Day Twelve

I finally finished my proposal! I sent in my draft to my professor, and the feedback he sent back, and I quote" Sangeetha, I think it looks great, especially considering how briefly we have discussed the project" So, hopefully this entire project will actually work out so I can get some good data. Basically this is a really rough overview of what it does.

A computational biology analysis of the genetic linkage between adrenal gland weight and anxiety behavioral assays by methods of singular value decomposition

Specific Objectives

Aim One: To find a correlation between a non-behavioral trait and a set of behavioral traits to investigate if indirectly related behaviors may be influenced by the same genetic factors.  Specifically, the non-behavioral trait of interest in this study is the adrenal gland weight and the behavioral traits are anxiety test assays. The study will attempt to show that the adrenal gland weight has an effect on anxiety in general. This analysis will be completed using singular value decomposition (SVD) as well as running quantitative trait loci (QTL) scans using the statistical open source software R. A set of overlapping QTLs and genes will be formed to compare with the gene expression analysis.

Aim Two:  To conduct a gene expression data analysis on all of the genes mapped thus far in the BXD inbred mouse cross in order to find similar expression patterns among genes. This analysis alike the phenotype trait analysis is done using singular value decomposition and QTL scans. In the end, a set of genes with its corresponding gene ontology annotations will be formed that represent the greater proportion of genes whose gene expression are explained by the patterns found by SVD. QTL scans will be performed on the SVD gene expression patterns to identify genetic loci that influence these patterns.   

Aim Three: To compare the gene lists between the gene expression analysis as well as the phenotype trait analysis for overlap. After completing the singular value decomposition on both the gene expression data for the BXD inbred mice cross and the phenotypic trait data, overlapping QTL scans can be found.

 If you want my actual proposal to read if you're interested. I can probably send it to you.