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Genome browser: Visualizing data in chromosomal coordinates

Step 1: Visualizing results

Genomica's genome browser allows you to visualize data in chromosomal coordinates, similar to the common web genome browers but with expanded viewing capabilities. More importantly, Genomica provides a suite of statistical analysis tools that perform statistical comparisons between data that is represented in chromosomal coordinates.

All the data is represented in chromosome tracks. Tracks are quite diverse in terms of the different objects that they can represent. For example, the sample tracks that come with Genomica include tracks for displaying: colored boxes (e.g., useful for representing genes); graphs; impulse graphs; ovals; and colored bar graphs (e.g., useful for representing tiling expression measurements). After loading an expression file into Genomica, you can load such gxt track files using the 'Chromosome' --> 'Load Track From File...' or the 'Chromosome' --> 'Load Track From Repository...' menu. Using the control panel on the left within the chromosome viewer, you can navigate to the exact locations you want to view; select a single or multiple chromosome display and control which chromosomes will be displayed; select which tracks will be displayed and change the visual properties for each track; search for items within the tracks loaded; view the items in each track as a table; and print the current view into an image; The result of loading the Genomica sample tracks should look something like this:

Step 2: Loading your own track

You can also load your own tracks into Genomica. The format is quite simple and you can use the above examples as a guideline. The format is xml, but the data part is tab-delimited with one line for each item displayed, with the following columns for each item:
  • Column 1: Chromosome name
  • Column 2: Unique identifier
  • Column 3: Start coordinate (in basepairs)
  • Column 4: End coordinate (in basepairs)
  • Column 5: Index of the feature type (a number between zero and the number of types minus 1)
  • Column 6: Real-valued number
This data part is wrapped by an xml header (again, look at the sample tracks to see examples). The xml contains various display properties of the track. All of these can be controlled visually within the Genomica GUI so you do not need to use them when creating your own tracks. However, one field is important to fill in, and this is the "FeatureTypes" field. This field is a string representation of all the different types that you have, where the index of the first type is zero, the index of the second type is 1, etc.. Recall that these index types are used in Column 5 of the chromosome track file format. The types are written as strings, with different types separated by a semi-colon. For example, to specify two types named "Induced" and "Repressed", we would write FeatureTypes="Induced;Repressed".

Step 3: Browsing a chromosome track as a table

A very useful feature that we implemented in Genomica's genome browser is the ability to traverse all the items of a particular chromosome track as a spreadsheet-like table, while in parallel seeing in the chromosome viewer, what the region around the selected chromosome item looks like. In this way, you can for instance load several tracks and display only the genes in the table view, such that clicking on each gene will then show all the data in the chromosome viewer that appears in the gene area and some selected number of basepairs flanking the gene. As another example, when analyzing ChIP-chip data, you can select a table view on regions that are called as significantly bound by some analysis program, and browse the items in the table, each time viewing the data that supports the call that was made in that region of the chromosome in which the call for significant binding was made. To open a table view on a selected chromosome track, click the "T" image from the left control panel of the chromosome viewer.
As an example, the following is a screenshot from Genomica when using this option of browsing a particular track in a table view: