title: A novel method to identify pathways associated with renal cell carcinoma based on a gene co-expression network.
abstract: The aim of the present study was to develop a novel method for identifying pathways associated with renal cell carcinoma (RCC) based on a gene co-expression network. A framework was established where a co-expression network was derived from the database as well as various co-expression approaches. First, the backbone of the network based on differentially expressed (DE) genes between RCC patients and normal controls was constructed by the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database. The differentially co-expressed links were detected by Pearson's correlation, the empirical Bayesian (EB) approach and Weighted Gene Co-expression Network Analysis (WGCNA). The co-expressed gene pairs were merged by a rank-based algorithm. We obtained 842; 371; 2,883 and 1,595 co-expressed gene pairs from the co-expression networks of the STRING database, Pearson's correlation EB method and WGCNA, respectively. Two hundred and eighty-one differentially co-expressed (DC) gene pairs were obtained from the merged network using this novel method. Pathway enrichment analysis based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and the network enrichment analysis (NEA) method were performed to verify feasibility of the merged method. Results of the KEGG and NEA pathway analyses showed that the network was associated with RCC. The suggested method was computationally efficient to identify pathways associated with RCC and has been identified as a useful complement to traditional co-expression analysis.
authors.affiliation: Department of Neurology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250021, P.R. China.
authors.forename: Xiyun
authors.initials: X
authors.lastname: Ruan
authors.affiliation: Department of Urology, Shandong Provincial Qianfoshan Hospital Affiliated to Shandong University, Jinan, Shandong 250014, P.R. China.
authors.forename: Hongyun
authors.initials: H
authors.lastname: Li
authors.affiliation: ICU, Affiliated Hospital of Jining Medical University, Jining, Shandong 272129, P.R. China.
authors.forename: Bo
authors.initials: B
authors.lastname: Liu
authors.affiliation: Department of Urology, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong 250013, P.R. China.
authors.forename: Jie
authors.initials: J
authors.lastname: Chen
authors.affiliation: Department of Urology, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong 250013, P.R. China.
authors.forename: Shibao
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Department of Urology, Shandong Provincial Qianfoshan Hospital Affiliated to Shandong University, Jinan, Shandong 250014, P.R. China.
authors.forename: Zeqiang
authors.initials: Z
authors.lastname: Sun
authors.affiliation: Department of Urology, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong 250013, P.R. China.
authors.forename: Shuangqing
authors.initials: S
authors.lastname: Liu
authors.affiliation: Department of Urology, Shandong Provincial Qianfoshan Hospital Affiliated to Shandong University, Jinan, Shandong 250014, P.R. China.
authors.forename: Fahai
authors.initials: F
authors.lastname: Sun
authors.affiliation: Department of Urology, Shandong Provincial Qianfoshan Hospital Affiliated to Shandong University, Jinan, Shandong 250014, P.R. China.
authors.forename: Qingyong
authors.initials: Q
authors.lastname: Liu
mesh_terms: D001499:Bayes Theorem; D002292:Carcinoma, Renal Cell / Q000235:genetics*; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D056726:Genetic Association Studies / Q000379:methods*; D020022:Genetic Predisposition to Disease; D006801:Humans; D007680:Kidney Neoplasms / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis