Identify enriched motifs in promoters (GTRD) (workflow)

Workflow title

Identify enriched motifs in promoters (GTRD)

Provider

geneXplain GmbH

Workflow overview

Description

 This workflow is designed to find individual motifs enriched in the promoters of the input gene set as compared with a background set (No set).

In the first part of the workflow, the enriched motifs are identified by the method analyses/Methods/Site analysis/Search for enriched TFBSs (genes). 

Site search is done with the help of the GTRD library of the positional weight matrices, PWMs, namely with the profile moderate threshold. The enriched motifs are filtered with Adj_site_FE>1.0, and a filtered profile is created using the method, ‘Create profile from site model table’. 

This filtered profile is used to run Site search on gene set on the promoters of the input gene set.

The output Sites from this method are converted into Ensembl genes and annotated further with gene description and gene symbol. These Ensembl genes are the Transcription factor genes.

The results folder consists of several files and folders. The table Enriched Motifs contains those site models, here GTRD matrices, which are enriched in the Yes set in comparison with the No set.

 

 

 

Parameters

Input Yes gene set

Input No gene set

Profile

Species

Filter by TFBS enrichment fold

Filter for column Adj. site FE

Start promoter

End promoter

Result folder