Visualizing metabolic network dynamics through time-series metabolomics data

Buchweitz, L. F.; Yurkovich, J. T.; Blessing, C.; Kohler, V.; Schwarzkopf, F.; King, Z. A.; Yang, L.; Johannsson, F.; Sigurjonsson, O.; Rolfsson, O.; Heinrich, J.; Draeger, A.

doi:10.1101/426106

bioRxiv · 10.1101/426106

Visualizing metabolic network dynamics through time-series metabolomics data

Buchweitz, L. F.·Yurkovich, J. T.·Blessing, C.·Kohler, V.·Schwarzkopf, F.·King, Z. A.·Yang, L.·Johannsson, F.·Sigurjonsson, O.·Rolfsson, O.·Heinrich, J.·Draeger, A.

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Abstract

New technologies have given rise to an abundance of -omics data, particularly metabolomics data. The scale of these data introduces new challenges for the interpretation and extraction of knowledge, requiring the development of new computational visualization methodologies. Here, we present a new method for the visualization of time-course metabolomics data within the context of metabolic network maps. We demonstrate the utility of this method by examining previously published data for two cellular systems--the human platelet and erythrocyte under cold storage for use in transfusion medicine.\n\nThe results comprise two animated videos that allow for new insights into the metabolic state of both cell types. In the case study of the platelet metabolome during storage, the new visualization technique elucidates a nicotinamide accumulation which mirrors that of hypoxanthine and might, therefore, reflect similar pathway usage. This visual analysis provides a possible explanation for why the salvage reactions in purine metabolism exhibit lower activity during the first few days of the storage period. The second case study displays drastic changes in specific erythrocyte metabolite pools at different times during storage at different temperatures.\n\nIn conclusion, this new visualization technique introduced in this article constitutes a well-suitable approach for large-scale network exploration and advances hypothesis generation. This method can be applied to any system with data and a metabolic map to promote visualization and understand physiology at the network level. More broadly, we hope that our approach will provide the blueprints for new visualizations of other longitudinal -omics data types.\n\nAUTHOR SUMMARYProfiling the dynamic state of a metabolic network through the use of time-course metabolomics technologies allows insights into cellular biochemistry. Interpreting these data together at the systems level provides challenges that can be addressed through the development of new visualization approaches. Here, we present a new method for the visualization of time-course metabolomics data that integrates data into an existing metabolic network map. In brief, the metabolomics data are visualized directly on a network map with dynamic elements (nodes that either change size, fill level, or color corresponding with the concentration) while the user controls the time series (i.e., which time point is being displayed) through a graphical interface. We provide short videos that illustrate the utility of this method through its application to existing data sets for the human platelet and erythrocyte. The results presented here give blueprints for the development of visualization methods for other time-course -omics data types that attempt to understand systems-level physiology.

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Buchweitz, L. F., Yurkovich, J. T., Blessing, C., Kohler, V., Schwarzkopf, F., King, Z. A., Yang, L., Johannsson, F., Sigurjonsson, O., Rolfsson, O., Heinrich, J., Draeger, A.. 2018-09-26. Visualizing metabolic network dynamics through time-series metabolomics data. https://doi.org/10.1101/426106

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