Q9. Some of the annotation types are highlighted in bold in the “Entity Properties” dialog. What does that mean?

The annotation types in bold are the annotations that are supported for mapping pathway entities of the respective experiment type in GeneSpring.

Q8. Is it possible to determine which annotations to display for each gene in the Entity Properties dialog?

Yes, you can select the desired annotations by using the “Properties Filter” drop-down icon in the Entity Properties dialog.

Q7. Where do I get annotation information on pathway nodes in KEGG pathways?

The annotation information on pathway nodes can be found in the Entity Properties dialog.
Double-click on the node to open the corresponding dialog.

Q6. Why do I see multiple genes for one node in a KEGG pathway? Why are multiple entities selected when I select a single node in a KEGG pathway?

Some nodes in KEGG pathways may represent multiple entities. For example, different isoforms of the protein, subunits of proteins, members of the same gene family, etc. . All entities under the node get selected when you select the node on the pathways.
Mouse over the node of interest to view all the entities under the node in the tooltip. You can also select the node to filter the heatmap below to limit it to only the entities represented by the node. Specific entities under the node can then be selected from the heatmap.

Q5. Why are some genes/proteins grayed out in the pathway viewer?

A pathway node in KEGG pathway is grayed out if that entity is absent in the organism of your experiment.

Q4. What are the prerequisites for working with KEGG pathways?

To be able to work with KEGG pathways:
a. you should be working with GeneSpring 13.0 and
b. you should be a licensed user of KEGG.

Q3. Is it possible to limit Single Experiment Analysis to KEGG pathways?

Single Experiment Analysis provides an option to select the pathway source in Step 1 of the wizard-driven workflow. Select “KEGG” to limit your analysis to KEGG pathways.

Q2. Can I import KEGG pathways that I had saved on my system after downloading them from the KEGG FTP site?

No, KEGG pathways can only be imported into GeneSpring from the Agilent server or .update file.

Q1. How can I download KEGG pathways?

To download KEGG pathways, please go to GeneSpring Tools -> Import Pathways from KEGG ->From Agilent server.

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