Frequently Asked Questions
Yes, genes in an experiment can be mapped to chromosomal location in Genome Browser of GeneSpring. The mapping is based on chromosome number, start and end locations.
Following are required for Genome Browser:
•Build information for the organism of your experiment – Build is information of the chromosomes present in the organism and their lengths
•Chromosome number, start and end position for the probes/genes in the technology of your experiment. - This information is required to show data in Genome Browser.
To run Genome Browser, please download the build for the organism of your experiment. To download a build go to “Annotations -> Annotation Manager -> List -> From server”. Select the Organism and build of your interest and download them and then try to run Genome Browser.
GeneSpring provides you with the option to create your organism and build in the tool.
•Go to “Annotations -> Annotations Manager -> Create”
•Select “New Organism”
•Enter Common name, Scientific name and Taxonomy ID
Create New Build
•Go to “Annotations -> Annotation Manager -> Click on the Organism of interest -> Create”
•Select “New Build”
•Enter a name, build source and browse for the file with chromosome name and length information.
Chromosome name and length without any header should be present in a file for creating a build. For example
GeneSpring supports .tsv,.txt and .gz files for a build creation.
You may contact GeneSpring support to obtain a file based update. After the file based update is obtained, please go to “Annotations -> Annotations Manager -> List -> From file -> Select the .update file”. It will list all the annotations present in the update file, select the interested ones and click update.
To delete an organism created from “Annotations -> Annotation Manager”, please go to the Annotations Manager -> Select the Organism -> Click Delete.
Yes, you can select a specific region in a chromosome in either of the following ways:
a. Enter the region of interest in the chromosomal coordinates
b. Browse through the chromosome : Below are the options to browse through the chromosome in Genome Browser:
- Use zoom function from tool bar
- Use double click to zoom in and shift+double click to zoom out.
- Use shift + mouse drag to zoom in.
Yes, data from a specific region can be exported from Genome Browser in following two ways:
- From spreadsheet: Follow the steps below for the same:
- Select the region of interest
- Go to Spreadsheet
- Right-click on the spreadsheet and select Export as entity list/ Export as text.
- From Data Track : Right-click on track for export options.
To find a specific Gene or probe in Genome Browser, go to spreadsheet and use “Find” option. The selected entity will be highlighted in the spreadsheet as well as the tracks.
Data from different experiments can be plotted on Genome Browser. To view the data, drag and drop the entity lists of interest on Genome Browser, it will be added as a track and can be viewed along with the other existing tracks.
Yes, it is possible to view list associated values (p-value, Fold change, etc) on Genome Browser. Please follow the steps below:
• Right-click on the track of interest
• Go to Edit track properties
• The list associated value columns are visible as check boxes in the Edit track properties Dialog. Select the required data and it will be added in the same track as one more feature. Click ok.
List associated values are also shown in the spreadsheet.
Yes, it is possible to view raw data on Genome Browser using the steps below:
- Launch Genome Browser
- Drag and Drop the experiment
- Select the interpretation and samples or conditions
- Click ok
- Right-click on the data track
- Select “Edit track properties”
- Select “Raw” in region view
- Click ok
The mapping of probes in Genome Browser is done using chromosome number and location. The chromosome number is expected to be in alphanumeric (chr1) or only numeric characters. If the format is alphanumeric then all the alphabets should be lowercase. The error could occur if the chromosome number has uppercase in them.
The Genome Browser is launched on the organism of your experiment. Check the organism of your experiment to ensure that it is the same as the organism of the build.
To check the organism of an experiment, right-click on the experiment name and select “Inspect Technology”. You have the option to change the organism in the Technology Inspector window.
Yes, the builds will continue to work. The builds from previous version will be called as “Segments”.
Yes, you may export images in the following two ways:
- Right-click on the track of interest -> Export as -> Image. This will export individual track.
- Go to the Tool bar in Genome Browser -> Select “Export selected track as image” -> Select the tracks of interest -> Specific a folder to save images. This feature enables you to export one or more than one track together.
To change the sequence of tracks go to the “Reorder” icon in the icon bar. Following this, select the track of interest and arrange it in the order of preference using up or down arrow.
Merge icon is used to bring different tracks together. This option is highlighted when two data tracks are selected and both tracks have only one feature enabled.
Data distribution over all chromosomes can be obtained by editing track properties from Right-click operations. Go to Edit track properties -> Chromosome View -> Select feature of interest.
This will show the data for the selected chromosome in Genome browser area. To view all the chromosomes together, go to “Chromosome tab” on the left of Genome Browser.
Similar is the case if you wish to view data for a particular feature for the whole genome. Right-click on the track of interest and select Edit track properties. Go to Genome View and select the required feature and click ok. It will enable this feature in Genome View.
Yes, annotation information present in a file can be imported in GeneSpring. You may use any of the following methods:
- Drag and Drop a file on Genome Browser: To use this feature, follow the steps below:
- Launch Genome Browser
- Drag and drop the file of interest
- Provide a name to the feature and select a template
- In the subsequent step, define the data type and the column types for each of the columns.
- Add annotations from annotation manager: To use this feature, follow the steps below:
- Go to “Annotations -> Annotations Manager"
- Select the Organism and build
- Right-click on the build
- Select the annotation type of interest
- Import the file.
Please refer to GeneSpring manual for details on supported file formats.