tag:blogger.com,1999:blog-36768584.post3614895844524115419..comments2024-03-03T18:49:34.382-05:00Comments on Omics! Omics!: Wishing I Had Been A Referee: A Renaissance for Tagamet?Keith Robisonhttp://www.blogger.com/profile/04765318239070312590noreply@blogger.comBlogger5125tag:blogger.com,1999:blog-36768584.post-3186424247338486672011-08-30T13:47:02.020-04:002011-08-30T13:47:02.020-04:00Hi, thanks for noticing the papers. Yes, we cited...Hi, thanks for noticing the papers. Yes, we cited the Connectivity Map in the papers, of course. Of course the Connectivity Map is a great resource, generously contributed to the public by a well-funded lab. I think one key that may not have been clear is that we could find so many disease profiles using free, publicly-available resources.<br /><br />To me, it is incredible that, due to increasing requirements from journals and funding agencies, that molecular measurements are available in the public (i.e. NCBI GEO, EBI ArrayExpress, etc).<br /><br />Several investigators have used Connectivity Map to make similar predictions, and we cite several of these, but to my knowledge, very few have actually tried their predictions in pre-clinical animal models.<br /><br />You are right that we didn't provide a list of the exact experiments we downloaded from NCBI GEO, and that would have been useful. We did provide a smaller list in our previous publication, including the specific disorders used in this paper. See here for details and the list: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000662#s4<br /><br />Best wishes -- Atul Butteatulbuttehttps://www.blogger.com/profile/01752712849667426905noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-75462313157848478222011-08-30T05:01:10.204-04:002011-08-30T05:01:10.204-04:00I can't help but wonder who are these reviewer...I can't help but wonder who are these reviewers and why they didn't ask some of these same questions. Seems to be a rampant problem in this field.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-25502297907539901022011-08-29T15:12:18.077-04:002011-08-29T15:12:18.077-04:00Actually both papers are essentially a minor tweak...Actually both papers are essentially a minor tweak of Connectivity Map. Very surprising it got into STM.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-61547846388685544612011-08-29T09:29:50.416-04:002011-08-29T09:29:50.416-04:00Yes, thank your for pointing that out -- I meant t...Yes, thank your for pointing that out -- I meant to explicitly cite Dr. Stegmaier's work with Todd Golub which pioneered this approach -- I believe they have initiated clinical trials based on it, but I don't know if any of those panned out.Keith Robisonhttps://www.blogger.com/profile/04765318239070312590noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-49885967255438386312011-08-29T09:24:18.157-04:002011-08-29T09:24:18.157-04:00Kim Stegmaier developed a similar strategy at the ...Kim Stegmaier developed a similar strategy at the Broad, called gene expression based high-throughput screening (GE-HTS). I'm sure you're probably well aware of this technology, but just in case, they have also come up with some interesting findings over the years.Anonymousnoreply@blogger.com