Reviews On Enhancer Prediction Methods

Question

[Diana]

Hi,

Has anyone come across some good recent reviews on enhancer prediction tools and transcription factor binding prediction tools?

Edit: I'm looking for a review article that compares different existing tools for enhancer prediction/transcription factor binding site prediction so I can get an idea about the efficiencies of different methods

Thanks!

Answer 1

[PoGibas]

There is Encode thread enhancer discovery and characterization so you might want to start there.

Edit
New method announced - STARR-seq (can be used to identify and quantify enhancer activity).
science.1232542 January 17 2013

[PoGibas]

Added some new information to my previous answer.

Answer 2

[Rad]

I don't think such a review exists, that said, you can still gather the papers on enhancer predictions methodologies, the most famous paper is chromHMM, but there are some other methodologies based on machine learning techniques like SVM for example. As we don't know yet everything about enhancers in term of functional properties and epigenetic ones, I think it is better to start with all review on enhancers (I guess you did). If you are developing a tool on enhancer predition, my advice is to use experimental data as foreground/background which is in term of data quantity not that much. A lot of tools especially those based on SVM are trainined on a very few amount of experimental data (known enhancers, may be a couple of handreds) which makes it a bit hard to make a solid statement on prediction efficiency. The only way to confirm the accuracy is to do a functional analysis of upstream and downstream regions for an approximation.