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 Cereals Free – Triticum Aestivum by checking the Multispecies selector at the top left of the website header. If you aren’t, click the selector and change to the correct Resource/Species combination, or click here.
Exercise 2 query:
Keyword Search:
color OR flavon* OR proanthocyanidin
| Gene List Search |
|---|
| TRAESCS3D02G468400 |
| TRAESCS2B02G038700 |
| TRAESCS2A02G025700 |
| TRAESCS2A02G527700 |
| TRAESCS2D02G530600 |
| TRAESCS2B02G558400 |
| TRAESCS3B02G257900 |
| TRAESCS3A02G226600 |
| TRAESCS3D02G224600 |
| TRAESCS2D02G493400 |
| TRAESCS6A02G369700 |
| TRAESCS6B02G406400 |
| TRAESCS6B02G405900 |
| TRAESCS3B02G280700 |
| TRAESCS4A02G085900 |
| TRAESCS3B02G006300 |
| TRAESCS3B02G007400 |
| TRAESCS4A02G206800 |
| TRAESCS3B02G006100 |
| TRAESCS3A02G464900 |
Pro tip: to get even more out of your network, 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 out other genes.
Exercise steps
1. Open Gene List Search in the “SEARCH TYPE” panel on the left.
2. Copy the “Exercise 2 query” query above by pasting the “Keyword Search” into the Keyword search of the Wheat KnetMiner instance.
In bubbles, directly underneath the search box, you can see numbers. Hover over these bubbles to understand what they mean.
3. Copy/paste the Gene List Search from the table above into the Gene List Search on the interface.
4. Hit search and take a look at your results in Gene View. Find the MYB1 gene and click it’s Gene Accession to make a Network.
5. Hide the publication nodes by clicking the orange publication nodes card in the Graph Explorer on the right of the network.
6. Click the Refresh Layout button on the top left of the view, to clean up the knowledge graph.
7. Find our gene of interest (MYB1) – it should have a double blue border and an orange highlighted label, as it’s the seed gene used to create the network. Click on it and open the Info Box on the right of the screen. What’s the gene’s source?
8. Which gene(s) is/are 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!)
