Weighted Gene Co-Expression Network Analysis Identifies Key Modules and Central Genes Associated With Bovine Subcutaneous Adipose Tissue

Sheng, Hui; Pan, Cuili; Wang, Shuzhe; Yang, Chaoyun; Zhang, Junxing; Hu, Chun‐Li; Hu, Honghong; Xue, Feng; Yang, Mengli; Lei, Zhaoxiong; Gao, Yuhong; Wang, Zhong; Ma, Yan

doi:10.3389/fvets.2022.914848

Cited by 3 publications

(4 citation statements)

References 37 publications

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“…In PLXND1 gene deficient zebrafish visceral adipose tissue, the induction of COL5A1 promotes adipocyte proliferation and differentiation, culminating in hyperplastic visceral adipose tissue morphology and reduced lipid accumulation ( Minchin et al, 2015 ). Moreover, COL5A1 has been deemed a hub gene associated with bovine subcutaneous adipose tissue by WGCNA, which is consistent with our results ( Sheng et al, 2022 ). Increasing evidence suggests that COL6A3 expression is distinctly correlated with adipose tissue mass, adipocyte size, weight gain or loss, insulin resistance, and inflammation ( Pasarica et al, 2009 ; Dankel et al, 2014 ; McCulloch et al, 2015 ).…”

Section: Discussionsupporting

confidence: 93%

“…Recent investigations have verified that the COL1 network is the last to form and remains well organized during the later stage of adipocyte differentiation, and the extracellular network of COL5 and COL6 is formed in the middle stage of adipocyte differentiation and maintained until the late stage of adipocyte differentiation ( Sheng et al, 2022 ). Another study has designated COL1A2 , COL5A1 , COL6A3 as DEGs in obese and healthy adipocyte excised from subcutaneous tissue in humans.…”

Section: Discussionmentioning

confidence: 99%

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Identification of crucial modules and genes associated with backfat tissue development by WGCNA in Ningxiang pigs

Chen,

Ren,

et al. 2023

Front. Genet.

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Fat deposition is an economically important trait in pigs. Ningxiang pig, one of the four famous indigenous breeds in China, is characterized by high fat content. The underlying gene expression pattern in different developmental periods of backfat tissue remains unclear, and the purpose of this investigation is to explore the potential molecular regulators of backfat tissue development in Ningxiang pigs. Backfat tissue (three samples for each stage) was initially collected from different developmental stages (60, 120, 180, 240, 300, and 360 days after birth), and histological analysis and RNA sequencing (RNA-seq) were then conducted. Fragments per kilobase of transcript per million (FPKM) method was used to qualify gene expressions, and differentially expressed genes (DEGs) were identified. Furthermore, strongly co-expressed genes in modules, which were named by color, were clustered by Weighted gene co-expression network analysis (WGCNA) based on dynamic tree cutting algorithm. Gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) enrichment were subsequently implemented, and hub genes were described in each module. Finally, QPCR analysis was employed to validate RNA-seq data. The results showed that adipocyte area increased and adipocyte number decreased with development of backfat tissue. A total of 1,024 DEGs were identified in five comparison groups (120 days vs. 60 days, 180 days vs. 120 days, 240 days vs. 180 days, 300 days vs. 240 days, and 360 days vs. 300 days). The turquoise, red, pink, paleturquoise, darkorange, and darkgreen module had the highest correlation coefficient with 60, 120, 180, 240, 300, and 360 days developmental stage, while the tan, black and turquoise module had strong relationship with backfat thickness, adipocyte area, and adipocyte number, respectively. Thirteen hub genes (ACSL1, ACOX1, FN1, DCN, CHST13, COL1A1, COL1A2, COL6A3, COL5A1, COL14A1, OAZ3, DNM1, and SELP) were recognized. ACSL1 and ACOX1 might perform function in the early developmental stage of backfat tissue (60 days), and FN1, DCN, COL1A1, COL1A2, COL5A1, COL6A3, and COL14A1 have unignorable position in backfat tissue around 120 days developmental stage. Besides, hub genes SELP and DNM1 in modules significantly associated with backfat thickness and adipocyte area might be involved in the process of backfat tissue development. These findings contribute to understand the integrated mechanism underlying backfat tissue development and promote the progress of genetic improvement in Ningxiang pigs.

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Section: Discussionsupporting

confidence: 93%

Section: Discussionmentioning

confidence: 99%

Identification of crucial modules and genes associated with backfat tissue development by WGCNA in Ningxiang pigs

Chen,

Ren,

et al. 2023

Front. Genet.

