EEL - Enhancer Element Locator


Enhancer Element Locator, or EEL, is a tool for locating distal gene enhancer elements in mammalian genomes by comparative genomics.

Database access

We have computed EEL alignments between orthologous genes from human and many other species. The results are available on our mysql server at http://sysdb.cs.helsinki.fi/u/tkt_bsap/EELweb/.

The data is regularly updated with some synchronization with ENSEMBL database, which we use as source of genomic information. The current database is also available via DAS service behind url http://sysdb.cs.helsinki.fi/das. Add the EEL track named NCBI35cis to current Ensembl version as follows:

  1. Open Ensembl genome viewer, for example near MYC gene.
  2. Click "Manage your data" on the left panel and choose "Attach DAS".
  3. Write "http://sysdb.cs.helsinki.fi/das/NCBI35cis" into the box "or other DAS server" and press "Next".
  4. Tick the box "NCBI35cis" and press "Next".
  5. Choose species "Homo_sapiens" (default) and press "Next".
  6. Choose coordinate system "Chromosome NCBI35" and press "Next".
The DAS source should be attached and the track NCBI35cis should be visible in the browser. You can also view the track directly in ENSEMBL release 50.

Genome wide data download

The data used in the paper is available here along with up-to-date computations with more current genome assemblies.

Usage

Instructions for using the Enhancer Element Locator is available here. A straightforward protocol for EEL usage is also published in Nature Protocols.

Download

The EEL-1.1 software is available for download in various forms under the GNU General Public Licence. Please choose appropriate distribution:
  1. Standalone Windows. Just install and use on Microsoft Windows.
  2. EEL-1.0 Compiled MacOS X. Compiled binary package for Apple/PowerPC users. No graphical user interface and needs either PYTHONPATH set or extracted in /System/ directory.
  3. EEL-1.0.1 Fancy MacOS X. For Apple/PowerPC users. Contains Mac specific graphical user interface.
  4. Compiled Windows. If you already have python installed on your computer, you can try this precompiled package with Python scripts.
  5. Source. This works with everyone with enough patience. For Linux users this is preferable distribution, others should be prepared for more or less work to get everything running (need at least C++-compiler and Python).

Transcription factor motifs

You can obtain transcription factor motifs from databases such as JASPAR or use the motifs used in the CELL article.

Installation

Apple MacOS X

Download the version compiled for Mac OS X from here. Start the Terminal program and uncompress the package with command 
tar -zxvf MacEEL-1.1.tar.gz
Follow the instructions in file EEL/MacEEL GUI INSTALL.rtf.

Linux and non-listed OSes

Download the source package from here. Uncompress the package by 
tar -zxvf EEL-1.1.tar.gz
Finally go the EEL-1.1 directory and issue the command 
python setup.py install
Now you should be able to launch eel with command 
eel

Microsoft Windows

Click the link for standalone Windows EEL above and follow the instructions on the installer.

References