February 2018

From OpenWetWare

Week 1 (2/5-2/9)

  • Adjusted significance values for edge deletions
  • Created a figure to illustrate which edge deletions caused significant changes and which caused no changes

Research Meeting

  • Went over abstracts
  • Submitted app to the symposium

Week 2 (2/12-2/16)

  • began work on poster for the symposium, mostly the background info
  • will be using spreadsheet that Maggie made to calculate minMSE (also for use in the future)

Research Meeting

  • all abstracts are submitted
  • turned in application and dues for Tri Beta

Week 3 (2/19-2/23)

  • calculated MSE:minMSE for each deletion network
    • only one was significant
  • looked at differences in edge weights in each deletion network compared to the intact network

Research Meeting

  • clustering deletions to see which are most similar or most different to the intact network
  • work with Brandon to make a heat map of the edge weight changes in each deletion

Week 4 (2/26-3/2)

  • worked on figures for poster

Research Meeting

  • went over poster figures with Dr. Fitzpatrick
  • Notes
    • unweighted db5 network
      • explain more about what it is
    • LSE:minLSE graph
      • sort from smallest to largest
      • color db5 line with a different color
      • fit improves in 5 cases
      • dHMO1-CIN5: what does it look like over time with and without that edge. CIN5 vs. time with and without HMO1-CIN5 edge
      • dHMO1-YOX1: yox1 vs. time with and without MSN2, and with and without HMO1
      • dZAP1-ACE2: ACE2 vs. time with and without the ZAP1 edge
      • Put the mean of the data and standard error on the graphs
      • Also show a deletion vs time where the model got worse
    • MSE:minSME ration and Production Rates
      • may not need the whole picture, maybe just a table to talk about the t tests
    • Some type of MSE:minMSE visual
      • experiment with things, run them by Dr. D and Dr. F
    • Edge Heat Map (table legend to be reformatted)
      • The edge deletions that change a lot are associated with central genes (lots of edges going to and from them: CIN5, MSN2).
      • Perhaps have not gotten the dynamics of GCR2-MSN2 right quite yet
      • Interesting to illustrate where these things are in the network
      • HMO1-CIN5 and ZAP1-ACE2 potentially have a pretty big ripple effect.
      • HMO1-YOX1 and MSN2-YOX1 end at a dead end.