Screening of differentially expressed genes associated with non-union skeletal fractures and analysis with a DNA microarray

The purpose of this study was to identify the feature genes that are associated with non-union skeletal fractures using samples of normal union and non-union skeletal fracture microarray data. The gene expression profile GSE494 was downloaded from the Gene Expression Omnibus database and included 12 samples based on three different platforms (GPL92, GPL93 and GPL8300). Each of the platforms had four sets of expression data, two from normal union skeletal fracture samples and two from non-union skeletal fracture samples. The differentially expressed genes within the three platforms of expression data were identified using packages in R language and the differentially expressed genes common to the three platforms were selected. The selected common differentially expressed genes were further analyzed using bioinformatic methods. The software HitPredict was used to search interactions of the common differentially expressed genes and then FuncAssociate was used to conduct a functional analysis of the genes in the interaction network. Further, the associated pathways were identified using the software WebGestalt. Under the three different platforms, GPL92, GPL93 and GPL8300, the numbers of differentially expressed genes identified were 531, 418 and 914, respectively. The common gene CLU and its interacting genes were most significantly associated with the regulation of sterol transport and the osteoclast differentiation pathway. Upregulation of the gene CLU was identified by comparing data for normal union and non-union skeletal fracture samples. According to the function of CLU and its interacting genes, it was concluded that they inhibit the normal healing process following a fracture, and result in non-union skeletal fractures through the regulation of sterol transport and the pathways of differentiation in osteoclasts.