Analyze promoters on the geneXplain platform
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 (1).
At the first step, the input table is converted into a table with Ensembl Gene IDs (2).
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.
Site search is done with the help of the #TRANSFAC
® library of the positional weight matrices (#PWMs).
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.
The result of this step is a list of PWMs the hits of which are overrepresented in Yes set versus No set. Default No set in the workflow is a set of housekeeping genes for the corresponding species.
Next, the list of PWMs is converted into a table of transcription factors (3).
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.
It is possible to get a #visualization
of TFBS for individual genes (4).