I believe I might have found a common regulatory element for a dozen E coli genes/loci, however I need to find further evidence, preferably using bioinformatics. Can anyone help show me how can I prove these genes are co-expressed or not? Is there any database for expression of e.coli genes? or any other means to provide further evidence that my element is real.
There are certain databases where you can find the possible regulons of different putative regulators including the Regprecise database. Similarly, Genome 2D is also very useful online server which may help you in to find the co-expression pattern of genes.
I would urge all commentators to remember the differences between proof of function and possible function. Bioinformatics is quite useful, but has limitations, especially for proof of function, which usually needs in vivo work. Muhammad says it quite clearly: "... certain databases where you can find possible regulons of different putative regulators..." This says it quite well, I think.
As said above there are no bioinformatics tools that can prove your regulatory element as functional or "real". The only way to confirm the regulation of gene(s) expression by a regulatory element (enhancer, promoter...) is to perform biological experiments ("wet lab" work) where you mutate / invalidate / test your regulatory elements, for example with reporter constructs (luciferase assays). In E.coli, it shouldn't be too difficult to set up or to find collaborators to do the job. Good luck with your work!
to Muhammad: Any names or links of databases that I can access online?
Fabrice is exactly right! You've still got to do the work in the lab; otherwise, all you may have are probabilities.
to Alina: I found a common DNA motif that is represented at 15 different positions in e.coli and many other bacteria simply with bioinformatics. I found it may act as an attenuator. I do not have the infastructure to do wetlab. that is why I want to publish a communication and seek for funding with it.
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