ArticleGenes & genomics2021
Using weighted gene co-expression network analysis (WGCNA) to identify the hub genes related to hypoxic adaptation in yak (Bos grunniens).
Article in Genes & genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 2 of them syntheses that pooled it.
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20 citing papers in PubMed, 2 syntheses or guidelines pooled it, 28 citations in OpenAlex.
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- Genetic Variation and Haplotype Structure ofLife (Basel, Switzerland) · 2026Article
- Multi-Omics Analysis Reveals New Insights into Yak Lung Under High-Altitude Adaptation.Animals : an open access journal from MDPI · 2026Article
- Study on the mechanism of action of HuaZhuoKeLi in modulating LCN2-mediated cellular pyroptosis to ameliorate ulcerative colitis.Scientific reports · 2026Article
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- A comprehensive study on the longissius dorsi muscle of Ashdan yaks under different feeding regimes based on transcriptomic and metabolomic analyses.Animal biotechnology · 2024Article
- Whole genome resequencing-based analysis of plateau adaptation in Meiren yak (Animal biotechnology · 2024Article
- Cloning, bioinformatics analysis and expression of the cysteine dioxygenase type 1 (CDO1) gene in domestic yak.Frontiers in veterinary science · 2024Article
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- Nd-Mn Molecular Cluster with Searched Targets for Oral Cancer Imaging.Molecular imaging and biology · 2023Article
- Genomic selection analysis of morphological and adaptation traits in Chinese indigenous dog breeds.Frontiers in veterinary science · 2023Article
- Genome-wide identification and in-silico expression analysis of carotenoid cleavage oxygenases gene family inFrontiers in plant science · 2023Article
- Identification of key sex-specific pathways and genes in the subcutaneous adipose tissue from pigs using WGCNA method.BMC genomic data · 2022Article
- Integration of RNA-seq and ATAC-seq identifies muscle-regulated hub genes in cattle.Frontiers in veterinary science · 2022Article
- Identification of the hub genes related to adipose tissue metabolism of bovine.Frontiers in veterinary science · 2022Article
- Transcriptome analysis of pika heart tissue reveals mechanisms underlying the adaptation of a keystone species on the roof of the world.Frontiers in genetics · 2022Article
- Integrative analysis identifies potential ferroptosis-related genes of hypoxia adaptation in yak.Frontiers in veterinary science · 2022Article
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7 authors at 1 institution in 1 country.
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Abstract
backgroundAs a mammal living at the highest altitude in the world, the yak has strong adaptability to the harsh natural environment (such as low temperature, scarce food, especially low oxygen) of Qinghai-Tibet Plateau (QTP) after a long process of natural selection.
objectiveHere, we used Weighted Correlation Network Analysis (WGCNA), a systematic biology method, to identify hypoxic adaptation-related modules and hub genes. The research of the adaptability of yak against hypoxia is of great significance to identify the genetic characteristics and yak breeding.
methodsBased on the transcriptome sequencing data (PRJNA362606), the R package DESeq2 and WGCNA were conducted to analyze differentially expressed genes (DEGs) and construct the gene co-expression network. The module hub genes were identified and characterized by the correlation of gene and trait, module membership (kME). In addition, GO and KEGG enrichment analyses were used to explore the functions of hub genes.
resultsOur results revealed that 1098, 1429, and 1645 DEGs were identified in muscle, spleen, and lung, respectively. Besides, a total of 13 gene co-expression modules were detected, of which two hypoxic adaptation-related modules (saddlebrown and turquoise) were found. We identified 39 and 150 hub genes in these two modules. Functional enrichment analyses showed that 12 GO terms and 18 KEGG pathways were enriched in the saddlebrown module while 85 GO terms and 22 KEGG pathways were enriched in the turquoise module. The significant pathways related to hypoxia adaptation include FoxO signaling pathway, Thermogenesis pathway, and Retrograde endocannabinoid signaling pathway, etc.
conclusionsIn this study, we obtained two hypoxia-related specific modules and identified hub genes based on the connectivity by constructing a weighted gene co-expression network. Function enrichment analysis of two modules revealed mitochondrion is the most important organelle for hypoxia adaptation. Moreover, the insulin-related pathways and thermogenic-related pathways played a major role. The results of this study provide theoretical guidance for further understanding the molecular mechanism of yak adaptation to hypoxia.
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