EPDnew, the Homo sapiens (human) curated promoter database

Overview

Version: 004
Coverage: 25503 promoters, 17785 genes
Genome assembly: H. sapiens (Feb 2009 GRCh37/hg19)
Gene annotation UCSC known genes (30-Jun-2013)
Based on data from: Riken/ENCODE CAGE data downloaded from UCSC,
FANTOM5 data,
EPD (old)
Documentation files Promoter assembly pipeline description
Statistics and quaility control report

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 tools

  • EPD selection tool: Promoter subset selection based on EPD-supplied annotation.
  • 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.

Analysis tools

  • 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 positions.

How-To Documentation: OProf , FindM and ChIP-Cor .

Viewer

The following is an example of the EPDnew viewer for the promoter MAPK1_1:

Last update Dec. 2016