In silico analysis of expression data during the early priming stage of liver regeneration after partial hepatectomy in rat
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Li Yin1,2,3, Xueqiang Guo1, Chunyan Zhang1, Zhihui Cai1,3 and Cunshuan Xu1,2
1College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
2State Key Laboratory Cultivation Base for Cell Differentiation Regulation and Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang 453007, Henan Province, China
3Luohe Medical College, Luohe 462002, Henan Province, China
Cunshuan Xu, email: [email protected]
Keywords: liver regeneration; priming stage; in silico analysis; GSEA; Cnot3
Received: June 27, 2017 Accepted: December 05, 2017 Published: January 27, 2018
The priming stage is the first step of liver regeneration (LR). This stage is characterized by the transition from G0 to cell cycle for 4 hours in rat. In this study, individual gene level and gene set level (GSEA) was performed to identify the candidate genes and significantly changed biological processes at 2 h after partial hepatectomy (PH). The leading edge analysis is performed to identify the key genes and iRegulon was employed for transcription factor (TF) analysis. A total of 53 differentially expressed genes were identified using RMA package based on R language at 2 h after PH, including the transcription factor, enzyme and cytokine. As the most important genes in our analysis, Socs3 was selected with a special analysis so as to find the pathways correlate to the expression of it. The changed significantly pathways in LR involved response to stress, ATP metabolism, and regulation of cell cycle mainly. Several transcription factors were identified including Stat5a, Cnot3 and zfp384. Taken together, at the early priming stage of LR in rat, the liver is experiencing some changes including response to stress, activated ATP metabolism and inhibition of cell cycle. Our analysis provided a detailed and comprehensive map for further research of the early priming stage of LR in rat.
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