The Gene Set View allows you to view track data over a set of genes or genomic coordinates. At control panel, go to "Genomic view" → "Gene Set View" to view options.
Click tab "Custom gene set" to show following panel. You can enter a list of genes or genomic coordinates, or even mix the two types for input. Without further configurations, you can directly submit your input content and run Gene Set View:
Click the "KEGG pathways" tab to show following panel:
To search KEGG pathways by keyword, enter them in the text field on left and press button , a list of matching pathways will be displayed. To run Gene Set View on one of them, click pathway ID:
If you already know the pathway ID, enter it in the second text field on right and run Gene Set View on it. Make sure the pathway ID belongs to the genome you're working with.
If you submit gene set via above two ways without any changes, gene body will be displayed as indicated. To change to other gene parts for display, press button , a small panel will pop out prompting you to choose a type of gene part to be displayed:
Checking radio button to select a gene type. Then click elsewhere to dismiss the panel. The text in the main panel has been updated following selection:
If the pre-defined gene parts don't meet your requirement, you can use custom region selection tool by checking option "custom region...":
A ruler appears in the gene part selection panel. Using the green/red sliders you can define the length of upstream/downstream region flanking an "origin", where it could be one of the three choices (transcription start site, stop site, or entire gene body).
Press on the slider and move it to select a length. In the example, 2500 bp is selected for both upstream and downstream of transcription start site. Same way of selecting 5 kb region centered on transcription start site:
In a nutshell, running Gene Set View means replacing chromosome using list of gene segments or chromosomal intervals for horizontal axis. Many Browser components will be updated in accordance with this change:
When running the Gene Set View, you couldn't run the genomic juxtaposition or contig view. If you go to the genomic juxtaposition control panel, you will see following:
You have to turn off Gene Set View and back to genomic view to run these functions.
In the newly displayed panel, click tab "Add / remove" to show functions to add to or remove from existing gene set:
In order to add items to existing list, enter gene names or genomic coordinates in the text area. Items will be added by pressing button.
In order to remove items, use the box on the right of text area. Inside the box lists existing items. Mark items for removal by clicking button :
To unmark, click button again. Once done marking, click button to remove marked items.
Click tab "Change part" to show its panel:
Same as described above, click button to change gene part.
Click tab "Sort" to show options on how genes would be sorted:
By chromosomal order and location will arrange genes by chromosomal order (chr1, chr2, ...) and left most genomic coordinate and the order of appearance in same chromosome.
By length can be from short to long or reverse. Following is example of length-sort from short to long:
By average track score requires selecting a heatmap track, so that gene will be sorted based on their average track score.
When you choose such options, a panel will be displayed prompting you to choose a track:
At this stage, you can either click the button to choose a track from the pop-out panel:
Or right click on a track and select it via menu option:
Once selected, the track name will be printed on the panel:
Following example shows sorting of genes by ascending average score on a track:
The Gene Plot is a very useful downstream function following the Gene Set View. An entire chapter is devoted on this feature.
Last modifed: 1/2/2012