Weighted gene co-expression network analysis (WGCNA) is often used to analyze multi-sample (>15) data, identify co-expressed modules, and explore the relationship between modules target traits in systematic biology. In order response to  Magnaporthe oryzae  infection rice near iso-genic lines (NIL) carrying different broad-spectrum resistance genes. We analyzed expression pattern o...

Abstract Background Long intergenic non-coding RNAs (lincRNAs) are capable of regulating several tumours, while competitive endogenous RNA (ceRNA) networks great significance in revealing the biological mechanism tumours. Here, we aimed to study ceRNA network lincRNA glioblastoma (GBM). Methods We obtained GBM and normal brain tissue samples from TCGA, GTEx, GEO databases, performed weighted ge...

The biology of sperm, its capability of fertilizing an egg and its role in sex ratio are the major biological questions in reproductive biology. To answer these question we integrated X and Y chromosome transcriptome across different species: Bos taurus and Sus scrofa and identified reproductive driver genes based on Weighted Gene Co-Expression Network Analysis (WGCNA) algorithm. Our strategy r...

Human clear cell renal cell carcinoma (ccRCC) is one of the most common types of malignant adult kidney tumors. We constructed a weighted gene co-expression network to identify gene modules associated with clinical features of ccRCC (n = 97). Six hub genes (CCNB2, CDC20, CEP55, KIF20A, TOP2A and UBE2C) were identified in both co-expression and protein-protein interaction (PPI) networks, which w...

Melanoma is a fatal skin malignant tumor with poor prognosis. We found that long noncoding RNA BASP1-AS1 essential for the development and prognosis of melanoma. The methylation, sequencing, copy number variation, mutation data, sample follow-up information melanoma from Cancer Genome Atlas (TCGA) were analyzed using weighted gene co-expression network analysis 366 samples common to three omics...

Anthocyanin is the key factor that results in attractive color of sweet cherry fruits. However, information regarding coloration and potential mechanisms underlying anthocyanin biosynthesis limited. In this study, we found accumulation varied flesh peel, while content increased sharply dark red (DR) stage. Correlations between concentrations RNA sequencing (RNA-seq), constructed with Weighted G...

Systemic lupus erythematosus is a diffuse connective tissue disease mediated by autoimmunity and characterized immune inflammation. The purpose of this study to explore candidate key genes cell infiltration involved in the pathogenesis systemic erythematosus. Intersection derived from differentially expressed between patients healthy individuals are identified weighted gene co-expression networ...

Abstract Chronic Infection of Hepatitis B virus (HBV) is one risk factor hepatocellular carcinoma (HCC). Much effort has been made to research the process HBV-associated HCC, but its molecular mechanisms carcinogenesis remain vague. Here, weighted gene co-expression network analysis (WGCNA) was employed explore co-expressed modules and hub/key genes correlated HCC. We found that most significan...

This study aimed to identify more biomarkers associated with osteosarcoma progression via lncRNA-mRNA co-expression network. Dataset GSE99671 was downloaded from GEO database. The mRNAs and lncRNAs that were differentially expressed between tumor normal samples screened out. Functional enrichment analysis of carried out, followed by weighted gene correlation network (WGCNA). Based on the mRNAs,...

Abstract Background Cognitive reserve (CR) is susceptibility to brain damages, which impacts the development of Alzheimer’s disease (AD). Whereas CR associated with certain subnetworks connectivity, little research has been done on identifying genes that contribute these subnetworks. In this study, we linked regional variation in brain‐wide gene expression. We utilized Allen Human Brain Atlas (...