Computation
Overview
Our group was focused on merging the following lists: human ortholog (List 1) + expression in glial cells (List 2) + altered in ALS (List 3) + possible communication (List 5). We found 77 communication gene candidates, which we then separated based on whether those genes were up or down regulated. Finally, we took those gene candidates to FlyBase to get the correlating stocks that we will order.
Merging Lists
List 1: Human Ortholog
We are looking for genes that are also expressed in humans. We used the website https://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl for identifying human orthologs for our genes of interest.
List 2: Expression in Glial Cells
List 3: Altered in ALS
We took our list of genes that are over or under expressed in ALS from Atilano et al who expressed polyGR to observe effects.
List 4: Expression in the Mushroom Body
Get the list of genes that express plasma membrane proteins from flybase.
flybase.org > Tools > Search/Browse Portals > QueryBuilder > Build a new query > Choose Expression Patterns in Data Class > Type membrane in Subcellular Localization > Click Finish Editing > Click Run Query > Click on gene (count) > Export ID list
Bringing all the lists together
A Google Colab notebook describes the way we merged all the lists together and got all the stocks.
Sorting Up/Down Regulated
We wrote a program to sort through our list of genes and compare with a spreadsheet of sorted upregulated and downregulated genes. We now had our final list of genes and knew which ones were downregulated or upregulated.
Getting Stocks
We created a module for crawling flybase.org. You can call the get_stocks method with gene name or id and stock type and it will crawl the website and return the matched stocks.
