Visualization

IAMBEE analysis can be followed in real-time after the data submission. You can observe a summary of the data submitted as well as the progress of the analysis. Keep in mind the runtime analysis, we suggest to run an initial analysis using the sample data, this will give you an idea of how the program works.

To gain a quick insight into the obtained inferred sub-network, it can be visualized using the online tool by clicking Visualize Results button on the results page.

IAMBEE has an stochastic nature, this is reflected in the sub-networks inferred as result. Please note that even when using the same parameters the results can be slightly different.

Understanding the Visualization

The inferred sub-network is visualized by drawing the genes/gene products as dots or nodes and the interactions as edges. The canvas containing the final network is delineated by a dash line, you can zoom in and out using the mouse wheel or the equivalent in touch-pad.

Additionally, to drag the whole network you can click an empty space in the canvas, hold and move to the desired point. Similarly, each of nodes is draggable by clicking on the node, hold and drag to the desired point.

Nodes

The nodes visualized correspond to a mutated gene with a possible relevance in the adaptive phenotype studied. Note that each node has an outer pie circle with the same number of divisions, this being the number of conditions present in the mutation file.

A colored part indicates a mutation in that gene in one particular condition. e.g. The nodes in the figure above share the color salmon in one of the divisions this indicated that these genes are mutated in that condition. Similarly, the green division is present in two of the three nodes, this indicates that the genes are mutated in this particular condition but the gene b3517.

Edges

The interactions defined in the network file and present in the inferred sub-network are observable as arrows connecting nodes. The color of the edge represents the function of the interaction as explained in the legend.

The edge opacity depicts the probability of that edge involved in the phenotype. Clearer the arrow means that is more likely to be involved.