Worked+on+paper+9-11-12

Worked on paper to update figures and description of results C:\kurt\storage\CIM Research Folder\kwhittem\Papers\My Possible Papers\smc1\9-11-12 Paper Modifications Here are the notes on the figures from Kathy "C:\kurt\storage\CIM Research Folder\DR\2012\9-11-12\Figure notes from Kathy 9-13-12.pdf" Shen also sent his modified figures "C:\kurt\storage\CIM Research Folder\kwhittem\Papers\My Possible Papers\smc1\9-11-12 Paper Modifications\modified figs from Shen 9-13-12.ppt" Note that the original files are embedded in the powerpoint and can be opened by double clicking the image. Also note that only the 1st 4 figures in the powerpoint are needed in the paper.

I first started with the motif peptide figure. "C:\kurt\storage\CIM Research Folder\DR\2012\9-11-12\smc motif table.svg" Here's another version of the table that just contains the top blast result. "C:\kurt\storage\CIM Research Folder\DR\2012\9-11-12\smc motif table just top blast result.xlsx"

I may want to add BLAST results to this table.

BLASTed PMREGS In order to see some smc-like results I set the output to output more than 20,000 results (the maximum). I wrote some java code to extract the smc lines from the blast results here "C:\kurt\storage\CIM Research Folder\DR\2012\9-11-12\java code to extract smc lines.txt"

BLAST results were saved to the shared drive S:\Research\Cancer_Eradication\Users\kwhittem\kwhittem\Raw Data Often Originally on Research Drive\2012\9-11-12\BLAST Results

In Figure 7a and b with the PQRE and HEE heatmaps, Kathy thought it would be good to indicate which peptides were "specific". I think I'll indicate which ones were different from naive (in the 108 peptide list).

Need the PQRE list, the HEE list, and then I need to find the union of these lists with the 108 peptide list. PQRE-like peptide list TISKYVMVEPMRQHEEWGSC AVSHQEMNEGEQGPMREGSC RVGEMPMREYDISGGSGGSC WKPVPMRDFRTQPLMGDGSC LGGLSPMRETVVWWHWHGSC VNIWTNYPMRQGVNKGEGSC VMVKSPMRQADDYSKAGGSC LAQMLWPMRQMEEIRVTGSC FNFAQPKERQMPMRDFVGSC FPRKRNWWNTGPMREMNGSC RFVNWNPQRERRIRTIEGSC

HEE-like peptide list KHEESDRHTTHKEQESRGSC DHNRENHHSNHKHHEEHGSC PHEEYMRQFHSAGQPTFGSC DHRFWIKDMQYTIHEEPGSC VIGNYGREAFRAHEENHGSC QIPALGPFKHEELIGAYGSC IADQMDIDHEENGVFNIGSC ISIRTLHEETTAYPKVSGSC APPRLGGYFSHDHEEELGSC LTSQYHEESLLQFAIAIGSC NRETESKNHSTHEETQRGSC QMVLNKAWNDHEETMWHGSC IIKDHEEASSSKIQVAAGSC NQQPKHEEALQLGPYHKGSC KLIDHLRMNLKKEQHEEGSC HHNRFTGPKHEEIVSVRGSC NEVAKDHQMYQNHEEKIGSC GWAKARAWHYQPHEEQWGSC TISKYVMVEPMRQHEEWGSC

Now I can compare these lists with the 108 SMC1fs peptides Some Java code to get the union "C:\kurt\storage\CIM Research Folder\DR\2012\9-12-12\paper\code for union with 108.txt"

Here are the union lists pqre_like_peptides [TISKYVMVEPMRQHEEWGSC, AVSHQEMNEGEQGPMREGSC, RVGEMPMREYDISGGSGGSC, LGGLSPMRETVVWWHWHGSC, FPRKRNWWNTGPMREMNGSC] hee_like_peptides [TISKYVMVEPMRQHEEWGSC]

Changed the 3D bar graph figure so that there weren't 2 blue colors and also reversed the order of the legend so it matched the order of the graph.

Some Comments to give back to Kathy:

You asked why we "chose to do the experiment with these 2 motifs? No binding with the others or what??" We chose the PQRE and HEE motifs because these are the two most prevalent motifs.

You mentioned that the PQRE and HEE heatmap descriptions were mislabeled so that they were reverse. However, this does not appear to be the case unless I have missed something.

We talked about indicating which peptides were SMC1fs specific in the PQRE and HEE heatmap figure. There are multiple ways one could define something as being SMC1fs specific. I chose to mark which peptides were in the 108 peptide list that distinguished SMC1fs sera from naive sera.

You were curious about whether the SMC sample in figure 5 with the 3D bar graph should be the 17mer or a 27mer. It should be the 17mer just as it was originally.

You were curious about the p values of the PQRE-like peptides presnet in the PQRE and HEE heatmap that did not come up positive. Some of the peptides that look specific do have low p values (still above the 0.0001 threshold of course otherwise they would have been included in the 108 peptide list). However, some look kind of specific but don't have low p values. The p values for the HEE and PQRE peptides can be found here: "C:\kurt\storage\CIM Research Folder\DR\2012\9-13-12\smc paper\p values of peptides 9-13-12.xlsx" I'm not sure if you wanted to comment on this issue in the paper. I have just left commentary about this out for now.

Note that in the document I changed the font from Calibri to Arial since we have to use one of these approved fonts: Arial, Courier, Times, Symbol.

sent e-mail to Kathy on 9-14-12 https://mail.google.com/mail/u/0/?ui=2&shva=1#sent/139c618b1192751d