Tech Notes

Q. Why can't I see any genes on my pathway?

A. There can be several reasons why no genes are displayed on the pathway(s). Follow this guideline to help you solve the problem:

1. GeneSpring will only display the objects selected in the Navigator: make sure that the "all genes" list is selected in order to maximize the number of genes that will be displayed on the pathways. If some genes appear after selecting the "All Genes" list, it may mean that none of the genes from the previously selected gene list are found on the pathway.
   
   If still no genes are displayed on the pathway, and you are using KEGG "map" pathways, KEGG organism-specific pathways, or GenMapp pathways, go to point 2. If you are using other pathways, go to point 5.
   
   
2. KEGG or GenMapp pathways are using gene annotations to map genes onto the pathway images. Make sure that your genome contains annotations before proceeding. At the very least, your genome should have GenBank IDs for each gene. You can verify this by double-clicking on the "All Genes" list, then select "Configure Columns". Check the box "GenBank" and click OK.
   
   If your genome contains GenBank IDs, go to point 3. If it doesn't, go to point 4.
   
   
3. If your genome has GenBank IDs, select "GeneSpider: Update Annotations from Silicon Genetics" option from the Annotations menu. Click "Start" to begin updating.
   
   When the annotation update is complete, the KEGG pathways should display some genes onto their image. For a quick assessment of how many pathways contain mapping genes, right-click on the pathway folder and select "Make Gene Lists". If you are using GenMapp pathways, go to point 5. If you are using KEGG pathways, and still no genes appear on the pathways, go to point 6.
   
   
4. If your genome doesn't have any annotations, nor GenBank IDs, enter that information in the file called 'yourgenome_ORFs.txt' in your genome folder (each genome is saved in the GeneSpring data directory) with the appropriate entries, then go to point 3. If you can't obtain GenBank IDs, go to point 6.
   
   
5. If you have installed GenMapp pathways prior to update the genome's annotations, delete the pathway folders by right-clicking on each one and selecting "Delete". Then import the pathways again into GeneSpring by dragging the zipped file downloaded from our website (http://www.silicongenetics.com/cgi/SiG.cgi/Support/pathways.smf). Restart GeneSpring. If still no genes appear on the pathway images, go to point 6.
   
   
6. If you are using other pathways, or if your genes don't map the pathways due to a lack of annotations, map the genes onto the pathway images manually. Please see "How do I import pathways graphics files into GeneSpring and how do I draw genes onto them?" for details on the procedure.