Gene Ontology Graphs
The Gene Ontology structure can be described in terms of a graph, where each GO term is a node, and the relationships between the terms are edges between the nodes. GO is loosely hierarchical, with child terms being more specific than their parent terms. A child term may have more than one parent term. There exist different types of relationships between child and parent terms: is a (is a subtype of); part of; has part; regulates, negatively regulates, and positively regulates. Children that represent a more specific instance of a parent term have is a relationship with the parent. Children that are a constituent of the parent term have a part of a relationship.
The three GO categories (cellular component, biological process, and molecular function) are each represented by a separate root ontology term.
OmicsBox offers the possibility of visualizing the hierarchical structure of the gene ontology by directed acyclic graphs (DAG). OmicsBox integrates a viewer for graph visualization. It allows fast navigation and zooms on the GO DAG. OmicsBox provides various ways for the joint analysis of groups of annotated sequences.
It is possible to generate these graphs in OmicsBox:
Simple GO Graph: Generates the GO graph of the provided GOs.
Colored Graph: Generates the GO graph from a text file.
Combined Graph: Generates the GO graph to visualize the annotation results.
These functionalities are available under the functional analysis → Gene Ontology Graph and the Combined Graph on the side panel once a sequencing project has been loaded.
Simple GO Graph
The "Make GO Graph'' function allows visualizing any set of GO terms/Ids and these have to be provided by the user (figure 2).
Figure 1: Simple GO Graph
Figure 2: Simple GO ID Graph
We can generate a GO graph from a text (.txt) file which contains a list of GOs and the desired color for each of them. It is also possible to label groups of GOs with the same name. Figure 4 shows an example that was created introducing the following text file:
GO:0000003 6 Group A GO:0040007 8 Group B GO:0050896 1 Group B
The text file has to follow a simple structure, to be processed correctly. It may contain from 2 to 3 columns in each line. The first column has to contain a GO, the second a number (0.0 to ) and the optional third column contains a text that will be written into the octagon of the corresponding GO. The columns must be separated with a tabulator character.
According to the example above Group B has two GO IDs that contain different values. It is also possible to differentiate these GO IDs by coloring according to their values. In order to color the octagon according to the value, you should select the gradient color on the next page on the color graph configuration window (see figure 6).
Figure 3 Colour Configuration Window
Figure 4: Coloured GO Graph by Group
Figure 5: Coloured GO Graph by Group value
Figure 6: Select Colour to differentiate values within the same group.