Skip to main content
Figure 3 | BMC Bioinformatics

Figure 3

From: iVUN: interactive Visualization of Uncertain biochemical reaction Networks

Figure 3

Analysis of parameter correlations in the JAK2/STAT5 signaling pathway. By linking the graph view (A) with the Pearson correlation matrix (B), scatter plots and histograms (C), our visual analytics systems iVUN allowed for a step-by-step exploration of the MCMC sample obtained for the JAK2/STAT5 signaling pathway [34]. The graph view (A) shows the reactions (links), states (nodes), and outputs (subsets of nodes surrounded by a semitransparent area). The sample mean of fluxes and states is mapped to the color of links and nodes respectively. The Pearson correlation matrix (B) facilitates the efficient search for pairs of strongly correlated parameters. The selection of individual parameter pairs in the Pearson correlation matrix followed by the automatic highlighting of associated edges in the graph view (A) allows for the identification of these parameters in the BRN. In the JAK2/STAT5 signaling pathway, pairs of strongly correlated parameters in general influence similar states and outputs of the network. In addition, there are some parameters that alter several reaction fluxes, e.g., 'SOC3Inh', and which therefore correlate with many parameters. This yields clusters of strong parameter-wise correlations, which are recognizable in the matrix view. Beyond the analysis of linear correlations using the Pearson correlation matrix, scatter plots (C) reveal nonlinear correlation structures as shown for 'SOCS3RNADelay' and 'SOCS3RNATurn'. The parameter sample for the JAK2/STAT5 signaling pathway shows only few strongly nonlinear correlations, although histograms (C) reveal that, e.g., the distribution for the parameter 'SOCS3RNATurn' is bimodal.

Back to article page
\