Analyze promoters (GTRD)

Created: 2013-11-13 16:34:21      Last updated: 2015-04-17 13:45:02

This workflow is designed to search for putative transcription factor binding sites, TFBS, on the promoters of an input gene set.

As input, any gene or protein table can be submitted. The input table contains genes under study, and it is called “Yes” set.
At the first step, the input table is converted into a table with Ensembl Gene IDs.

At the next step, promoters are analyzed for potential cis-regulatory sites. Promoters in this workflow are defined as sequences from -1000 to +100 relative to the transcription start sites, as they are annotated in Ensembl.
Site search is done with the help of the TRANSFAC® library of the  positional weight matrices, PWMs, namely with the profile vertebrate_non_redundant_minSUM.
At the same step, frequencies of putative TFBSs are compared between Yes set and No set to identify sites overrepresented in Yes set versus No set. Default No set in the workflow is a set of housekeeping genes for the corresponding species (as they are published in PMID: 19534766)
The result of this step is a list of PWMs the hits of which are overrepresented in Yes set versus No set.

Next, the list of PWMs is converted into a table of transcription factors. Two tables are produced, with Ensembl Gene IDs and with Entrez IDs.
Finally, both tables with transcription factors are annotated with additional information, gene description and gene symbols.

The output is a new folder with several tables, including a summary of the predicted TFBSs, genomic tracks of the Yes and No promoters  and sites, as well as the tables with transcription factors potentially regulating the genes in the Yes set.

What is the geneXplain type?

The geneXplain platform is an online toolbox for a broad range of bioinformatic and systems biology applications. It is developed by geneXplain GmbH. The technology behind the geneXplain platform is BioUML (, which has been built, improved and supported for many years at the Institute of Systems Biology in Novosibirsk. The individual workflows (geneXplain type), or Bricks, are unified under a standardized interface.
To run the workflows you just need to register for a free account here:

You get a password from BioStore to login the platform. It is open for everyone.

After clicking the workflow link (bottom) you can immediately enter the platform and execute the workflow via simple drag and drop of uploaded data files in your project.

Workflow_Analyze promoters (GTRD)

This workflow is available together with a valid TRANSFAC® license.

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