Frequently Asked Questions
The following Target Prediction databases are available from GeneSpring version 12.5 onwards:
- TargetScan (updated from the version available in previous versions of GeneSpring)
All Target Prediction databases have to be downloaded prior to analysis. They can be downloaded using the Annotations Manager: Annotations > Annotations Manager > List > From Agilent server.
If you are unable to obtain the updates from the Agilent server, for example due to internet connectivity issues, you can contact GeneSpring support to obtain file based updates. To update from file, go to Annotations > Annotations Manager > List > From file and select the update file you received from GeneSpring support.
The context percentile filters for TargetScan analysis were moved from the workflow to the Options window and can be accessed and edited via Tools > Options > NGS > Small RNA > Target detection > Target Scan going forward from GeneSpring version 12.5.
The filters have to be changed in the Options window before starting the analysis to be applied. GeneSpring applies these filter settings to all subsequent analyses until you change them again in the Options window.
Yes, it is required to download the new version of the TargetScan database in GeneSpring 12.5 before you start the analysis. The old version of the database will not work in GeneSpring 12.5.
Similarly, you have to download any of the other Target Prediction databases available from GeneSpring 12.5 onwards (see Q1.) using the Annotations Manager (see Q2.) before you start any analyses that require them.
GeneSpring uses either MIMAT ID or mirBase accessions for Target Detection analysis. MIMAT IDs are used for TargetScan and microRNA.org databases, whereas mirBase accessions are used for PITA, PicTar and TarBase databases.
The hypergeometric method is used for calculating p-values for target genes. This is a new feature introduced in GeneSpring 12.5.
GeneSpring does not ask you to select a build in either of the following two cases:
- You have Target prediction databases downloaded for only one build.
- You are working in a small RNA experiment. In this case, the build information is directly taken from the experiment.
Yes, you can identify target genes that are present in the databases of your interest using the Find Targeted Genes option from the Results Interpretations section of the Workflow Browser by following these steps:
- In the Target Detection dialog box, select the entity list containing the active regions for which you want to identify target genes.
- Select all the databases of interest.
- Select the Report only the entities supported by all the selected target prediction databases option.
- Click Next.
The resulting target genes are displayed.