“What’s the Answer?” Thread

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

BioStar Question of the Week:
Today’s question was more of a discussion topic, but an interesting one considering ENCODE, TFBS and prediction. It got a lot of views and interesting discussion:

ENCODE soon provides DNase I hypersensitivity data for the whole genome in a multitude of different tissues….The question is: has the in-silico prediction of enhancers, binding sites or partners still merit or will we be soon able to look-up the binding events of TFs in the different tissues?

Highlighted Answer:

Only one of several interesting answers and discussion:

I think there is a big difference between observing an event (ex. transcription factor binding to region X) and knowing why you observe it. To put it in another way .. if we can solve protein structures should we still try to predict how a protein might fold ? Prediction tries to encapsulates our knowledge of the system so I think the answer is that we will never stop trying to predict/model a system even if we can just easily measure it. Until we can model it we don’t really know how it works. If you are only interested in knowing where a TF might bind to then the observations are enough but if you want to know why a protein with those characteristics is binding to that DNA region then the observations are just the starting point.