TEAM
Genome Wide Association Studies on Mouse Data
Tony Macula, Adam Busis, Feride Kose, Mykhailo Kuian, Zachary Pollock
Single Nucleotide Polymorphism (SNP or "snip" ) data has been used to discovery associations between genotype (genes) and phenotypes ( disease). I am mathematician and a few biologists have indicated an interest. **What this team needs is someone proficient in Python.**
Here is a mouse data site:
https://phenome.jax.org/
and here is some data
https://phenome.jax.org/projects/Gatti2
genotype : https://phenome.jax.org/phenomedoc?name=QTL_Archive/gatti_2014/Gatti_2014_geno.csv
phenotype: https://phenome.jax.org/phenomedoc?name=QTL_Archive/gatti_2014/Gatti_2014_pheno.csv
The phenotype has individuals as rows and phenotypes as columns. The genotype file has individuals has columns and each marker (SNP) is a row. Here is video about one way to analyze single SNP relations.
https://www.youtube.com/watch?v=sOP8WacfBM8.
I would like to discover multiple SNP relationship to phenotypes.