WGCNA鉴定奶山羊妊娠至泌乳期乳腺发育关键基因

doi:10.11843/j.issn.0366-6964.2020.11.007

Abstract

Abstract: The purpose of this study was to select the key genes of mammary gland development at different physiological stages in dairy goats by weighted gene co-expression network analysis(WGCNA). GSE14008 mammary gland tissue microarray data set of dairy goats at different physiological stages (pregnancy 46 days, 70 days, 90 days, 110 days and 40 days postpartum) was downloaded from GEO database, and co-expression analysis was carried out using WGCNA package of R language. The target modules were selected by correlation analysis between the modules and physiological stages, and the hub genes were selected according to the connectivity degree. After enrichment analysis of the modules using DAVID website, the protein-protein interaction network of the modules was constructed using String website and the core genes were obtained using Cytoscape software, and finally the target genes were obtained from intersection of core genes and hub genes. A total of 8 443 genes from 18 samples were analyzed for co-expression of weighted genes. The 30 modules were obtained, and 4 target modules related to different physiological stages and 30 hub genes of each module were selected. Meanwhile, protein-protein interaction network of 4 modules and 20 core genes of each network were also obtained. Finally, 13 target genes related to mammary gland development were obtained from the 4 modules, which were UQCR, RGL2, NOTCH1, PTBP1, PPP5C, FZR1, UBE2L3, TNF, MAT2A, ITGB2, GPR18, JAK1 and CSN2 genes. The key processes of mammary gland development at different physiological stages and the genes that played the key role in these processes were elucidated by WGCNA, GO enrichment analysis, PPI network and other bioinformatics techniques, which provided a new idea and clue for the further research on the mechanism of mammary gland development.

Key words: WGCNA, mammary gland development, pregnancy, lactation, goat

CLC Number:

S827.2

GAO Huijie, ZHENG Huiling. Identification of Key Genes of Mammary Gland Development from Pregnancy to Lactation in Dairy Goats by WGCNA[J]. Acta Veterinaria et Zootechnica Sinica, 2020, 51(11): 2679-2688.

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Identification of Key Genes of Mammary Gland Development from Pregnancy to Lactation in Dairy Goats by WGCNA

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