Protein Network
This web page was produced as an assignment for Gen677 at UW-Madison Spring 2009
Background on String 8.0
The round balls demonstrate the actual proteins and the line show the interaction each protein has with each other. The color of the string is meant to illustrate how these interactions were determined. For example lime green means the interaction was found via text search, blue means Co-occurrence, which reflect the amount of conservation of the homologous protein in the specie. And Pink color line illustrates that interaction was determined by experiment.
Methods of Protein map search
I used the website String 8.0 to find other protein interactions that SIRT6 may have. I went about this by using an analysis of both mouse and human protein maps. I also had Drosophila as a choose for a map but when I clicked on it no protein interactions had been observed, so I did not use Drosophila in my analysis. The reason I used both human and mouse protein maps was 1) to look for possible overlap of proteins that they interact with 2) to also look for novel proteins that each may interact with but have been seen in the other species yet.
Protein map of Mouse SIRT6 interactions
From the protein map of mouse you can cleanly see that for humans most of my results came up as only being text based protein associations. And only SIRT1 showed co- occurrence meaning that it has a very similar sequence.
Protein map of Human SIRT6 interactions
In the protein interaction map of human you again see mainly text based protein interactions as determined by the green line. But of interest to me is the association of ELF5 to SIRT6 through actual experimental evidence.
Analysis
The string site was very useful and really gave a nice layout of protein network for SIRT6. While I did get quite a few protein interactions most of them where only found by text searches through the literature. And when I actually looked deeper into some of them I found that most really had no interaction with SIRT6. Or there were no papers containing interaction that SIRT6 may have with the protein. But one protein that really interested me was ELF5 in humans because that interaction had been shown directly in humans it was only seen in a 2 hybrid screen. So this is one protein I think would be interesting to see if SIRT6 actually interacts with. And to look for this interaction I could easily do a simple IP to determine if this interaction occurs. Overall the protein network was a interesting tool to use but most of the data didn't have actual interaction with SIRT6.
Mark Devries
Email [email protected]
last updated 1/22/09
http://www.gen677.weebly.com
