This web page was produced as an assignment for Gen677 at UW-Madison Spring 2009
GEO Profile of hypothalami of mice on a high fat diet
This is analysis of hypothalami from the GEO profile website was done with genetically identical inbred C57BL/6J males exhibiting high or low weight gain after several weeks on a high saturated fat diet.This experiment was done in the hopes that the results provide insight into the role of epigenetic mechanisms in the susceptibility to obesity. I found this expression profile interesting because SIRT6 gene levels seem to be clearly up in the high weight gainers while down in the low weight gainers. This seems odd because SIRT6 is usually activated when there is low NAD+ levels or low energy supplies, so I wouldn't really think that SIRT6 levels would increase in high weight gainer mice.
GEO profile of SIRT6 expression in immune resistant cancer cells
Analysis of a highly immune-resistant cancer cell line. The resistant cell line is produced by subjecting a susceptible cell line to multiple rounds of in vivo immune selection. Results provide insight into the molecular mechanisms underlying tumor immune evasion.
This is an interesting result because SIRT6 levels increase in cancer cells that are immune resistant and see that SIRT6 has some control on NF-kB gene it may allow for cancer cells to some how become resistant to the immune system by controlling inflammation so the immune system dosent come to where the cancer is.
GEO profile of SIRT1 overexpression mice
Analysis of transgenic hearts overexpressing Sirt1, a class III histone deacetylase. Sirt1 protects against apoptosis and mediates the survival of cardiac myocytes and neurons under stress in vitro. Results provide insight into the in vivo function of Sirt1 in the heart.
I found this microarray to be very interesting because it looks as if SIRT1 overexpression is inhibiting SIRT6 expression. This is interesting because SIRT1 could be regulating SIRT6 expression which maybe one way that SIRT6 is contoled. But one thing to watchout for with this experiment is that SIRT6 expression maynot be as robust in heart cells and also it maybe another protein that SIRT1 acts on that actually controlls SIRT6 levels.
Overall analysis
GEO was the best website for finding gene expression profiles of SIRT6 and how different conditions effected SIRT6 expression. This site did contain the actual gene profile of the SIRT6 knockout mice but I was unable to look at the actual heat map. So I choose just to use studies where people weren't looking directly at SIRT6, but found SIRT6 to either have increased or decreased expression levels depending on the different conditions used by the researchers. In all I was able to find some interesting studies where SIRT6 showed noticeable differences in expression levels. But I would have to say that the GEO site gives you so much data that it is overwhelming and I felt like the site could have done a better job of explaining how to search and what the results mean. Another note is that the each expression profile is
References
Barrett, T., Troup, D.B, Wilhite, S.E., Ledoux, P., Rudnev, D., Evangelista, C., Kim, I.F., Soboleva, A.,
Tomashevsky, M., and Edgar, R. (2007). NCBI GEO: mining tens of millions of expression profiles--database
and tools update. Nucleic Acids Research, 35(Database issue):D760-D765. doi:10.1093/nar/gkl887.
Mark Devries
Email [email protected]
last updated 1/22/09
http://www.gen677.weebly.com
