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| Welcome everyone to the GeneMANIA blog | === May 30, 2010 === 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). 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 [[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000779|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) 1. 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 kinase targets. 1. Download yeast expression data and filter the list of the potential kinase targets for those that are significantly |
GeneMANIA news and blog
May 30, 2010
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).
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) 1. 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 kinase targets. 1. Download yeast expression data and filter the list of the potential kinase targets for those that are significantly