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Liu J, Hua P, Hui L, et al. Identification of hub genes and pathways associated with hepatocellular carcinoma based on network strategy. Exp Ther Med. 2016;12(4):2109-2119doi: 10.3892/etm.2016.3599.
Liu, J., Hua, P., Hui, L., Zhang, L. L., Hu, Z., & Zhu, Y. W. (2016). Identification of hub genes and pathways associated with hepatocellular carcinoma based on network strategy. Experimental and therapeutic medicine, 12(4), 2109-2119. https://doi.org/10.3892/etm.2016.3599
Liu, Jun, et al. "Identification of hub genes and pathways associated with hepatocellular carcinoma based on network strategy." Experimental and therapeutic medicine vol. 12,4 (2016): 2109-2119. doi: https://doi.org/10.3892/etm.2016.3599
Liu J, Hua P, Hui L, Zhang LL, Hu Z, Zhu YW. Identification of hub genes and pathways associated with hepatocellular carcinoma based on network strategy. Exp Ther Med. 2016 Oct;12(4):2109-2119. doi: 10.3892/etm.2016.3599. Epub 2016 Aug 12. PMID: 27703495; PMCID: PMC5039750.
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Exp Ther Med. 2016 Oct;12(4):2109-2119. doi: 10.3892/etm.2016.3599. Epub 2016 Aug 12.

Identification of hub genes and pathways associated with hepatocellular carcinoma based on network strategy.

Experimental and therapeutic medicine

Jun Liu, Ping Hua, Li Hui, Li-Li Zhang, Zhen Hu, Ying-Wei Zhu

Affiliations

  1. Department of Radiology, Wuxi Second Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu 214002, P.R. China.
  2. Department of Internal Medicine, Wuxi Second Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu 214002, P.R. China.

PMID: 27703495 PMCID: PMC5039750 DOI: 10.3892/etm.2016.3599

Abstract

The objective of this study was to identify hub genes and pathways associated with hepatocellular carcinoma (HCC) by centrality analysis of a co-expression network. A co-expression network based on differentially expressed (DE) genes of HCC was constructed using the Differentially Co-expressed Genes and Links (DCGL) package. Centrality analyses, for centrality of degree, clustering coefficient, closeness, stress and betweenness for the co-expression network were performed to identify hub genes, and the hub genes were combined together to overcome inconsistent results. Enrichment analyses were conducted using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases. Finally, validation of hub genes was conducted utilizing reverse transcription-polymerase chain reaction (RT-PCR) analysis. In total, 260 DE genes between normal controls and HCC patients were obtained and a co-expression network with 154 nodes and 326 edges was constructed. From this, 13 hub genes were identified according to degree, clustering coefficient, closeness, stress and betweenness centrality analysis. It was found that reelin (

Keywords: centrality; co-expression network; hepatocellular carcinoma; hub gene; pathway; reverse transcription-polymerase chain reaction

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