nilgun

Hi Vishal,

Thanks for your email. I have been thinking of writing to you for a while. I am just so busy with lab work that I didn't get a chance. I am trying to finish up the remaining experiments so I can write the paper. We are close! When I met Scott, he asked me to contact you and ask you to write a methodical description of the microarray analysis you did that we can put in the methods section. I think the attached heap map (one on the right of the Brd4/p65/JQ1 cluster) you generated for Jess will be featured in Figure 1 so further details on how that particular figure was generated, what the analysis is, what is being compared exactly will greatly facilitate writing the computational part of the paper.

Scott wanted to make the microarray data a big part of the paper. As I write the paper he may request more analyses and I will contact you to ask for your help with these. Somethings we discussed are as follows:

Thanks a lot for all your help. I appreciate all the help. I will keep in touch. Best.
 * The current differentially expressed gene lists are comparing one hairpin to the control hairpin ( shBrd4 vs shRen). Some of these genes are changed in senescence (compared to growing) but some of them are not. Ideally we would only like to concentrate on those senescence-associated genes (differing between gro and sen) that are different between shBrd4 and shp65. Can this be done? (three way comparison or something? You may know that best way but I hope I made it clear what we would like). To navigate the current lists, I first find something that is different between shBrd4 and shp65. Then I have to go to the gro vs sen comparison to see if that gene is changing in senescence. If the lists already incorporated this, it would be so much more robust. I hope I am not asking for something crazy difficult :)
 * The other thing Scott is really interested in is comparing the genes different between shBrd4 and shp65 in senescence (Ideally these would be only changing-in-senescence genes as I described above). He then wants to do a motif search analysis on these genes. The idea is to see what is different in the promoters of those genes that are affected, for instance, by Brd4 knockdown but not p65 knockdown. Specifically he wants to know if there is any motif that jumps out of Brd4 regulated genes that you don't see in p65. Brd4 doesn't have a DNA binding domain and it associates with DNA indirectly through binding other transcription factors. This would probably be done easier if we had ChIP-Seq data for Brd4 and p65. I am working on that experiment but the data won't be available in less than two- three months from now . Do you think that there is any info that could be obtained from the microarray data regarding this? The ultimate aim is to say something about those Brd4-unique or p65-unique genes on the Brd4-p65 Venn diagram that fall outside the intersection region.

Nil