Kzebrows Week 15

Electronic Lab Notebook

Given the "Run Time 53" error when I tried to run my color set through MAPPFinder, I tried something else with the help of Dr. Dahlquist.

Opened Criterion-GO.txt file in Excel
Filtered Excel file:
- Number Changed by between 4 and 100
- Z score by greater than 2
- PermuteP by less than 0.05
- Adjusted P by less than 0.1

We decided to look at the criterion files for RX and RP -0pt5-10 and RX and RP -1-60. These were the samples at the smallest and largest time points at both concentrations, and by looking at the files and filtering them by the above criteria we were able to find some similarities:

RX and RP 0pt5-10 gene expression significantly increased: metabolic processes
RX and RP 0pt5-10 gene expression significantly decreased: ribosome
RX and RP 1-60 gene expression significantly increased: flagellar production
RX and RP 1-60 gene expression significantly decreased: metabolic processes

Next, with the help of Dr. Dahlquist, Erich and I decided that Erich would work on creating the gene mapp and I would work on creating color sets for each sample/time period. I created a final compiled raw data file by copying/pasting Erich's RP sample data into my RX sample data file. This file can be found on the OTS Files page under GenMAPP User Files.

Next I made sure the correct database build was being used in the GenMAPP program. I selected Data > Expression Dataset Manager and under Color Sets > Name I typed RX-0pt5-10. For Gene Value I typed Avg_LogFC RX-0pt5-10. I then added a New color set with the label "Increased", color red, and criterion "[Avg_LogFC RX-0pt5-10] > 0.25 AND [PValue_LogFC RX-0pt5-10] < 0.05." I added a second color set with the label "Decreased", color green, and criterion "[Avg_LogFC RX-0pt5-10] <-0.25 AND [Pvalue_LogFC RX-0pt5-10] < 0.05." I then saved this color set so it would appear on the mapp. I added 12 color sets, one for each sample/time period combo, starting with all RX-0.5 x MICs and then the corresponding 0.5 x MIC for RP. I then did the same for 1 x MIC. When I got to 1 x MIC at 30 minutes I encountered a GenMAPP error where the file could not be read. At that point I spoke to Dr. Dahlquist, who was able to fix it on my .gex file and upload that file, which I could then edit and use in order to proceed.

I then opened all of the Criterion files with Excel and made a compiled filtered file with the criteria above, the completed version of which is found here. I color coded each file (RP is blue, RX is pink) to highlight the top 10 GO terms for the different drugs at 1 x MIC at 60 minutes and 0.5 x MIC at 10 minutes (chosen because of their significance in the sanity check and out of our personal preferences with what we had already worked with) and put images of these tables in the team Power Point. I deleted all columns except for GO ID, name of GO term, number changed/present and percentage, number present/number in GO and percentage, regular p value, and adjusted p value.

Final PowerPoint Presentation