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Application of WGCNA and PloGO2 in the Analysis of Complex Proteomic Data
In this protocol we describe our workflow for analyzing complex, multi-condition quantitative proteomic experiments, with the aim to extract...
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Identification of unique transcriptomic signatures through integrated multispecies comparative analysis and WGCNA in bovine oocyte development
BackgroundCattle ( Bos taurus ) are a major large livestock, however, compared with other species, the transcriptional specificity of bovine oocyte...
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Identification and validation of seed dormancy loci and candidate genes and construction of regulatory networks by WGCNA in maize introgression lines
Key messageSeventeen PHS-QTLs and candidate genes were obtained, including eleven major loci, three under multiple environments and two with...
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WGCNA and transcriptome profiling reveal hub genes for key development stage seed size/oil content between wild and cultivated soybean
BackgroundSoybean is one of the most important oil crops in the world. The domestication of wild soybean has resulted in significant changes in the...
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Genetic architecture and key regulatory genes of fatty acid composition in Gushi chicken breast muscle determined by GWAS and WGCNA
BackgroundFatty acids composition in poultry muscle is directly related to its tenderness, flavour, and juiciness, whereas its genetic mechanisms...
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Identification of adult resistant genes to stripe rust in wheat from southwestern China based on GWAS and WGCNA analysis
Key messageIn this study, genome-wide association studies combined with transcriptome data analysis were utilized to reveal potential candidate genes...
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ARG1 as a promising biomarker for sepsis diagnosis and prognosis: evidence from WGCNA and PPI network
BackgroundSepsis is a life-threatening multi-organ dysfunction caused by the dysregulated host response to infection. Sepsis remains a major global...
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Comparative Transcriptome and WGCNA Analysis Reveal Molecular Responses to Salinity Change in Larvae of the Iwagaki Oyster Crassostrea Nippona
The Iwagaki oyster Crassostrea nippona is an important aquaculture species with significant potential for large-scale oyster farming. It is...
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GWAS across multiple environments and WGCNA suggest the involvement of ZmARF23 in embryonic callus induction from immature maize embryos
Key messageCombined GWAS, WGCNA, and gene-based association studies identified the co-expression network and hub genes for maize EC induction....
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GWAS Combined with WGCNA of Transcriptome and Metabolome to Excavate Key Candidate Genes for Rice Anaerobic Germination
Direct seeding of rice is a lightweight and simple cultivation method, which can effectively promote rice production. Anaerobic germination tolerance...
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Development and validation of an RBP gene signature for prognosis prediction in colorectal cancer based on WGCNA
BackgroundRNA binding proteins (RBPs) have been implicated in oncogenesis and progression in various cancers. However, the potential value of RBPs as...
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Identification of Key Genes and Pathways for Anaerobic Germination Tolerance in Rice Using Weighted Gene Co-Expression Network Analysis (WGCNA) in Association with Quantitative Trait Locus (QTL) Mapping
BackgroundRice is one of the most important food crops in the world, and with the development of direct seeding methods for rice, exposure to...
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Identification of hub genes that variate the qCSS12-mediated cold tolerance between indica and japonica rice using WGCNA
Key messageCold-tolerant QTL
qCSS12 -regulated 14 hub genes are involved in the chloroplastic biological processes and in the protein synthesis and...
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Integrated transcriptomic and WGCNA analyses reveal candidate genes regulating mainly flavonoid biosynthesis in Litsea coreana var. sinensis
Litsea coreana Levl. var. sinensis (Allen) Yang et P. H. Huang is a popular ethnic herb and beverage plant known for its high flavonoid content,...
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Root and shoot biology of Arabidopsis halleri dissected by WGCNA: an insight into the organ pivotal pathways and genes of an hyperaccumulator
Arabidopsis halleri is a hyperaccumulating pseudo-metallophyte and an emerging model to explore molecular basis of metal tolerance and...
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Identification of key sex-specific pathways and genes in the subcutaneous adipose tissue from pigs using WGCNA method
BackgroundAdipose tissues (ATs), including visceral ATs (VATs) and subcutaneous ATs (SATs), are crucial for maintaining energy and metabolic...
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Metabolic Networks: Weighted Gene Correlation Network Analysis
Weighted Gene Correlation Network Analysis (WGCNA) is used to build weighted gene networks representing direct interconnections among genes. This...
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Transcriptome sequencing analysis and WGCNA reveal the internal molecular mechanism that triggers programmed cell death in rice mutant zj-lm
A spontaneous lesion mimic mutant named ZheJing-lesion mimic ( zj-lm ) was characterized from the mutant library of Japonica rice ( Oryza sativa )...
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GWAS and WGCNA uncover hub genes controlling salt tolerance in maize (Zea mays L.) seedlings
KeymessageTwo hub genes
GRMZM2G075104 andGRMZM2G333183 involved in salt tolerance were identified by GWAS and WGCNA. Furthermore, they were verified...
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Using weighted gene co-expression network analysis (WGCNA) to identify the hub genes related to hypoxic adaptation in yak (Bos grunniens)
BackgroundAs a mammal living at the highest altitude in the world, the yak has strong adaptability to the harsh natural environment (such as low...
