A meta-analysis of public microarray data identifies gene regulatory pathways deregulated in peripheral blood mononuclear cells from individuals with Systemic Lupus Erythematosus compared to those without
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Date
2017
Journal Title
Journal ISSN
Volume Title
Publisher
BioMed Central
Abstract
BACKGROUND: Systemic Lupus Erythematosus (SLE) is a complex, multi-systemic, autoimmune disease for which the
underlying aetiological mechanisms are poorly understood. The genetic and molecular processes underlying lupus
have been extensively investigated using a variety of -omics approaches, including genome-wide association studies,
candidate gene studies and microarray experiments of differential gene expression in lupus samples compared to
controls.
METHODS: This study analyses a combination of existing microarray data sets to identify differentially regulated genetic
pathways that are dysregulated in human peripheral blood mononuclear cells from SLE patients compared to unaffected
controls. Two statistical approaches, quantile discretisation and scaling, are used to combine publicly available expression
microarray datasets and perform a meta-analysis of differentially expressed genes.
RESULTS: Differentially expressed genes implicated in interferon signaling were identified by the meta-analysis,
in agreement with the findings of the individual studies that generated the datasets used. In contrast to the
individual studies, however, the meta-analysis and subsequent pathway analysis additionally highlighted TLR
signaling, oxidative phosphorylation and diapedesis and adhesion regulatory networks as being differentially
regulated in peripheral blood mononuclear cells (PBMCs) from SLE patients compared to controls.
CONCLUSION: Our analysis demonstrates that it is possible to derive additional information from publicly
available expression data using meta-analysis techniques, which is particularly relevant to research into rare
diseases where sample numbers can be limiting.
Description
Keywords
Lupus, Systemic Lupus Erythematosus (SLE), Microarray, Gene expression, Meta-analysis
Citation
Kröger, W. et al. (2017). A meta-analysis of public microarray data identifies gene regulatory pathways deregulated in peripheral blood mononuclear cells from individuals with Systemic Lupus Erythematosus compared to those without. BMC Medical Genomics, 9: 66