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

Comments

Originally published at: http://dx.doi.org/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

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