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
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...
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| Format: | Article |
| Language: | English |
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BMC
2016-11-01
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| Series: | BMC Medical Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12920-016-0227-0 |
| _version_ | 1818426702281310208 |
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| author | Wendy Kröger Darlington Mapiye Jean-Baka Domelevo Entfellner Nicki Tiffin |
| author_facet | Wendy Kröger Darlington Mapiye Jean-Baka Domelevo Entfellner Nicki Tiffin |
| author_sort | Wendy Kröger |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-14T14:34:02Z |
| format | Article |
| id | doaj.art-67e1be4147d84cff95ea751143b42dea |
| institution | Directory Open Access Journal |
| issn | 1755-8794 |
| language | English |
| last_indexed | 2024-12-14T14:34:02Z |
| publishDate | 2016-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Medical Genomics |
| spelling | doaj.art-67e1be4147d84cff95ea751143b42dea2022-12-21T22:57:42ZengBMCBMC Medical Genomics1755-87942016-11-019111110.1186/s12920-016-0227-0A 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 withoutWendy Kröger0Darlington Mapiye1Jean-Baka Domelevo Entfellner2Nicki Tiffin3South African National Bioinformatics Institute/Medical Research Council of South Africa Bioinformatics Capacity Development Unit, University of the Western CapeSouth African National Bioinformatics Institute/Medical Research Council of South Africa Bioinformatics Capacity Development Unit, University of the Western CapeSouth African National Bioinformatics Institute/Medical Research Council of South Africa Bioinformatics Capacity Development Unit, University of the Western CapeSouth African National Bioinformatics Institute/Medical Research Council of South Africa Bioinformatics Capacity Development Unit, University of the Western CapeAbstract 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.http://link.springer.com/article/10.1186/s12920-016-0227-0LupusSystemic Lupus Erythematosus (SLE)MicroarrayGene expressionMeta-analysis |
| spellingShingle | Wendy Kröger Darlington Mapiye Jean-Baka Domelevo Entfellner Nicki Tiffin 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 Lupus Systemic Lupus Erythematosus (SLE) Microarray Gene expression Meta-analysis |
| title | 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 |
| title_full | 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 |
| title_fullStr | 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 |
| title_full_unstemmed | 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 |
| title_short | 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 |
| title_sort | 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 |
| topic | Lupus Systemic Lupus Erythematosus (SLE) Microarray Gene expression Meta-analysis |
| url | http://link.springer.com/article/10.1186/s12920-016-0227-0 |
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