This is exercise 2 of 4.
We’re now going to explore a list of differentially expressed genes (red vs. white grain) in the context of grain colour and PHS traits. Ensure that you are in Triticum Aestivum by checking the Multispecies selector at the top left of the website header.
Exercise 2 query:
color OR flavon* OR proanthocyanidin
|Gene List Search|
Pro tip: to get even more out of your KnetWork, consolidate American and British words in the Keyword Search, like: “colour OR color”.
In Gene View, you can use the interactive legend at the top by clicking on one or more symbols, e.g. pathways, phenotype, to retain genes with the selected evidence types and filter other genes.
1. Copy the “Exercise 2 query” query above by pasting the “Keyword Search” into the Keyword search of the Wheat KnetMiner instance.
In light grey, directly underneath the search box, you can see two numbers. The first number indicates the nodes in the wheat knowledge network that match the search terms. The second number indicates the number of genes in the wheat genome that have direct or indirect links to these search terms.
2. Copy/paste the Gene List Search from the table above into the Gene List Search on the interface (Figure 1).
3. Hit search and take a look at your results in Gene View. Find the MYB1 gene and select it to make a Network.
4. Hide the publication nodes by double-clicking the orange publication nodes square in the interactive legend underneath the network.
5. Click the Refresh button (Re-run the Layout) on the top left of the view, to clean up the knowledge graph.
6. Find our gene of interest (MYB1) and hold right click on it: what’s it’s source?
7. Which gene is it regulating? How can we know that for sure?
Bonus: which text-mined evidence is displaying seed color to co-occur with the TT2 gene? Is TT2 a wheat gene or related through an orthologue relationship with arabidopsis? How can you tell? (Follow the network connections!)
Figure 1 – Example 1 populated fields
On your version KnetMiner the number of documents and genes might be higher than in the above screenshot, as we’re constantly updating our Knowledge Graphs.