Weeks 4 and 5: Building a Gold Standard List

Over the past couple of weeks, Alex and I have been given the task of building our project’s gold standard list. This list will be comprised of genes known to be associated with Schizophrenia and genes known to be associated with cell motility; Alex was given the Schizophrenia half to research and I was given the cell motility half. Overwhelmed by the sheer volume of genes and pathways associated with cell motility, I began by looking up genes known to be associated with both Schizophrenia and cell motility. In our meeting, we briefly discussed how this might serve us later as a known positive we could use to test our algorithm.

I read through tons of articles and papers, many of which I found through references in previous papers we have read. In reading these papers, I was hunting for genes, pathways, and resources that were studied and employed by the researchers and found several that will be useful to us. The CAM pathway and associated genes appeared multiple times, and the resource KEGG was used by the majority of the researchers. My task over the past week has been to download data from KEGG, continue accumulating genes for our gold standard list, and begin adding “confidence details” to the genes – this is an important weight that will be added to the genes in our list and will be a measure of how “confident” we are that the gene is truly associated with either Schizophrenia or cell motility.