A Quick Update & Overview of Goals

Fall break is over and we’re back to work!

Before break, I found a great resource that summarizes cell motility proteins by grouping them by function; it includes chemotaxis, receptors, growth factors, rho family GTPases, adhesion, integrin-mediated signaling, cellular projections, cell polarity, and proteolysis. This resource constitutes a significant portion of the positive set of proteins involved in cell motility.

Over the past week, I have entered the next step in creating my positive set of proteins known to be participants in cell motility and schizophrenia. Because many papers cited pathways (in addition to specific proteins), it’s crucial to look at these pathways and comb proteins from them to add to the positive set. These pathways, which include the CAM pathway, FAK pathway, and Reelin pathway, were taken from KEGG, a pathway database. Unfortunately, the KEGG pathways download as unreadable XML files, so I must parse these files; I am currently using a parser developed by Anna Ritz. After I have parsed these pathways, my next small step is to see which, if any, proteins are involved in multiple pathways.

Once my positive set has come together, I will begin analyzing the GIANT network. This includes comparing KEGG proteins to the GIANT network as well as generating summary statistics of the GIANT network. I will go into more detail of what this entails as I complete this portion of my analysis, but it will include generating statistics such as degree distribution, average node degree (AND), average AND, and possibly a few others.