title: Identification of hub genes and pathways associated with retinoblastoma based on co-expression network analysis.
abstract: The objective of this paper was to identify hub genes and pathways associated with retinoblastoma using centrality analysis of the co-expression network and pathway-enrichment analysis. The co-expression network of retinoblastoma was constructed by weighted gene co-expression network analysis (WGCNA) based on differentially expressed (DE) genes, and clusters were obtained through the molecular complex detection (MCODE) algorithm. Degree centrality analysis of the co-expression network was performed to explore hub genes present in retinoblastoma. Pathway-enrichment analysis was performed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Validation of hub gene expression in retinoblastoma was performed by reverse transcription-polymerase chain reaction (RT-PCR) analysis. The co-expression network based on 221 DE genes between retinoblastoma and normal controls consisted of 210 nodes and 3965 edges, and 5 clusters of the network were evaluated. By assessing the centrality analysis of the co-expression network, 21 hub genes were identified, such as SNORD115-41, RASSF2, and SNORD115-44. According to RT-PCR analysis, 16 of the 21 hub genes were differently expressed, including RASSF2 and CDCA7, and 5 were not differently expressed in retinoblastoma compared to normal controls. Pathway analysis showed that genes in 2 clusters were enriched in 3 pathways: purine metabolism, p53 signaling pathway, and melanogenesis. In this study, we successfully identified 16 hub genes and 3 pathways associated with retinoblastoma, which may be potential biomarkers for early detection and therapy for retinoblastoma.
authors.affiliation: Department of Ophthalmology, The Second Hospital of Ji'nan, Ji'nan, China.
authors.forename: Q L
authors.initials: QL
authors.lastname: Wang
authors.affiliation: Department of Ophthalmology, The Ninth Hospital of Chongqing, Chongqing, China.
authors.forename: X
authors.initials: X
authors.lastname: Chen
authors.affiliation: Department of General Surgery, The Fourth Hospital of Ji'nan, Ji'nan, China.
authors.forename: M H
authors.initials: MH
authors.lastname: Zhang
authors.affiliation: Department of Medicine, Shandong Medical College, Shandong, China.
authors.forename: Q H
authors.initials: QH
authors.lastname: Shen
authors.affiliation: Department of Nursing, Shandong Medical College, Shandong, China.
authors.forename: Z M
authors.initials: ZM
authors.lastname: Qin
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D006801:Humans; D060066:Protein Interaction Maps; D015203:Reproducibility of Results; D012175:Retinoblastoma / Q000235:genetics* / Q000378:metabolism*; D015398:Signal Transduction