process

For the midterm, I wanted to visualize genes associated with disease to compare “normal” with “mutation.”  I quickly found that the amount of data available is substantial, but difficult to work with because of the number of points in any data set.

I decided to focus on the MAPT gene because of it’s association with Alzheimer’s.

The first step was gathering data about the normal MAPT gene.

DATA

NCBI is an incredible data resource and had good information about the MAPT gene amino acid sequence, and links to information about mutations.

Gene Abbreviation: MAPT

Here’s the atgc sequence of the normal MAPT gene, with the known mutations (and omissions) below.

Finding the mutations came from exploring a few different resources.
Snippet:

http://alsod.iop.kcl.ac.uk/Als/Overview/gene.aspx?gene_id=MAPT

http://www.genome.jp/dbget-bin/www_bget?hsa:4137

Mutation:

 
Simultaneously, I was working to create a graphic framework that would make sense to bring the data into.
 

Randomized initial graphics programming test (no data)

Turning Gene Sequence Data into Proteins

The biggest impact of changes in the sequence of amino acids in the atgc data, is a change in the proteins that the gene translates into. Using the data above, I translated the normal and mutated MAPT gene into proteins for the visualizations. Each protein can be abbreviated by one of the 26 letters of the alphabet.

Because of the massive number of datapoints, I once again limited the data to the proteins contained in the first 5’3′ reading frame. I hope in future iterations to figure out a way to keep all of the protein data from the normal and mutated genes while keeping the visualizations stripped down enough to make an impact in meaning.

Here are the normal and mutated MAPT gene sequences as proteins.

The next step would be to plot and compare the normal protein pattern with the mutated protein pattern.

Normal MAPT gene proteins

Mutated MAPT gene proteins

Comparison: gray are normal, white are mutations

I wanted to see these comparisons in physical form, and imagined having a 3D printed sculpture to present, but there wasn’t enough time for 3D modeling and printing. Instead, I used a laser cutter to etch the patterns into two pieces of clear acrylic that would be stacked in order to create comparisons.