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Genome Browser

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11.3 Genome Browser

The SVS Genome Browser provides both genetic position context and gene information. Contextual web links are also available for connecting to the Internet for information about a specific range or position in a chromosome via either the tool bar link out button, or by selecting a data point in the graph. The genome browser provides several annotation tracks. There are two default local tracks and several network tracks to enhance the exploration of results within the genome browser. See Features Unique to a Genome Browser for more information.

Obtaining a Genome Browser

A plot viewer is called a genome browser when a marker map is applied to a spreadsheet and:

  • The marker map is applied to row labels and columns of real, integer or binary values are plotted via Plot > Numeric Value Plot
  • The marker map is applied to either row labels or column headers, the data is either real, integer or binary and a Heat Map is plotted via Plot > Heat Map
  • The marker map is applied to columns of genotypic data and an LD plot is created via Plot > Linkage Disequilibrium
Features Unique to a Genome Browser

[Picture]

Figure 87: Region 7p12.3 Highlighted in a Genome Browser

There are several features in the Plot Viewer that are only available when the Plot Viewer is acting as a Genome Browser (see Figure 87). These features are detailed below.

Genome Browser Tool Bar Controls

A genome browser has special genome controls in the tool bar. These controls are:

  • Species selection: The species for the current genome map can be changed through this control. This causes the correct number and size of chromosomes to be drawn for the selected species.
  • Build selection: For species with multiple builds (such as Homo sapiens) the build can be selected via this menu. When multiple genome maps are available for a given build, they can be selected here by name. For example, user created genome maps created from a spreadsheet or marker map will usually use the same build as an existing map. See Creating a Genome Map.
  • Chromosome Selection: The zoom can be reset to a specific chromosome by selecting the chromosome from this menu. This behavior is equivalent to double clicking on the chromosome in the Full Domain View.
  • Genomic Zoom Region: A zoom region can be entered into this text box. Multiple formats are supported and interpreted as chromosome: start position to end position.
  • External Browser Links: Multiple external browsers can be accessed for the zoom region specified in the Genomic Zoom Region box. Regions spanning multiple chromosomes are not supported by the external browsers and will result in a warning when attempting to link out.

Full Domain View

The Full Domain View in a genome browser shades alternating chromosomes, creating chromosome “bands” for easy identification of chromosomal boundaries. The domain of the Graph View can be reset to that of a specific chromosome by double clicking on the desired chromosome band. This red zoom box can be resized by clicking and dragging the edges of the box to the desired size.

Graph Control Interface

The Graph Control Interface controls the display of the graphs in the Graph View. In the context of a Genome Browser, a chromosome shader can be used to shade alternating chromosomes in the same manner as in the Full Domain View. This option is located on the Graph Attributes tab for Graph Options. Also, the domain for the X-axis zoom control is specified by chromosome and position. Examples are:

  • Region: chr#
  • Region: chr#:StartPosition-chr#:EndPosition
  • Region: chr#:StartPosition-EndPosition
  • Region: chr#-chr#

There are several hyperlinks to online databases accessed by clicking on the tool bar link out button to obtain more information on particular regions of the genome. If there is a database without a hyperlink, the text in the Region text box can be copied by right-clicking and selecting “Copy”. This information can then be pasted into any genome browser.

Annotation Tracks

In a Genome Browser there are two top-level nodes in the Graph Control Interface, User Graphs and Annotation Tracks. From the Annotation Tracks node additional tracks can be added or removed. Parameters for a specified track can also be modified.

With the Annotation Track node selected, the control panel allows additional tracks to be added. There are two types of annotation tracks, local tracks and network tracks. Local tracks are stored in the annotations folder of the project and are available independent of network access. Network tracks are accessed on an as needed basis and the information downloaded is stored in a cache file for access up to 90 days after the download, after which the data is cleared from the cache, and re-downloaded as needed.

Default Local Tracks  There are two local tracks that are bundled in the SVS program in their entirety that can be accessed at all times even in the event that a network connection is not available.

Network Tracks  Network tracks are available from the Golden Helix, Inc. data server, http://data.goldenhelix.com. Various data sources are obtained and the data is compiled in a format for the Genome Browser to process and display. Additional sources can be made available on request. Information for a network track is downloaded only on an as needed basis. If a network track is requested and the zoom selected is the entire genome, then the entire track will be downloaded. Otherwise, only the information for the specified zoom will be downloaded and stored in a cache file for faster access after the project has been closed and reopened.

Add a Track  After selecting either the Add Network Track or Add Local Track tab, the displayed tracks can be sorted by clicking on a field name. Clicking on a track from either list selects the track and displays information about the track as well as a hyperlink containing more detailed track information on the current tab of the Data Console. Tracks can be added only from a single tab at one time. After track selections have been made click Add to add the selected track(s) to the displayed Annotation Tracks. Selections can be cleared by selecting Clear. By default, only tracks for the current genome map are displayed. Tracks for all genomes can be shown by clicking on Show tracks for all genome maps.

Hiding Annotation Tracks  An annotation track can be hidden from view without removing its configuration settings or data. To do this, un-check the box in front of the track name. This does not remove the track from the genome browser, but does remove it from the Annotation window. To re-show the track, check the box in front of the graph’s name.

Rename an Annotation Track Title  To rename an annotation track, right-click on the track name and select “Rename”. Renaming the track node will change the title of the track, which is displayed above the track in the Annotation Tracks window.

Reordering Annotation Tracks  Tracks can be reordered within the Annotation Tracks top-level node, preserving all track settings. To reorder a track, click on the track and drag it to the desired location. The effect of reordering tracks in the Annotation Tracks is that the track is placed below the location where it is dropped.
Multi-select operations are valid for moving tracks. These are: <Ctrl>-left-click selects multiple tracks one at a time, and <Shift>-left-click selects all tracks between the first and last selected track. All selected tracks will be moved to below the specified location from bottom to top of the list of tracks moved.

Delete an Annotation Track  To delete a track from the Genome Browser, right-click on the track name and select “Delete”. Multi-select operations are valid for deleting tracks. These are: <Ctrl>-left-click selects multiple tracks one at a time, and <Shift>-left-click selects all tracks between the first and last selected track. All selected tracks will be deleted.

Annotation Track Controls

Annotation track controls dictate the display of the title, the region, and the color of the features drawn. The track controls are displayed on two tabs. These tabs and their options are displayed below.

  • Graph:
    • Title: Check this box to display the annotation track title.
    • Region: Specify the region for the X-axis to span in this box. (Only available for numeric plots including LD and Heat Maps with genetic position for the X-axis.) Examples of formats for the region box are:
      • “chr#”
      • “chr#:StartPos-EndPos”
      • “chr#:StartPos-chr#:EndPos”
      • “chr#-chr#”
  • Color: The colors that are used to draw features for the track can be changed by clicking on the color buttons. Features cannot be renamed. Colors can be copied

Data Console

When data points are selected in the Graph View of a Genome Browser, information about the value of the point, as well as chromosome and position, are displayed in the Current tab of the Data Console. Some tracks include hyperlinks to online data bases for the specific chromosome and position of the data point are also available for obtaining more information about the specific region of the genome.

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