Enhancers and their RNA

== Overview

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This page aims both to give an overview of enhancer detection in FANTOM5 in general and then specific analyses made for the whole FANTOM 5 time courses. For more specifics, please see our satellite paper from phase 1.

== Background

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Identifying enhancers using CAGE tags Enhancers are , simplified, detected by looking for bidirectional CAGE tags clusters with balanced transcription not overlapping exons or known TSSs, with some additional expression constraints on top. These constrains are semi-arbitrary and will result in missing some known enhancers. Also, we avoid the proximal promoter region (-500 to -1), which may be too conservative.

== Associating enhancers with TSSs

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Associations are based on a very simple statistical test: a correlation test between the expression profile at the enhancer vs that of the TSS, based on CAGE. An additional contrains ois that we require that the distance between these is smaller than 500kb, for practical reasons (and few correlations are good at longer distances). At present, this is done using FAMTOM5 phase 1 samples, and not by individual time points, since the power is much higher.

== Analyses made on all time courses

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Please keep in mind that the enhancer detection approach works better on some time series. Data sets for these will be filled in in the next weeks.

Entire enhancer sets Enhancer sets from Phase 1 are here (link), as bed files.

Enhancer usage in time course X

Differential expression in time course X: time Y vs time Z

Motifs within enhancers

MARA