A comparative gene expression profiling of spondyloarthropathy and rheumatoid arthritis using oligonucleotide based microarrays

Comparative gene expression profiling of mononuclear cells from synovial fluid samples of rheumatoid arthritis (RA) and spondyloarthropathy (SpA) cases was performed. A total of 72 transcripts were found to be differentially expressed in RA compared to SpA, with p-value threshold of 0.05 and using the Benjamini-Hochberg False Discovery rate multiple comparison corrections. From the list, 57 transcripts were found to be upregulated in RA as compared to SpA and 15 downregulated by a fold change cut-off of 1.5-fold. The proposed study carried out mRNA expression profiling of mononuclear cells from synovial fluid samples of seven RA and five SpA cases. We have used 4X44K and 1X44K arrays from Agilent Technologies platform. Based on the RNA integrity, selected molecules were processed further using single-color microarray based gene expression. The raw data files obtained from this study were eventually analyzed with R package of the BioConductor suite.