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In silico analysis of expression data during the early priming stage of liver regeneration after partial hepatectomy in rat

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 pr...

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Autores principales: Yin, Li, Guo, Xueqiang, Zhang, Chunyan, Cai, Zhihui, Xu, Cunshuan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Impact Journals LLC 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5837750/
https://www.ncbi.nlm.nih.gov/pubmed/29545936
http://dx.doi.org/10.18632/oncotarget.24370
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author Yin, Li
Guo, Xueqiang
Zhang, Chunyan
Cai, Zhihui
Xu, Cunshuan
author_facet Yin, Li
Guo, Xueqiang
Zhang, Chunyan
Cai, Zhihui
Xu, Cunshuan
author_sort Yin, Li
collection PubMed
description 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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spelling pubmed-58377502018-03-15 In silico analysis of expression data during the early priming stage of liver regeneration after partial hepatectomy in rat Yin, Li Guo, Xueqiang Zhang, Chunyan Cai, Zhihui Xu, Cunshuan Oncotarget Research Paper 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. Impact Journals LLC 2018-01-27 /pmc/articles/PMC5837750/ /pubmed/29545936 http://dx.doi.org/10.18632/oncotarget.24370 Text en Copyright: © 2018 Yin et al. http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License 3.0 (http://creativecommons.org/licenses/by/3.0/) (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Paper
Yin, Li
Guo, Xueqiang
Zhang, Chunyan
Cai, Zhihui
Xu, Cunshuan
In silico analysis of expression data during the early priming stage of liver regeneration after partial hepatectomy in rat
title In silico analysis of expression data during the early priming stage of liver regeneration after partial hepatectomy in rat
title_full In silico analysis of expression data during the early priming stage of liver regeneration after partial hepatectomy in rat
title_fullStr In silico analysis of expression data during the early priming stage of liver regeneration after partial hepatectomy in rat
title_full_unstemmed In silico analysis of expression data during the early priming stage of liver regeneration after partial hepatectomy in rat
title_short In silico analysis of expression data during the early priming stage of liver regeneration after partial hepatectomy in rat
title_sort in silico analysis of expression data during the early priming stage of liver regeneration after partial hepatectomy in rat
topic Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5837750/
https://www.ncbi.nlm.nih.gov/pubmed/29545936
http://dx.doi.org/10.18632/oncotarget.24370
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