Dataset collection

Gene expression profiling studies were identified by searching PubMed (http://www.ncbi.nlm.nih.gov/pubmed). The following key words and their combinations were used: “osteoporosis,” “BMD,” “gene expression,” and “microarray.” The Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geowebcite) and ArrayExpress (http://www.ebi.ac.uk/arrayexpress/) were also used to identify and download relevant microarray datasets through September 2014. Studies were included in the analysis if they met the following criteria: (1) case-control studies for BMD or osteoporosis in human subjects, (2) gene expression raw data available, and (3) phenotype of subjects available. We conducted this meta-analysis in accordance with the guidelines provided in the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement (http://www.prisma-statement.org/) (S1 PRISMA Checklist) [17]. Raw data were downloaded from GEO and ArrayExpress websites. The following information was extracted from each identified study: Accession number, subjects, platform, number of cases and controls, tissue/cell type and raw gene expression data. Although the quantile or z-score for each study’s inclusion criteria is different, according to WHO definition [18], the low BMD group in all six studies can be classified into osteopenia/osteoporosis, while the high BMD group in all six studies can be classified into the normal.