GenMAPP-CS User Manual
The GenMAPP-CS GO-Elite tool identifies a minimal non-redundant set of Gene Ontology (GO) biological terms or pathways to describe a particular set of genes. The GO-Elite program also exists as a standalone program.
GO-Elite inputGO-Elite accepts input in two different formats:
- Files: An input file listing all data points to be queried (changed genes for example) and a denominator file containing all data points.
- Criteria defined as a GenMAPP Criteria set.
- From the Workspaces Action panel, select Run GO-Elite....
- In the GO-Elite interface, there are a number of parameters to define:
- Species to analyze: Select the appropriate species for your data.
- Primary identifier: Select the identifier used to import the data.
- Number of permutations: Indicates the number of permutations to run for the analysis. With increased permutations, you have more statistical confidence but also much longer run-times. The default value of 2000 is recommended for most analyses, but 0 is also acceptable.
- GO pruning algorithm: Select which method to use for pruning the GO hierarchy to produce non-redundant results, either Z-score, gene number or both. The z-score option will instruct the program to compare related GO terms based on their relative over-representation z-score, which is an indicator of degree of over-representation. Gene number compares the number of genes changed in the pathway/GO term. Combination uses the z-score times the log2 number of genes changed to rank related GO-terms. When two or more related GO terms are compared, GO-Elite chooses the GO-term with the highest scoring statistic based on the relative position of the terms in the GO hierarchy. It is recommended to try different methods for pruning and compare the results.
- Type of analysis: Select to run the analysis on pathways, GO terms or both.
- Z-score threshold: Select the threshold for pathway results. Any pathways with a Z-score under the threshold will not be reported. The default value of 1.96 is appropriate for most data sets.
- P-value threshold: Select the threshold for pathway results. Any pathways with a P-value over the threshold will not be reported. The default value of 0.05 is appropriate for most data sets.
- Minimum genes changed: Select the cutoff for number of changed genes on a pathway. Any pathways with fewer genes changed will not be reported.
- Input Source: Select either File or Criteria depending on your input. For criteria sets, it is possible to select more than one criteria for analysis, meaning GO-Elite will run analysis on each criteria separately.
Planned Feature: Currently GO-Elite analysis is only available for human, mouse, yeast and tuberculosis. It will be supported for all GenMAPP-supported species in the next release.
- When the analysis is complete, a summary of the analysis results will be displayed in the Status tab of the Results panel.
- Results for pathways and GO terms are displayed as lists in the GO and Pathway tabs respectively.
- Pathways in the results list can be opened by clicking the name of the pathway.