Fig. 4

Comparison of RAS-adjusted methods on the GSL pathway between NB +MYCN and GNB. Left dot plots illustrate the adjusted RAS values of NB +MYCN (“NB_MYCN_amp” in figure) and GNB, as well as the log2 fold-change between the two groups. The whiskers indicate the standard deviation. The color intensity of log2 fold-change points indicates the negative decimal logarithm of the adjusted p-values. On the right, the subgraph containing the GSL pathway is visualized. Nodes represent the gangliosides and edges are the metabolic reactions (arrows). The arrow color describes the log2 fold-change direction, where red means that the reaction is more active in NB +MYCN compared to GNB and blue means the reaction is stronger in GNB compared to NB +MYCN. Gray arrows represent reactions that are not significant (adjusted p-value \(> 0.05\)). The thickness of the arrow represents the relative log2 fold-change. The subplots show A) values from \(M_{W}\) (RAS values), B) \(M_{W_{1}}\) (RAS values adjusted by TP), C) \(M_{W_{2}}\) (RAS adjusted by the recursive TP), and D) \(M_{W_{3}}\) (RAS adjusted by TP of paths)