This week, I compared the brain tissue specific network from human base (http://hb.flatironinstitute.org) with the set of genes I collected associated with a higher risk of schizophrenia. This tissue specific network gives the probability that 2 genes interact with each other specifically in the brain. Genes that interact in regions other than the brain but still interact in the brain have a lower probability count. As expected, nearly all of the associated genes had at least a 0.1 probability, which is relatively high in terms of bioinformatic confidence. Notably, several of the genes interactions that had above a 0.9 probability involved cell adhesion genes.
Of the genes below the 0.1 confidence, most do have neural roles but simply have roles common to other parts of the body. For instance, mir-137 is involved in neural development but is also involved in tumor suppression for several cancers.
This upcoming week, I will be learning how to use NetworkX and will be gathering statistics from the Humanbase network with it.