Welcome to FluxomicsExplorer!

FluxomicsExplorer is a web-based application for the interactive exploration of changes in flux sampling data between two conditions of a single GEM with different constraints.

This demonstration is based on flux sampling data from the red blood cell (RBC) model iAB_RBC_283, which was constrained by extracellular metabolomics data of blood plasma samples taken at three different timepoints. FluxomicsExplorer was used to analyse and compare these different timepoints and their effect on the biological RBC system on a molecular level.

Blood plasma samples were taken from (semi-)professional athletes before (A), right after high-intensity training (B) and after 2h rest (C). The timepoints were analyzed by comparing them with eath other in FluxomicsExplorer resulting in 3 analyses: RBC_AB, RBC_BC and RBC_AC.

How to use:

  1. Use the reaction bar chart at the top for an overview of the flux sampling results. It shows in decreasing order the reactions with highest change between two conditions. The condition with the higher mean fluxes are marked by bar color. The asteriks above the bars also indicate if the change between both conditions is significant by Kruskal-Wallis. Try out and filter the chart to find a reaction easily by model ID or common name. You can also highlight all reactions that metabolize a specific metabolite by selecting one in the respective dropdown menu.
  2. By clicking on a certain reaction bar chart this will trigger the flux distributions histograms below to display higher detail about the reaction fluxes. On the left side are the flux distributions for both conditions situated, whereas on the right side is the flux difference distribution that was used to calculate the reaction scores above.
  3. For further information about metabolite distribution change one can examine the bar chart that displays the metabolite scores in the same manner as the reaction scores. This can give information and hints about change in metabolite turnover. Again by clicking the bars the histogram below will show a distribution of all reaction fluxes where the metabolite was metabolized. This can also show if production and consumtion is symmetrical or rather skewed in some direction by change in pathway flow.
  4. The network visualization employs a node-link diagram that shows the network between metabolites and reactions nodes. The edges mark either reaction or metabolite scores and can be changed accordingly. Networks are represented by pathways, that were collected from KEGG based on the model reactions. These can be selected by a dropdown menu, as well as different color scales and layouts. The network view can then be used to find relationships between different reactions and metabolites, examining different pathways, and following fluxes inside the network.
  5. The last visualization is a treemap based on BRITE functional hierarchy. Each rectangle represents a specific subsystem that has been retrieved from KEGG BRITE data. The corresponding subsystem reporter score is encoded using the same sequential color map used for the network visualization. A tooltip displays the subsystem name, subsystem score, and a list of reactions that are associated with this subsystem (i.e., that were used for the score calculation). Users can browse through the subsystem hierarchy by clicking on a rectangle, which will then expand to be the new root of the treemap. This way, child nodes can be inspected in greater detail. The interactive treemap visualization can be used in the analysis process to easily identify changed subsystems in the context of their functional embedding with the metabolism that is provided by the BRITE hierarchy.