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About the Course Module

Browsing Genomes

Enter the Course Module: 

The Browsing Genomes module uses the parasite Toxoplasma as an example to show how anyone who has internet access can use experimental results from scientists. Making data publicly available through databases like ToxoDB helps science move forward much more quickly than what would be possible without them. Like libraries, databases store and organize information in a structured way that allows users to find and use existing information as well as contribute new research findings for others to use.

Browsing Genomes gives you a tour of the ToxoDB database and a tool to explore its genome-related information. Then, it leads you through an activity using real data from an experiment that studied gene expression in different life stages of the Toxoplasma parasite.

Estimated Module Timing: 

Toxoplasmosis—reading and discussion: 10 minutes

ToxoDB—video and discussion: 15–20 minutes

GBrowse—video and discussion: 25 minutes

Hands-on GBrowse—browsing and discussion: 30–45 minutes

Additional Resources

CDC: Parasites—Toxoplasmosis (Toxoplasma infection)

Listen to Dr. Dubey discuss his work on toxoplasmosis and his induction into the United States Department of Agriculture’s Agricultural Research Service Hall of Fame (.mp4 or .wmv video, 4:47 min)


Data Questions

1. The blue gene has high expression in each of the four time points.

2. The red gene shows high expression in day3, day5, and day7, but low expression in the Tachyzoite.

3. In the Tachyzoite stage, only the blue gene shows high expression. Because the Tachyzoite stage is in human hosts, and day3, day5, and day7 are in cat hosts, you can see that the parasite’s red gene is not expressed much in humans but then becomes expressed highly when the parasite is found in a cat host. Gene TGME49_312970 (red gene) is up-regulated in the cat.


This may be a good time to remind students that they just looked at real data collected by researchers in a rigorous experiment. New genomic data continue to be added to ToxoDB as researchers complete other experiments on Toxoplasma gondii.


Advanced Question about Overlapping Gene Expression

There are actually three potentially interesting observations about the blue and red overlapping transcript expression on the RNAseq coverage plots.

1. Transcript expression from the opposing strand (i.e., blue transcript in the red gene area): This may be due to a couple of things: a) there is a certain amount of background expression, so if you zoom out to include 10 or 20 genes, you will see that there is always some level of reverse strand expression. Some of this may be relevant, which brings us to b) reverse strand noncoding RNA can, for example, serve a regulatory function in silencing gene expression. So in the case of the red gene, it is tempting to speculate that the reason the gene is not expressed in Tachyzoites is because of the silencing effect of the reverse strand transcripts (i.e., the blue gene expression in the Tachyzoites in the red gene region keeps the red gene from expressing itself).

2. RNA transcript going beyond the actual gene model (right side of the red gene, for example): This may indicate that the 5’ untranslated region of the red gene is longer in the cat stages.

3. Transcript in an intronic region: See, for example, the left side of the red gene. This may be because the gene model is incorrect and it should be a single exon instead of two, or it could mean that there are two alternative transcript variants of this gene—one where the left two exons are joined into one and the other where there are two exons.