BEM and the Art of Heat Maps

Sample heat map showing expression of 6 genes (listed down the side) for three samples from each of two treatments (A & B; labeled along the top).

The Benthic Ecology Meeting is coming up in a couple of weeks – which means I am trying to get my presentation finished up. I study gene expression in corals, comparing how genes are expressed differently in different parts of the colony. The best visual way that I know of to present gene expression data is through heat maps. Basically, these consist of a list of genes (transcripts) with the amount of expression in each of your samples – where the relative value of expression is color coded (usually red is high expression and blue is low expression).The example on the right shows how 6 genes from 3 different functional processes could be expressed. Genes 1 & 2 are consistently expressed more in in the A samples than the B samples. Both genes 1 & 2 are associated with one functional process, so this suggests that Process 1 is upregulated in treatment A. Genes 3 & 4 show the opposite pattern for genes in Process 2 [I should add that increased expression of an inhibitor would actually mean downregulation of a process… so it can be complicated]. Whereas genes 5 & 6 show no consistent pattern of expression among the two treatment groups. A functional process could be something like a signaling pathway involved in development, or a synthesis pathway involved in producing structural molecules.

Heat Map Eye Candy. This should probably be marine themed, but... well, feel free to imagine it is a spiny fish...

You can make heat maps in the program R, but the Broad Institute has a couple of relatively user-friendly programs that are more straight-forward and don’t require any coding. The one I just started to use is called GENE-E, and for my purposes it has some major benefits over the program that I used to use, GenePattern. I made a bunch of heat maps for my data, and it definitely helps me to see the data expressed this way in order to pick out patterns. But, all the tiny blue and red squares are making me a bit cross-eyed. So, on my nerd-break I crafted this… porcupine (in soothing fenerbahce colors).

Looking forward to finishing up this presentation and sharing my data with the world (of benthic ecologists) soon!

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