Abstract
BackgroundNetwork medicine aims to map molecular perturbations of any given diseases onto complex networks with functional interdependencies that underlie a pathological phenotype. Furthermore, investigating the time dimension of disease progression from a network perspective is key to gaining key insights to the disease process and to identify diagnostic or therapeutic targets. Existing platforms are ineffective to modularize the large complex systems into subgroups and consolidate heterogeneous data to web-based interactive animation.ResultsWe have developed PanoromiX platform, a data-agnostic dynamic interactive visualization web application, enables the visualization of outputs from genome based molecular assays onto modular and interactive networks that are correlated with any pathophenotypic data (MRI, Xray, behavioral, etc.) over a time course all in one pane. As a result, PanoromiX reveals the complex organizing principles that orchestrate a disease-pathology from a gene regulatory network (nodes, edges, hubs, etc.) perspective instead of snap shots of assays. Without extensive programming experience, users can design, share, and interpret their dynamic networks through the PanoromiX platform with rich built-in functionalities.ConclusionsThis emergent tool of network medicine is the first to visualize the interconnectedness of tailored genome assays to pathological networks and phenotypes for cells or organisms in a data-agnostic manner. As an advanced network medicine tool, PanoromiX allows monitoring of panel of biomarker perturbations over the progression of diseases, disease classification based on changing network modules that corresponds to specific patho-phenotype as opposed to clinical symptoms, systematic exploration of complex molecular interactions and distinct disease states via regulatory network changes, and the discovery of novel diagnostic and therapeutic targets.
Highlights
Network medicine aims to map molecular perturbations of any given diseases onto complex networks with functional interdependencies that underlie a pathological phenotype
Most current network platforms (e.g. Cytoscape [4], Gephi [5], Ingenuity Pathway Analysis (IPA) [6]), tools (e.g.VisANT [7], PATIKA [8], NAViGaTOR [9], GeneVis [10], yfiles [11], VANTED [12], Cancer PanorOmics [13]), custom R codes [14] generate static snapshots, which are inadequate at consolidating large-scale
PanoromiX is a comprehensive platform to enhance network model reproducibility, time-series interpretability, and data associability. This emergent tool of network medicine visualizes the interconnectedness of tailored genome assays to pathological networks and phenotypes for cells or organisms in a data-agnostic manner
Summary
The PanoromiX application accepts data in tab-delimited text files with the file extension .txt. It is used by the application to reference each node individually and perform operations such as linking and defining colors, shape and so on One can define both ‘Male’ and ‘Female’ nodes This field allows the user to enter a short paragraph of text (256 characters or less) containing a description, or additional information related to each node. It controls the dimensions or size of each node on screen This field allows the user to enter a numerical value (1–5) to display a time-point profile associated with the node. Valuable is PanoromiX’ interactive animation, which is very helpful in exploring and presenting time-series trends (Table 3, Additional file 4) This field must contain the id value of the node (from your corresponding nodes file) where the link will be drawn from. Browsers: IE 9, Firefox 31, Chrome 31, Safari 5.1, Opera 24, Opera Mini 8, iOS safari 7.1, Android Browser 4.4, or later
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