Abstract
BackgroundDuchenne Muscular Dystrophy (DMD) is an X-linked recessive disorder with its primary insult on the skeletal muscle. Severe muscle wasting, chronic inflammation and fibrosis characterize dystrophic muscle. Here we identify dysregulated pathways in DMD utilizing a co-expression network approach as described in Weighted Gene Co-expression Network Analysis (WGCNA). Specifically, we utilize WGCNA’s “preservation” statistics to identify gene modules that exhibit a weak conservation of network topology within healthy and dystrophic networks. Preservation statistics rank modules based on their topological metrics such as node density, connectivity and separability between networks.MethodsRaw data for DMD was downloaded from Gene Expression Omnibus (GSE6011) and suitably preprocessed. Co-expression networks for each condition (healthy and dystrophic) were generated using the WGCNA library in R. Preservation of healthy network edges was evaluated with respect to dystrophic muscle and vice versa using WGCNA. Highly exclusive gene pairs for each of the low preserved modules within both networks were also determined using a specificity measure.ResultsA total of 11 and 10 co-expressed modules were identified in the networks generated from 13 healthy and 23 dystrophic samples respectively. 5 out of the 11, and 4 out of the 10 modules were identified as exhibiting none-to-weak preservation. Functional enrichment analysis identified that these weakly preserved modules were highly relevant to the condition under study. For instance, weakly preserved dystrophic module D2 exhibited the highest fraction of genes exclusive to DMD. The highly specific gene pairs identified within these modules were enriched for genes activated in response to wounding and affect the extracellular matrix including several markers such as SPP1, MMP9 and ITGB2.ConclusionThe proposed approach allowed us to identify clusters of genes that are non-randomly associated with the disease. Furthermore, highly specific gene pairs pointed to interactions between known markers of disease and identification of putative markers likely associated with disease. The analysis also helped identify putative novel interactions associated with the progression of DMD.Electronic supplementary materialThe online version of this article (doi:10.1186/s13104-015-1141-9) contains supplementary material, which is available to authorized users.
Highlights
Duchenne Muscular Dystrophy (DMD) is an X-linked recessive disorder with its primary insult on the skeletal muscle
We evaluated differential mechanisms between dystrophic and healthy skeletal muscle using the following approach; first, co-expression networks were generated independently for healthy and dystrophic samples; second, clustering each of the co-expression networks resulted in several groups of biologically relevant genes for each condition; and preservation of modular topology from one condition was detected with respect to the second condition, allowing us to identify differences in gene connectivity patterns between conditions
Our results indicate that the modules exhibiting low preservation statistics contain several gene pairs that are likely to be associated with the disease progression
Summary
Duchenne Muscular Dystrophy (DMD) is an X-linked recessive disorder with its primary insult on the skeletal muscle. We identify dysregulated pathways in DMD utilizing a co-expression network approach as described in Weighted Gene Coexpression Network Analysis (WGCNA). We utilize WGCNA’s “preservation” statistics to identify gene modules that exhibit a weak conservation of network topology within healthy and dystrophic networks. Duchenne muscular dystrophy (DMD), is a lethal form of dystrophinopathy characterized by marked deficiency or absence of subsarcolemmal cytoskeletal protein- dystrophin. Absence of this protein is caused due to frame shift mutations of the dystrophin gene [1]. We utilize a co-expression networks approach to gain insights into molecular interactions dysregulated in dystrophic skeletal muscle with respect to healthy muscle
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