From GeneWeaver Wiki
The GeneSet Graph Tool
Why Use the GeneSet Graph Tool
- The GeneSet Graph is designed for the user in need of a partitioned display to illustrate just how tied genes are to one another. For example: a user in need of a GeneSet Graph would look for visual references more than chemical references or references by utility. A GeneSet Graph can also help pick apart the most valuable or most occurring genes depending on the user's preference.
Understanding the GeneSet Graph Tool
- The GeneSet Graph Tool presents a partitioned display of genes and GeneSets. Genes are represented by elliptical nodes, and GeneSets are represented by boxes. The least-connected genes are displayed on the left, followed by the GeneSets, then the more-connected genes in increasing order to the right. Genes and GeneSets are connected by colored lines to show what genes are in which GeneSets. In this way, the GeneSet Graph displays the bipartite graph of the genes and GeneSets, but modifies the display of the gene partition to make it easier to visually interpret.
Using the GeneSet Graph Tool
- Access the GeneSet Graph Tool through the My Projects tab under the Analyze Genesets option.
- To generate a GeneSet Graph, you must first select GeneSets from a project. Projects may be created and updated by uploading GeneSets, searching the GeneWeaver database, or through the use of other tools in the ODE system. See the documentation for uploading GeneSets, Search, or Manage GeneSets to learn more about these functions. From the Analyze GeneSets tab, select “My Projects”. To select an entire project or multiple projects for analysis, check the box next to the project name. To select individual GeneSets within a project, click on the ‘!’ beside the project name and check individual GeneSets using the checkboxes. Next, click on the GeneSet Graph icon in the Analysis tools box to the left of the project list. (For users that want to change options, press the green '+' sign before they start the tool).
- When enabled, this option will suppress the display of GeneSets which are not connected to any displayed genes. This helps remove unnecessary information for users that only want relations. This is only relevant when MinDegree is greater than 1.
- Include homology to integrate multi-species data. If excluded, data from multiple species will be segregated into distinctly separate graphs.
- The minimum number of connections for a displayed gene. A value of 2 means that any displayed genes must be found in at least two of the input gene sets. Increasing this value will basically shift the resulting gene display left. Since lower-order overlaps are generally more likely and more numerous than higher-order intersections, this can quickly reduce the number of genes displayed and make the result more manageable.