Document Type
Article
Original Publication Date
2015
Journal/Book/Conference Title
Bionformatics and Biology Insights
Volume
2015
Issue
Suppl. 3
DOI of Original Publication
10.4137/BBI.S29470
Date of Submission
April 2016
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by complex interplay among immune cell types. SLE activity is experimentally assessed by several blood tests, including gene expression profiling of heterogeneous populations of cells in peripheral blood. To better understand the contribution of different cell types in SLE pathogenesis, we applied the two methods in cell-type-specific differential expression analysis, csSAM and DSection, to identify cell-type-specific gene expression differences in heterogeneous gene expression measures obtained using RNA-seq technology. We identified B-cell-, monocyte-, and neutrophil-specific gene expression differences. Immunoglobulin-coding gene expression was altered in B-cells, while a ribosomal signature was prominent in monocytes. On the contrary, genes differentially expressed in the heterogeneous mixture of cells did not show any functional enrichment. Our results identify antigen binding and structural constituents of ribosomes as functions altered by B-cell- and monocyte-specific gene expression differences, respectively. Finally, these results position both csSAM and DSection methods as viable techniques for celltype-specific differential expression analysis, which may help uncover pathogenic, cell-type-specific processes in SLE.
Rights
© the authors, publisher and licensee Libertas Academica Limited.
Is Part Of
VCU Biostatistics Publications
Comments
Originally published at: http://dx.doi.org/10.4137/BBI.S29470