Susan Study

  • Start Date: 09 Sep 2004
  • Research Drive Directory: Kasper/040603/
  • Data Type: MassSpec
  • Notes:
  • Status:
    1. normal: 100% complete
    2. tumor: 100% complete


Analysis Requests : 2 data sets - normal and tumor


  • originally it has 9 time points, the investigator combine them into 6 time points
  • four samples in each time points : AP VP DP LP, each sample is the average of 6 mice.


  • 4 time points and 3 samples (AP VP DLP—DLP is the combination of DP&LP)

Step I: based on normal find out proteins that have the following pattern

timepoint ½ 3 4/5 6 10/15 40
cond N N F F F F
cond N N N F F F
cond N F F F F F
cond F N F F F F
cond F F N F F F
cond F F N N N N
cond F N N N N N

Totally generate 7 conds * 4 sample types (AP VP DP LP)= 28

Step II: pair wised comparison totally 6*5=30 based on normal set(data from step I result 1-5).
    • AP vs. VP
    • AP vs. DP
    • AP vs. LP
    • VP vs. DP
    • VP vs. LP
    • DP vs. LP

Step III: based on tumor set:get the pattern from step I, based on pattern 1-5, find out following patterns:

    • AP week10 week15
      ON ON
      OFF ON
      ON OFF
    • VP week 12 week17
      ON ON
      OFF ON
      ON OFF
    • DLP week10 week15
      ON ON
      OFF ON
      ON OFF


  • summary sheet: \KASPER\040603\deliverable
  • normal data set: \KASPER\040603\deliverable\normal_result
  • tumor data set: \KASPER\040603\deliverable\tumor_result

Change Log:

  • Sept. 22th: change timepoint of cloumn AK from 1 week to 12 weeks
  • Sept. 22th: delete 3 samples of 18 weeks in tumor data set.
  • Oct. 4th: change column AK type VP back into week 1.
  • Oct. 22th: change question #1 and #3 in tumor set (change week18 to week15)

Contact Info:

  • Primary Study Contact Person: Susan Kasper


Topic revision: r5 - 29 Oct 2004, JoanZhang

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