Identify the signature genes for diagnose of uveal melanoma by weight gene co-expression network analysis.
OBJECTIVE
To 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.


METHODS
Gene 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).


RESULTS
In 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.


CONCLUSIONS
From WGCNA analysis and hub gene calculation, we identified RPS15A, PTGDS, CD53 and MSI2 might be target or diagnosis for uveal melanoma.
Department of Ophthalmology, West China Hospital, Sichuan University, Chendu 610041, Sichuan Province, China ; Molecular Medicine Research Center, West China Hospital, Sichuan University, Chendu 610041, Sichuan Province, China.
Kai
K
Shi
Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, Gansu Province, China.
Zhi-Tong
ZT
Bing
Molecular Medicine Research Center, West China Hospital, Sichuan University, Chendu 610041, Sichuan Province, China.
Gui-Qun
GQ
Cao
College of Electrical Engineering, Northwest University for Nationalities, Lanzhou 730030, Gansu Province, China.
Ling
L
Guo
Department of Ophthalmology, West China Hospital, Sichuan University, Chendu 610041, Sichuan Province, China ; Molecular Medicine Research Center, West China Hospital, Sichuan University, Chendu 610041, Sichuan Province, China.
Ya-Na
YN
Cao
Molecular Medicine Research Center, West China Hospital, Sichuan University, Chendu 610041, Sichuan Province, China.
Hai-Ou
HO
Jiang
Department of Ophthalmology, West China Hospital, Sichuan University, Chendu 610041, Sichuan Province, China ; Molecular Medicine Research Center, West China Hospital, Sichuan University, Chendu 610041, Sichuan Province, China.
Mei-Xia
MX
Zhang
gene ontology; microarray data; weighted gene co-expression network analysis