So here is a challenge which I am sure many people face.
An academic does an experiment and finds a particular protein A-protein B interaction in vitro which may be important in a disease. How do you go about finding molecules to test experimentally that might up or down regulate protein B ?
Fortunately there have over the past decade or so been many gene expression studies where human or animal cells / organisms have been exposed to different drugs at different concentrations. You could just go to one or more database and look for examples of were your gene of interest goes up or down. You could also google, use PubMed etc..with varying chances of success.
I have had cause to try this a few times when when one of the groups I have been working with came up with target X of interest.
Yesterday evening I found several resources and the differences in accessibility was quite interesting.
1st The Connectivity Map from the Broad Institute, funded by NHGRI in 2009 and 2010 each time to the tune of close to $1M. This requires you to register and after doing this it would let me get in. I was very annoyed by the fact this database even requires this.
2nd A smaller Japanese database of anticancer drugs and gene expression data works on a similar principal but this required no password, login etc.
3rd GEO from the NCBI was easy to use, it did not have any relevant results but it did not require a login etc.
4th Expression Atlas from EMBL-EBI was also very easy to access and required no login.
So I sent a short email to the Connectivity Map folks at the Broad asking what requires them to require a login and why it did not work.
Is there a list of similar databases somewhere, is there a definitive meta-database that allows you to search across them. I am sure instead of finding individual papers from x or y group touting there algorithm or database for doing these searches it might be good to have just one definitive place to go. Small request. For the $2M spent on Connectivity Map that was not too helpful. Perhaps there should be a mandate that any database thats meant to be publically accessible should not require a password, login , registration. If it works for 3 out of the 4 databases above why can it not work for all? And of course this does not apply to commercial tools.
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