Andrew Cal

Lab Blog

 See what I've been up to: lab blog

Contact Infomation

Office: Erman Hall, Room 305

Address: 1103 East 57th Street, Chicago, IL 60637

Email: cal _ uchicago _ edu

Fax: 773-702-9740

Phone: 773-834-4055

Cell: 312     3079 075

Species-wide Regulatory Variation

Although molecular genetic studies with Arabdiopsis thaliana commonly use a only a handful of inbred ecotypes, the species is rich in phenotypic and life history diversity. I hope to use genomic resources developed in this model organism to better understand how genetic variation has allowed for the colonization of disparate environments. We have the tools in hand to interrogate how genetic variation affects gene expression. Studies involving recombinant inbred lines have revealed a large number of expression differences between pairs of inbred accessions (West et al 2007,  Keurentjes et al 2007). My goal is to map global expression difference while surveying species wide diversity. To do this, I have randomly crossed a over 200 inbred lines that represent diversity from across several continents. Genotyping by array hybridization has given us a high resolution haplotype map of the accession I have used, allowing for linkage disequilibrium mapping of expression QTL's.

About me

When I am not being a sixth year PhD candidate in Molecular Genetics and Cell Biology, I like to print T shirts, make science diagrams with my nephews in crayon, and play in the Hyde Park's finest hardcore punk band, gun with occasional music(RIP), and another screamyish band where I get to wear cardigans, an open letter.  

 An example of Association mapping of transcript level, for the gene ACD6 (AT4G14400) across >200k SNPs:

The most significant association for this gene also shows alleles specific expression:

(ONLY PLANTS HETEROZYGOUS AT THE DECTION SNP (with alleles A or B) are shown, grouped based on the genotype at the most significant snp from above. The left group is plants where Allele A is on the same molecule (chromosome) as the repressive allele of the associated snp, the right bar is transcript ratio A/B when allele A is on the same molecule as the promotive allele. The middle bar the A/B ratio when the above SNP is homozygous ie. would not expect allele specific expression). Boxes show the interquartile range, with wiskers being the most extream value within 2 IQ ranges and circles, and circles representing values outside of 2 IQ range above or below the median.