GeneMANIA news and blog

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This is a temporary home for some informal news and blog-style writing about GeneMANIA. In terms of news, we will use this space to talk about upcoming GeneMANIA releases and changes. In terms of blogs, we will walk you through some of the types of analyses that you can do with GeneMANIA. There's lots to talk about; we need a lot of space to show you just how powerful a research tool GeneMANIA can be. What we talk about here is meant to supplement our OpenHelix video tutorial (which will be available shortly) and our Nucleic Acids Research webserver submission (which has just been accepted).

May 30, 2010

Today I am going to work through an example analysis featured in a recent PLoS Computational Biology education article by Curtis Huttenhower and Oliver Hofmann entitled "A Quick Guide to Large-Scale Genomic Data Mining". It's a nice introduction to some of the databases and tools that you can use to do that types of analysis that GeneMANIA was designed to make easy. You can read the article here.

In their paper, Curtis and Oliver have worked through an example of finding potential yeast cell cycle kinase targets. Paraphrasing their workflow, the steps involved are the following:

1. Download a list of yeast genes assigned the Gene Ontology annotations "cell cycle" and "protein kinases activity" (there's 51 such genes)
2. Download interaction databases to find other genes whose protein products have physical interactions with those of the genes in our list of cell cycle kinases. These are potential targets.
3. Download yeast expression data and filter the list of the potential kinase targets for those that are significantly co-expressed with one of our cell cycle kinases.

Sounds easy enough, but it's not. See for yourself. After you download the initial list of yeast cell cycle kinases, there's 25 more steps before you get your final list. Some of those steps involve installing specialized software and some of them involve downloading all of the yeast gene expression data in Gene Expression Omnibus. It would probably take you all day long, if you were lucky.

On the other hand, GeneMANIA is designed to make this type of analysis easy. We've already downloaded all the data you need and put it into a convenient format. All you need to do is enter a gene list. Here's their list of 51 yeast cell cycle kinases. Now here's what you need to do:

1. Open the text file, select your gene list and copy it to your clipboard.

2. Go to GeneMANIA

3. Choose "yeast" from the list of species. Please wait a few seconds for the yeast networks to load -- sorry about the wait, we're working on fixing that.
4. Select your gene lis
5. Click on the gene box. It will open up with the default gene list already highlighted, so if you paste your own list into the box, your list will overwrite the default list.
6. Open up the advanced options panel. At the top left, besides "Enable" click on "none". This will deselect all of the default networks. Now click on the checkboxes besides "Co-expression" and "Physical interactions".
7. In the "Number of gene results" part of the advanced options panel (it's at the bottom), select "50" genes. This should be a good place to start from.
8. Click "GO"

That's it, you are done, now you have to wait about thirty seconds (maybe a minute) for GeneMANIA to run your analysis and upload the network display to your computer. GeneMANIA will find the co-expression and physical interaction networks most relevant to your query (i.e. those related to cell cycle) and then find the list of 50 genes that are most highly connected to the cell cycle kinases in your query list. Once GeneMANIA comes back you can examine the list by clicking on the Genes tab (it's on the right, near the top). You can save your result by choosing the "Save" menu item (it's on the left, near the top).

You can also navigate through the network to see whose connected to who. Right now, the network is a big ball of purple. That's because there are a lot of co-expression relationships among the genes in your query list (and the result list). Turn off the display of co-expression networks by clicking on the Networks tab (beside the Genes tab) and clicking the check box besides "Co-expression". I like to reset the network layout after I do this (choose the "Actions" menu and click reset layout).