Fig 1. Experimental set up and analyses of expression profiling data.

(A) Schematic overview of sampling. MB: myoblasts cultured in growth medium. MT: myotubes cultured in differentiation medium. TNF: myotubes cultured in differentiation medium with TNF-α. IGF: myotubes cultured in differentiation medium with IGF-1. (B) Gene expression data were analyzed by hierarchical clustering, principal component analysis (PCA), and dynamic PCA among others. Moreover, the profiling data were clustered by applying the self-organized tree algorithm (SOTA) as well as pathway association enrichment analyses. Furthermore, genes adversely regulated by differentiation and TNF-α were identified. Finally, TNF-α-regulated genes were compared with results of other studies. The study identified novel insights into the gene expression mechanisms and kinetics of early skeletal myocyte differentiation and how this is modified by TNF-α.