EPDnew, the Homo sapiens (human) curated promoter database
Promoter Selection and Analysis tools
Various tools allow you to analyse promoters from EPD and/or to
select subsets of promoters. In order to analyze the complete EPD
promoter set, go directly to one of the analysis pages. If you
prefer to first select a subset of promoters, go to one of the
selection pages. From the output of the selection pages you can then
directly navigate to one of the analyses pages, or you can continue
with another selection page to refine your promoter selection.
selection tool: Promoter subset selection based on
ChIP-Cor : Promoter subset selection based on
experimental data or genome annotations residing in the
MGA repository. Example: select promoters that have more
than 100 H3K4me3 ChIP-seq tags data between -100 and +100
relative to the TSS.
FindM : Promoter subset selection based on DNA motif
occurrences. Example: select promoters that have (or
don't have) a c-Myc binding site between -100 and +100
relative to the TSS.
ChIP-Cor : Generation of an aggregation plot
(feature correlation plot) for a specific genome
annotation features. Example: Distribution of
nucleosomes (MNase-seq tags) near promoters, e.g.
from -1000 to +1000 relative to the TSS.
ChIP-Extract : Extraction of
specific chromatin features around each promoter in
table format. The output is a table with rows
representing each promoter and columns the feature
tag occurance at a specific distance. Example:
Distribution of nucleosomes (MNase-seq tags) near
each promoter, e.g. from -1000 to +1000 relative
to the TSS. Useful for downstream analysis in R,
for example to classify promoters according to
differences in feature distribution.
OProf: Generate a motif occurrence profile
around TSS positions. Example: Generate a plot
showing the occurrence frequency of TATA-boxes
between -100 to +100 relative to the TSS.
FindM Extract DNA motif positions near transcription
start sites. Example: extract coordinates of
CCAAT-boxes located between -150 and -50 relative to a
TSS. The output is set of CCAAT-box positions that can
be further analysed in the same way as a set of TSS
The following is an example of the EPDnew viewer for the promoter MAPK1_1