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The new era of autoimmune disease research

DOI: 10.1186/ar3335

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Microarray analysis and gene expression profiling allow patterns of gene expression in diseases and developmental processes to be assessed. Advances in biological databases have enabled the large-scale expression profiling data to be processed and the foundation for biological interpretation to be laid. Despite this, a major limitation involves the interpretation of massive amounts of microarray data. In microarray analysis, which is often used to identify differentially expressed genes, genes that are expressed at higher or lower levels than controls are of interest. In the previous issue of Arthritis Research & Therapy, Lee and colleagues [1] conducted gene expression and bioinformatics analyses between healthy individuals and patients with systemic lupus erythematosus (SLE) and provided insights into biological and functional abnormalities in SLE as well as abnormal regulatory networks. Such analyses - that is, gene ontology analysis, which is used to classify genes into functionally related gene groups, and network pathway analysis, which identifies relationships among these genes - provide an additional layer of insight that cannot be achieved by focusing on individual molecules [1].Lee and colleagues [2] previously demonstrated, by DNA microarray and bioinformatics analyses, that genes related to the immune response were differentially expressed in patients with SLE compared with healthy controls. Other studies have also reported increased expression of IFN-inducible genes (that is, the 'IFN signature') in peripheral blood cells from patients with SLE [2-4]. Many groups are currently looking into pathological roles of plasmacytoid dendritic cells (pDCs) and IFN-inducible genes in SLE since pDCs are major producers of IFN-α [4-7]. Given that SLE is a systemic disease that influences multiple organs, Lee and colleagues [1] emphasized the importance of assessing biological and cellular abnormalities associated with SLE other than those related to the immune respo

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