After running Protein Identification STAT Compare tool, you can find the gene ontology column to run GO analysis. Click ‘run’ or ‘re-run’ to start gene ontology analysis. In the backend analysis, the IP2 uses Ontologizer9

Figure 12.1.1: Gene Ontology run page

In the next page, select organism. For background analysis to generate p-value, there are two options. Users can use GO database as background and all identified genes as study group. Another option is to define all identified genes as ‘background’ and regulated genes as ‘study group’. In this case, users will need to type in a p-value threshold based on IDStat results to define the study group. When it is ready, click the run button.

Figure 12.1.2: Gene Ontology options

GO analysis provides results for three different categories – biological process, cellular component, and molecular function. By default, the IP2 picks and displays the top 20 most significant GO terms based on enrichment analysis. To find out all GO terms, users can click the ‘Gene Ontology Analysis output file’ link to download all results.

Figure 12.1.3: Biological process

Figure 12.1.4: Cellular component

Figure 12.1.5: Molecular function

On the bottom of GO result pages, users can customize the results by selecting GO terms of their interest, then click the re-filter button.

Figure 12.1.6: GO term customization

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