What I did today
- We had completed the calculations from the Schade data. What we noticed was that we needed to check the degradation rates for the 15 genes in our network.
- We took the raw half-life values of the genes from the Belle paper. the Belle paper was published in 2006, "Quantification of protein half-lives in the budding yeast proteome".
- Unfortunately 3 out of the 15 genes in our network did not have half-life values in this paper.
- To calculate the degradation rates from the half-life we used the equation =ln(1/2)/the half-life. We compared them to Stephanie Kuelbs' degradation rates and they were similar
- We could not leave those genes with zero values because that would misguide our function.
- We decided to take the average degradation rates of 203 genes from the Harbison's paper, Transcriptional regulatory code of a eukaryotic genome, published in 2004. The genes in this paper were compared to the genes in Belle's paper.
- The main reason why we decided to take the average of the 203 genes instead of only the genes in our network is because we might change the network later. If we were to change it, then the values would not have gone with that data. Since we are taking the average of the 203 transcription factors, then it accounts for the entire network, even if we were to change it.
- We took the median of the 203 genes.
- From the 203 gene list and the 3000 gene list, 135 genes were overlapped.
- Dr. Fitzpatrick suggested that for statistical purposes we took out the high and low 10% values. They are considered outliers. We also wanted the average to have less variation.
- Fortunately, our average was really close to the median.
- The average value that was obtained and replaced the genes that did not have degradation rates was -0.0193.