D-Light on Promoters

D-Light on Promoters is a simple client-server based system for quering and viewing annotation data on promoter sequences. By default, the underlying database is filled with transcription factor binding site (TFBS) data during server setup. Users may add also other arbitrary annotations at any time.

Right after the server installation (or using our public D-Light server) a user can query precalculated data of predefined promoter and PFM (Position Frequency Matrix) sets and view them in a graphical manner. For more advanced usage, however, users may add own data sets (PFMs, promoter sequences, precalculated annotation sets). D-Light allows for querying single TFBSs or pairs of TFBSs. Cross-genome searches verify the matches in homologous genes.

For sensitive and/or multi user environments the system provides a user management such that users can create personal accounts and upload/remove personal data, which are invisible for other users but can be queried in the context of the public content.

We provide a public D-Light server containing 2 kB up-/downstream promoters from Human, Mouse and Rat annotated with predicted TFBS using the JASPAR core vertebrata PFMs. The client links located in navigation bar (left) access this server by default.

D-Light version 2 (Update August 2016)

We have recently updated the D-Light database to the latest genome assembly and JASPAR PFM data. Please note that user related data (user accounts, queries, and uploaded data) as well as ENCODE data were not migrated to D-Light version 2.

The original D-Light version 1 including all user related data is available on this server until August 2017. In order to access these data, either change the port numbers in the D-Light configuration file (dlightApplet.properties; port=8083, portDAS=8084) or simple download the corresponding standalone client (Standalone v1 database 2013). Please do not hesitate to contact us, if you have any further questions.

All changes:
  •  JASPAR 2016 PFMs – The D-Light database now provides the current version of the JASPAR PFMs, which now includes 519 vertebrate PFMs (509 of those PFMs have at least hit with the default D-Light p-value cutoff).
  • New genome assemblies: On our public web service we now provides hg38 (as default), hg19, mm10 and rn5. Other updated releases and several new genomes are available for a local D-Light installation.
  • Please note that due to the increased number of promoters and annotations the database size increased by a factor of six and hence the response time for certain queries may also slightly increase.

Technical Details:

The client is written in Java (using the GenoViz SDK) and will run on any operating system supporting Java 1.6 or later. It is available as a Java Web Start application or as a standalone application for local installation. The server uses solely open source components such as MySQL , MyDAS and Python and runs on Unix like operating systems.

Both, client and server are also provided as GNU GPL licensed source code.

We recently encountered problems when using the applet or web-start client with the latest OpenJDK/IcedTea 7 Java version. Please use the standalone client in this case. We are sorry for this inconvenience and try to resolve this problem as soon as possible.