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“…The weighted co-expression network (WGCNA) is a systems biology method that can analyze microarray data to explore the correlation between genes ( Langfelder & Horvath, 2008 ). It can distinguish the associations between different gene sets and between trait phenotypes and gene sets, and gather highly related genes into the same module ( Sheng et al, 2022 ). The genes in the module can be organized by connectivity.…”

Section: Introductionmentioning

confidence: 99%

Identification of key genes in bovine muscle development by co-expression analysis

Zhang

Sheng

Pan

et al. 2023

PeerJ

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Background Skeletal muscle is not only an important tissue involved in exercise and metabolism, but also an important part of livestock and poultry meat products. Its growth and development determines the output and quality of meat to a certain extent, and has an important impact on the economic benefits of animal husbandry. Skeletal muscle development is a complex regulatory network process, and its molecular mechanism needs to be further studied. Method We used a weighted co-expression network (WGCNA) and single gene set enrichment analysis (GSEA) to study the RNA-seq data set of bovine tissue differential expression analysis, and the core genes and functional enrichment pathways closely related to muscle tissue development were screened. Finally, the accuracy of the analysis results was verified by tissue expression profile detection and bovine skeletal muscle satellite cell differentiation model in vitro (BSMSCs). Results In this study, Atp2a1, Tmod4, Lmod3, Ryr1 and Mybpc2 were identified as marker genes in muscle tissue, which are mainly involved in glycolysis/gluconeogenesis, AMPK pathway and insulin pathway. The assay results showed that these five genes were highly expressed in muscle tissue and positively correlated with the differentiation of bovine BSMSCs. Conclusions In this study, several muscle tissue characteristic genes were excavated, which may play an important role in muscle development and provide new insights for bovine molecular genetic breeding.

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“…WGCNA is often used to construct the co-expression module and identify hub genes (HUBG) within each module by describing patterns of correlation between genes based on similarities in gene expression profiles [ 27 ]. Moreover, WGCNA has been widely utilized to explore the relationship between genes and tissues for the identification of the HUBGs for various tissues in mammals, including cancer tissues in the human [ 28 ], subcutaneous adipose [ 29 ], and multiple tissues in cattle [ 21 ], brains in pigs [ 30 ], and skin and hair follicle in goats [ 31 ].…”

Section: Introductionmentioning

confidence: 99%

Expression Profile of Housekeeping Genes and Tissue-Specific Genes in Multiple Tissues of Pigs

Pan

Cai

Wang

et al. 2022

Animals

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Pigs have become an ideal model system for human disease research and development and an important farm animal that provides a valuable source of nutrition. To profile the all-sided gene expression and their biological functions across multiple tissues, we conducted a comprehensive analysis of gene expression on a large scale around the side of housekeeping genes (HKGs), tissue specific genes (TSGs), and the co-expressed genes in 14 various tissues. In this study, we identified 2351 HKGs and 3018 TSGs across tissues, among which 4 HKGs (COX1, UBB, OAZ1/NPFF) exhibited low variation and high expression levels, and 31 particular TSGs (e.g., PDC, FKBP6, STAT2, and COL1A1) were exclusively expressed in several tissues, including endocrine brain, ovaries, livers, backfat, jejunum, kidneys, lungs, and longissimus dorsi muscles. We also obtained 17 modules with 230 hub genes (HUBGs) by weighted gene co-expression network analysis. On the other hand, HKGs functions were enriched in the signaling pathways of the ribosome, spliceosome, thermogenesis, oxidative phosphorylation, and nucleocytoplasmic transport, which have been highly suggested to involve in the basic biological tissue activities. While TSGs were highly enriched in the signaling pathways that were involved in specific physiological processes, such as the ovarian steroidogenesis pathway in ovaries and the renin-angiotensin system pathway in kidneys. Collectively, these stable, specifical, and co-expressed genes provided useful information for the investigation of the molecular mechanism for an understanding of the genetic and biological processes of complex traits in pigs.

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Weighted Gene Co-Expression Network Analysis Identifies Key Modules and Central Genes Associated With Bovine Subcutaneous Adipose Tissue

Cited by 3 publications

References 37 publications

Identification of crucial modules and genes associated with backfat tissue development by WGCNA in Ningxiang pigs

Identification of crucial modules and genes associated with backfat tissue development by WGCNA in Ningxiang pigs

Identification of key genes in bovine muscle development by co-expression analysis

Expression Profile of Housekeeping Genes and Tissue-Specific Genes in Multiple Tissues of Pigs

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