Closed dondi closed 2 years ago
During this weekly session I went to YeastMine and selected the regulators tab. From there I was able to get all of regulator genes, and search for the targets of each regulator. YeastMine provided code to do this, so I am currently creating a file to generate all of the regulator and target genes.
During the meeting @kdahlquist mentioned that I should generate 2 adjacency matrices, a 295x295 regulator by regulator matrix that is primarily used in GRNmap, as well as the 295x???? regulator by target matrix.
200x6000 regulator X target
I'm not sure how many genes SGD will classify as a regulators, it will be ~175-250.
I created the script to generate the regulators by regulators adjacency matrix as well as the regulators by targets adjacency matrix. There were 294 genes classified as regulators, and I generated all of their targets. Some genes did not have a standard name, so in the script they are not currently in the matrices.
When there is no standard name, we need to substitute the systematic name instead.
I made the appropriate fix and regenerated the adjacency matrices.
Decided at the meeting to commit this work to a new top-level folder called database. .gitignore will also be revised to avoid accidental committal of files produced by these scripts
This is complete
SGD may be YeastMine. We want to look for regulation information there if available.
In the absence of API availability, we may need to develop a mechanism for storing the GRNs in our own database, and importing into them based on published files.