10.3389/fphys.2019.00278.s003
Jianbin Zhang
Jianbin
Zhang
Qiangqiang Nie
Qiangqiang
Nie
Chaozeng Si
Chaozeng
Si
Cheng Wang
Cheng
Wang
Yang Chen
Yang
Chen
Weiliang Sun
Weiliang
Sun
Lin Pan
Lin
Pan
Jing Guo
Jing
Guo
Jie Kong
Jie
Kong
Yiyao Cui
Yiyao
Cui
Feng Wang
Feng
Wang
Xueqiang Fan
Xueqiang
Fan
Zhidong Ye
Zhidong
Ye
Jianyan Wen
Jianyan
Wen
Peng Liu
Peng
Liu
Image_2_Weighted Gene Co-expression Network Analysis for RNA-Sequencing Data of the Varicose Veins Transcriptome.TIF
Frontiers
2019
weight gene co-expression network analysis
RNA-sequencing
varicose veins
interferon
GBP5
guanylate-binding protein 5
2019-03-19 04:54:41
Figure
https://frontiersin.figshare.com/articles/figure/Image_2_Weighted_Gene_Co-expression_Network_Analysis_for_RNA-Sequencing_Data_of_the_Varicose_Veins_Transcriptome_TIF/7860779
Objective<p>Varicose veins are a common problem worldwide and can cause significant impairments in health-related quality of life, but the etiology and pathogenesis remain not well defined. This study aims to elucidate transcriptomic regulations of varicose veins by detecting differentially expressed genes, pathways and regulator genes.</p>Methods<p>We harvested great saphenous veins (GSV) from patients who underwent coronary artery bypass grafting (CABG) and varicose veins from conventional stripping surgery. RNA-Sequencing (RNA-Seq) technique was used to obtain the complete transcriptomic data of both GSVs from CABG patients and varicose veins. Weighted Gene Co-expression network analysis (WGCNA) and further analyses were then carried out with the aim to elucidate transcriptomic regulations of varicose veins by detecting differentially expressed genes, pathways and regulator genes.</p>Results<p>From January 2015 to December 2016, 7 GSVs from CABG patients and 13 varicose veins were obtained. WGCNA identified 4 modules. In the brown module, gene ontology (GO) analysis showed that the biological processes were focused on response to stimulus, immune response and inflammatory response, etc. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis showed that the biological processes were focused on cytokine-cytokine receptor interaction and TNF signaling pathway, etc. In the gray module, GO analysis showed that the biological processes were skeletal myofibril assembly related. The immunohistochemistry staining showed that the expression of ASC, Caspase-1 and NLRP3 were increased in GSVs from CABG patients compared with varicose veins. Histopathological analysis showed that in the varicose veins group, the thickness of vascular wall, tunica intima, tunica media and collagen/smooth muscle ratio were significantly increased, and that the elastic fiber/internal elastic lamina ratio was decreased.</p>Conclusion<p>This study shows that there are clear differences in transcriptomic information between varicose veins and GSVs from CABG patients. Some inflammatory RNAs are down-regulated in varicose veins compared with GSVs from CABG patients. Skeletal myofibril assembly pathway may play a crucial role in the pathogenesis of varicose veins. Characterization of these RNAs may provide new targets for understanding varicose veins diagnosis, progression, and treatment.</p>