Anthony J. Wavrin Week 14

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Week 19 Assignment

Electronic Lab Notebook

  1. Dr. Fitzpatrick had made an input file that was originally for other data but, I used it as a template to make the input file for my data (dHMO1).
  2. Using my previously made network file (adjacency matrix), I imported it to the template file in the "network", "network_weights", and "network_thresholds" spreadsheets. In doing this, i corrected the network so only the gene names were used instead of the protein names.
  3. I corrected the list of the standard names and looked up the systematic names of the genes using YEASTRACT and put that into all the appropriate spreadsheets.
  4. I then looked up the correct protein degradation rates for the genes in the network using this file and used the average degradation rate of 0.027182242 for proteins that were not listed and put them into the corresponding rows in the spreadsheet "degradation_rates".
  5. Using the function degradation rate X 2, I calculated the production rates and inputted those into the corresponding rows in the spreadsheet "production_rates".
  6. Using the excel file I created in the week 9 assignment, I searched for the average log change of expression for times 15, 30, and 60 minutes by searching the systematic name of each gene and input that data into the spreadsheet "log2_concentrations".
  7. Next using the same excel file from week 9, I had to compute the standard deviation for each log fold change for each gene in the network. This was done by creating two new spreadsheets, one that carried of the data points and had the calculations for the st. dev. and the other was solely the standard deviations, which was then inputted into the spread sheet "concentration_sigmas".
  8. Lastly, I changed the spreadsheet so the function would be plotted every 5 minutes from 0 to 60 minutes and entered the thresholds for all genes to 0.

dHMO1 Input File

Original Assignment