang¹, Yu Xiao^{1

5

6}

Affiliations

¹ Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China.
² Department of Urology, The Fifth Hospital of Wuhan, Wuhan, China.
³ Department of Endocrinology, The First Affiliated Hospital of Zhejiang University, Hangzhou, China.
⁴ Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
⁵ Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China.
⁶ Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.

Abstract

Human clear cell renal cell carcinoma (ccRCC) is one of the most common types of malignant adult kidney tumors. We constructed a weighted gene co-expression network to identify gene modules associated with clinical features of ccRCC (n = 97). Six hub genes (CCNB2, CDC20, CEP55, KIF20A, TOP2A and UBE2C) were identified in both co-expression and protein-protein interaction (PPI) networks, which were highly correlated with pathologic stage. The significance of expression of the hub genes in ccRCC was ranked top 4 among all cancers and correlated with poor prognosis. Functional analysis revealed that the hub genes were significantly enriched in cell cycle regulation and cell division. Gene set enrichment analysis suggested that the samples with highly expressed hub gene were correlated with cell cycle and p53 signaling pathway. Taken together, six hub genes were identified to be associated with progression and prognosis of ccRCC, and they might lead to poor prognosis by regulating p53 signaling pathway.

Keywords: Clear cell renal cell carcinoma (ccRCC); Co-expression network analysis; DAVID, Database for Annotation, Visualization and Integrated Discovery; DEG, differentially expressed gene; DEGs, differentially expressed genes; GS, gene significance; GSEA, enrichment analysis and gene set enrichment; HPA, human protein atlas; Hub genes; MEs, module eigengenes; MS, module significance; PPI, protein-protein interaction; Prognosis; Progression; SAM, significance analysis of microarrays; STRING, search tool for the retrieval of interacting genes; TCGA, the cancer genome atlas; TOM, topological overlap matrix; WGCNA, weighted gene co-expression network analysis; ccRCC, clear cell renal cell carcinoma.