Tuesday, January 25, 2011

A GeneMANIA usage example.

Here's a protocol that highlights some of the newer features of GeneMANIA.

1) Choose “yeast” from the species box
2) Press "example" underneath the gene box to fill it with the default list
3) Open the advanced options panel by clicking on “Show advanced options”
4) Choose “50” genes from the “Number of gene result” box
5) Press “GO” at the upper right corner of the interface
6) Wait.

While you are waiting, GeneMANIA is assigning a percentage weight to each of the networks according to how much more connected genes in your input are to each other compared to genes in the rest of the network. Then it is making a new, list-specific composite network that’s equal to a weighted average of the selected networks. Then the GeneMANIA engine will do label propagation on the composite network to score all the other genes in the networks according to how strongly associated they are to the query genes. Once this process is done, GeneMANIA takes the top 50 most highly associated genes and displays them, along with the query genes, in a browse-able network.

Once the network returns, you'll see that there are a lot of interactions among the genes in the network but you might notice that the input genes (whose nodes are coloured in gray) fall into two groups. The network layout uses a random initialization, so it's similar but not exactly the same every time. We will now make the groupings clearer by colouring nodes according to their function.

7) Open the function tab
8) Hover over “M Phase” in the networks tab – see the genes annotated with M Phase change colour. Most of the genes in the network have this annotation. Click on the “plus” sign to colour the nodes
9) Find “double-strand break repair” in the list of annotations. When you hover on top of it, the nodes with the annotation will change colour. Click on the “plus” sign besides it to colour the nodes with that annotation. This recolours some of the nodes because they have multiple annotations.
10) Continue down the list until you find “anaphase-promoting complex”, click on the “plus” sign beside it to colour these nodes.

Now you can easily see that GeneMANIA recovered the two distinct functional groupings.

You can now save the result of your analysis either as a publication-ready figure or a spreadsheet with a list of all of your interactions.

11) Click on the “Save” menu. If you choose “Save report as PDF”, you’ll get a PDF report of your analysis, if you choose “Save network as text”, you’ll get a tab-delimited text file with all of your interactions.

Note that the physical interactions alone nicely distinguish the two functional groups of nodes. To see this, you can do the following:

12) Click on the Networks tab
13) In the networks tab, uncheck all the boxes except the one beside "Physical interactions"
14) Choose “Reset layout” in the Actions menu.The anaphase promoting complex is tightly linked together, but the DNA damage repair genes are more loosely connected.

That's all for now.