Worked on paper 9-11-12

2015-01-13

azim58 - 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&amp;shva=1#sent/139c618b1192751d

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