Figure 3

(a) Manhattan plot of differentially expressed (DE) spectral features. The left and right column of plots represented the positively and negatively charged peaks. Four temporal phases were arranged chronologically from top to bottom; the top row with two plots were linked to the Early phase and next three rows of plots were linked to Mid, Late and LR phases, respectively. The negative log transformed hypergeometric p-values of each spectral feature were presented in each plot, where the p-values measured the significance of divergence of the putative metabolites from the pre-TBI baseline. The red colored dots demonstrated highly significant spectral features [− log(p-value) > 3] and among these red dots, the HMDB-annotated spectral features were marked with their corresponding putative metabolite names. (b) Venn diagram of the Differentially abundant putative metabolites across the four temporal phases. The longitudinal distribution of these metabolites suggested that nearly 37% of them were consistently perturbed in at least two temporal phases starting from Early. These putative metabolites are listed in Table 2. (c) Network linked to dystrophy of muscle. This network was inferred from a group of DE miRNAs and differentially abundant putative metabolites. Angiogenesis emerged as one significant and pertinent network linked to muscular dystrophy. In the network, the rectangular, oval and hexagonal nodes represent biofucntions, miRNAs and putative metabolites, respectively. The rhombus shaped nodes were inserted to connect two molecules of interest, although the regulations of these molecules inside the rhombus nodes were not determined by present set of assays. The four segments of the bar at the bottom of each miRNAs and putative metabolites documented the regulations in four temporal phases arranged chronologically from left to right. The red-, green- and yellow-colored segments represented up-, down and unchanged regulations in comparison to the pre-TBI baseline. The edges represent the relationship between two nodes; the arrow-headed edges represent activation, and the straight-lined edges represent association between two nodes.