Gene Ontology Graphs
OmicsBox aims to be a visual-oriented tool. This means that special attention is paid to show information through graphs, coloring and charts.
Directed Acyclic Graphs
OmicsBox offers the possibility of visualizing the hierarchical structure of the gene ontology by directed acyclic graphs (DAG). This functionality is available to visualize results at different stages of the application and although configuration dialogs may vary, there are some shared features when generating graphs.
Software. OmicsBox integrates a viewer based on the ZVTM framework developed by Emmanuel Pietriga at the INRA (France) for graph visualization (, ). This high-performing vectored visualization framework allows fast navigation and zooms on the GO DAG. A graph overview is permanently shown at the upper right corner of the graphical tab to easy follow exploring across the DAG surface. Zoom in/out is supported on the mouse wheel and fast zoom to readability is reached by double click on a DAG node. Information about the current node is given on the lower application bar
Node Filters. A potential drawback during drawing Gene Ontology DAGs where numerous sequences are involved is the presence of an excessive number of nodes that would make the graph hard to visualize and will demand large memory resources. OmicsBox allows modulation of graph size by introducing node filters that depend of the type of graph considered. Additionally, there are a maximum possible number of nodes to be displayed.
Coloring mode. OmicsBox highlights nodes proportionally to some parameter of the analysis which result is visualized on the DAG. By this intensity variation of node color relevant terms get more visual weight which is a useful way to guide visual inspection of the results.
Graph element legend
The GO Graphs are displayed in different shapes. In order to understand what does each shape mean the Graph Legend (Figure 1) will provide you with this information.
octagon: Annotated GO Terms
square: Intermediate GO Terms
ellipsis: GO Terms linked to a Blast Hit
Figure 1: Graph Legend that shows the graph shapes
Gene Ontology term obtained by mapping which can directly be associated with one ore more BLAST hits. (GO-Accession, maximum hit e-value assigned, max. hit similarity assigned, number of hits belonging to this)
Non-annotated GO term node (GO term name, mean e-value of all hits contributing to this node, max. e-value, max. Similarity, number of Hits contributing to this node, Annotation Algorithm Score)
Annotated GO term node (GO term name, mean e-value of all hits contributing to this node, max. e-value, max. Similarity, number of Hits contributing to this node, Annotation Algorithm Score)
There exist two types of relationships between child and parent terms. Children that represent a more specific instance of a parent term have an 'instance of' or 'is a' relationship to the parent. Children that are a constituent of the parent term have a 'part of' relationship.
Pies and Bar Charts
Some of the results obtained by the Data Mining tools present in the application (see Quantitative Analysis section) are displayed either as a Bar or Pie charts. Similarly to the DAGs, parameters for modulating the size of these graphs are available at their configuration menus. As these charts are very much related to the Data Mining functions they correspond, they will be explained together in the next section.