For this week’s tip we highlight a new tool, NetGestalt, which offers some interesting visualization strategies for large-scale biological data in the context of pathways. I see a lot of need for this, and am pleased to be introduced to this tool. (And they have Venns! I ♥ Venns!)
I found out about it from a recent blog post by Will Bush of Getting Genetics Done. They have a great eye for useful tools, and he has more details about the functionality of NetGestalt that you should go and read. As far as I can tell there’s no publication associated with this yet–you are getting breaking information from their departmental retreat–so you will want to explore the manual that they have for further information. But they have also created a series of handy videos–and that’s how they became this week’s video tip!
This is just the first introductory video, be sure to go over to their site and see the others. They cover adding tracks and track types, analysis, and layout features.
You may also wish to explore another tool from this group–WebGestalt. This tool adds helpful context to lists of genes. That’s another issue that continues to be a big need. But now with the opportunity to go further and add layers of more data on to your analysis with NetGestalt, you should be able to mine some really useful directions from your data.
WebGestalt (a prior tool from this group, for adding useful information to lists of genes): http://bioinfo.vanderbilt.edu/webgestalt/
Zhang, B., Kirov, S., & Snoddy, J. (2005). WebGestalt: an integrated system for exploring gene sets in various biological contexts Nucleic Acids Research, 33 (Web Server) DOI: 10.1093/nar/gki475
Edit to add: I’m bumping this because the NetGestalt paper is now out.
Shi, Zhiao, Wang, Jing, & Zhang, Bing (2013). NetGestalt: integrating multidimensional omics data over biological networks Nature Methods, 10, 597-598 DOI: 10.1038/nmeth.2517