ArticleInternational journal of ophthalmology2015
Identify the signature genes for diagnose of uveal melanoma by weight gene co-expression network analysis.
Article in International journal of ophthalmology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
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- Psoriasis Associated Hub Genes Revealed by Weighted Gene Co-Expression Network Analysis.Cell journal · 2023Article
- Exploring the molecular mechanism of comorbidity of autism spectrum disorder and inflammatory bowel disease by combining multiple data sets.Journal of translational medicine · 2023Article
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- Identification of 5 microRNA biomarkers associated with the prognosis of uveal melanoma.Medicine · 2022Article
- Identification of hub genes in the subacute spinal cord injury in rats.BMC neuroscience · 2022Article
- Identification of co-expression hub genes for ferroptosis in kidney renal clear cell carcinoma based on weighted gene co-expression network analysis and The Cancer Genome Atlas clinical data.Scientific reports · 2022Article
- Identification of Key Modules and Genes Associated with Major Depressive Disorder in Adolescents.Genes · 2022Article
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- Identification of a Novel Cancer Stemness-Associated ceRNA Axis in Lung Adenocarcinoma via Stemness Indices Analysis.Oncology research · 2021Article
- Weighted gene co-expression network analysis reveals that CXCL10, IRF7, MX1, RSAD2, and STAT1 are related to the chronic stage of spinal cord injury.Annals of translational medicine · 2021Article
- Construction of co-expression modules related to survival by WGCNA and identification of potential prognostic biomarkers in glioblastoma.Journal of cellular and molecular medicine · 2021Article
- Potential Novel Modules and Hub Genes as Prognostic Candidates of Thyroid Cancer by Weighted Gene Co-Expression Network Analysis.International journal of general medicine · 2021Article
- Hub Gene and Its Key Effects on Diffuse Large B-Cell Lymphoma by Weighted Gene Coexpression Network Analysis.BioMed research international · 2021Article
- Identification of a Five-Gene Prognostic Signature Related to B Cells Infiltration in Pancreatic Adenocarcinoma.International journal of general medicine · 2021Article
- Identification of Potential Cytokinin Responsive Key Genes in Rice Treated With Trans-Zeatin Through Systems Biology Approach.Frontiers in genetics · 2021Article
- Identification of co‑expression modules and hub genes of retinoblastoma via co‑expression analysis and protein‑protein interaction networks.Molecular medicine reports · 2020Article
- Weighted gene correlation network analysis reveals novel regulatory modules associated with recurrent early pregnancy loss.Bioscience reports · 2020Article
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7 authors.
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No grant is acknowledged in the PubMed record.
Abstract
aimTo identify and understand the relationship between co-expression pattern and clinic traits in uveal melanoma, weighted gene co-expression network analysis (WGCNA) is applied to investigate the gene expression levels and patient clinic features. Uveal melanoma is the most common primary eye tumor in adults. Although many studies have identified some important genes and pathways that were relevant to progress of uveal melanoma, the relationship between co-expression and clinic traits in systems level of uveal melanoma is unclear yet. We employ WGCNA to investigate the relationship underlying molecular and phenotype in this study.
methodsGene expression profile of uveal melanoma and patient clinic traits were collected from the Gene Expression Omnibus (GEO) database. The gene co-expression is calculated by WGCNA that is the R package software. The package is used to analyze the correlation between pairs of expression levels of genes. The function of the genes were annotated by gene ontology (GO).
resultsIn this study, we identified four co-expression modules significantly correlated with clinic traits. Module blue positively correlated with radiotherapy treatment. Module purple positively correlates with tumor location (sclera) and negatively correlates with patient age. Module red positively correlates with sclera and negatively correlates with thickness of tumor. Module black positively correlates with the largest tumor diameter (LTD). Additionally, we identified the hug gene (top connectivity with other genes) in each module. The hub gene RPS15A, PTGDS, CD53 and MSI2 might play a vital role in progress of uveal melanoma.
conclusionFrom WGCNA analysis and hub gene calculation, we identified RPS15A, PTGDS, CD53 and MSI2 might be target or diagnosis for uveal melanoma.
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