Interacting with the UCSC Genome Browser

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Using the UCSC genome browser to view genomic data.

Open the UCSC genome informatics page.

  • The horizontal and vertical blue menus provide access to the tools.
  • Particularly useful links are Genomes, Blat and Tables.
  • Clicking on any of these will take you to pages that have pull-down menus that control organism and assembly.
  • Important: Different organisms and assemblies have different amounts and types of associated data.
  • ALWAYS be aware of the assembly you are using.

Click the “Genomes” link to go to the browser gateway page.

  • Note the useful information located at the bottom of the page. This can vary by assembly but can include:
  1. Sample position queries - examples of how to query the database.
  2. Assembly details - General assembly information
  3. Summary Statistics - Detailed statistics of the active assembly

Prabhakar et al., use the 2004 human assembly so activate this assembly

  • One of the genes in their list is protocadherin 10. 
Search for the gene by typing: "Protocadherin 10" into the 
"position or search term" box and click "submit".
  • The hyperlinked results are organized into sections. Each section corresponds to different "tracks" of data in the database. Everything listed contain matches to the "Protocadherin 10" search term.
  • The data at UCSC Genome Informatics is grouped into sets of related information called "Tracks"
  • Click the first hit in the "Known Genes" group correspond to the gene we are looking for.

The Genome Browser

  • The genome browser is the central visualization tool of the UCSC Genome Informatics Group.
  • Most everything is hyperlinked and adjustable

Browser.png

  • Restore the visualization to default by clicking the "default tracks" button under the image. Settings from previous settings can be retained.
Positional and scale controls are located above and below the browser image (red boxes)
  • zoom and movement buttons
  • coordinate window
  • coordinate bar in view - click re-centers and zooms in 3x
  • Dragging across the upper track is a zoom to selection function.
  • move start and end functions
Data organization and track controls (blue boxes)
  • Like the search results, the information displayed in the browser window is organized according into tracks of data. The kinds of tracks being displayed and the ways they are presented can be controlled.
  • NOTE: This human assembly is mature, heavily annotated and extensively analyzed. Other genomes and less mature assemblies have less associated information.
  • The buttons "default tracks" and "hide all" will do as their name suggests.
  • The "configure" button displays a list of the available data with display options.
  • The bottom of the page consists of a series of pull-down menus. Each is associated with a type of data and the options control display mode.
  • IMPORTANT: Useful details about each track can be obtained by clicking the hyperlinked track name. 
In the "Genes and Gene Predictions Tracks" section, use the 
pull-down menu to set the "Known Genes" track to full. 
Click the "refresh" button.

Note:After changes are made to the pull-down menus, refresh is required for them to take effect. 


Click the "1.5x" button in the "zoom out" section. You can see 
that one of the PCDH10 isoforms is shown in it's entirety. 
The other 2 extend off the screen to the right.
  • The visual cues that you see in the "Full" display of known genes are:
    • Arrowheads indicate the strand of the gene.
    • Thin lines are introns, medium lines are non-coding portions of the mRNA,

thick lines are coding region.

    • In some cases, colors indicate annotation quality. 
Adjust the zoom to display all of each PCDH10 isoform. Use the 
various zoom tools to adjust the display accordingly. 
You can enter coordinates:

chr4:134,423,873-134,472,358

Examine the menu items beneath each track. The options such as:
"hide", "dense", "full" and "pack" correspond to different display modes.
To understand what these do, turn the "Spliced ESTs" track 
in the "mRNA and ESTs Tracks" section to full and click refresh.
The EST data will appear in the window. 
Change the spliced EST display option to "Dense" and refresh. 
Try the "Pack" option.
  • The actual effects of these different options are described HERE
  • Efficient access to controls for all the different types of data, as well as other display options, can be accessed by clicking the "configure" button. 
Select this button so you can see all the information associated 
with this assembly.
  • Every track is hyperlinked to more information. 
Click on the multi-exon isoform of PCDH10 labeled with PCDH10 
in the known gene track to open a gene information page.
  • The tracks in the browser window can be rearranged by dragging the left-hand side track names.

Known Gene Pages

  • Known genes are attached to a large amount of data in the UCSC tool.

KgIndex.png 

Look at the different kinds of data displayed on this page. 
In general terms, what kinds of human tissues express PCDH10? 
Does D. melanogaster have a homolog? 
What GO terms are attached to this gene product?

view position:

chr4:134,416,924-134,482,511 

of the May2004 human assembly. If you are not there, paste those 
coordinates into the "position/search" window. 
Also set the "Known Genes" and "Spliced ESTs" tracks should be set to "Full".

Notice that one of the spliced ESTs (DA219615) shares an exon with the known 
multi-exon isoform of PCDH10 but it's 3' end is located outside the displayed 
area. Adjust the display so the the end of this EST can be seen. 
One easy way to do this is to click the "move end" button (set at 2.0) three times. 
The region being displayed should now be:

chr4:134416924-134488579
  • This EST documents an uncharacterized isoform of human PCDH10 that uses an alternative 3' end. It may be differentially regulated and could have a different protein coding sequence.
Retrieved from "http://rous.mit.edu/index.php/Interacting_with_the_UCSC_Genome_Browser"
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