Unveiling transcription factor regulation and differential co-expression genes in Duchenne muscular dystrophy

BACKGROUND: Gene expression analysis is powerful for investigating the underlying mechanisms of Duchenne muscular dystrophy (DMD). Previous studies mainly neglected co-expression or transcription factor (TF) information. Here we integrated TF information into differential co-expression analysis (DCEA) to explore new understandings of DMD pathogenesis. METHODS: Using two microarray datasets from Gene Expression Omnibus (GEO) database, we firstly detected differentially expressed genes (DEGs) and pathways enriched with DEGs. Secondly, we constructed differentially regulated networks to integrate the TF-to-target information and the differential co-expression genes. RESULTS: A total of 454 DEGs were detected and both KEGG pathway and ingenuity pathway analysis revealed that pathways enriched with aberrantly regulated genes are mostly involved in the immune response processes. DCEA results generated 610 pairs of DEGs regulated by at least one common TF, including 78 pairs of co-expressed DEGs. A network was constructed to illustrate their relationships and a subnetwork for DMD related molecules was constructed to show genes and TFs that may play important roles in the secondary changes of DMD. Among the DEGs which shared TFs with DMD, six genes were co-expressed with DMD, including ATP1A2, C1QB, MYOF, SAT1, TRIP10, and IFI6. CONCLUSION: Our results may provide a new understanding of DMD and contribute potential targets for future therapeutic tests. VIRTUAL SLIDES: The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/13000_2014_210