Identify enriched motifs in promoters (GTRD) (workflow)

Workflow title

Identify enriched motifs in promoters (GTRD)

Provider

geneXplain GmbH

Workflow overview

Description

This workflow finds transcription factor binding sites, TFBS, enriched in the promoters of an input gene set as compared to the promoters of the backgrounds set. Site search is done with the help of the GTRD library of positional weight matrices, PWMs, namely with the profile moderate threshold.

In the first part of the workflow, the enriched motifs are identified by the method Search for enriched TFBSs (genes). Filtered enriched motifs serve as a basis to construct a specific profile, and this profile is run on the promoters of the input gene set, method Site search on gene set.

Yes set and NO set is the gene sets for which you wish to analyse the promoters. By default the workflow uses a subset to 300 genes randomly taken out of the human housekeeping genes as NO set. Filter by TFBS enrichment fold: In this field you can specify the enrichment fold (FE) to filter the motifs. By default it is 1.0, which means all motifs with FE>1.0 will be reported in the resulting table and the same motifs will serve to create a specific profile. If you want to use highly-enriched motifs, you can specify higher thresholds, e.g. 1.1, 1.2 etc, or even 2.0 or 3.0 depending on your Yes and No sets. The promoter region is -1000 to +100 relative to the TSS.

The result folder contains several files and folders including site search results, annotated transcription factors, Profile table and table with Enriched motifs.

The table Enriched Motifs contains those site models, here GTRD matrices, which are enriched in the Yes set in comparison with the No set. Each row of the output table represents the result for one PWM from the input profile.  Profile presents only those PWMs with adj. site FE >1. Site search analysis output serves to visualize enriched motifs in the promoters. The table Transcription factors Ensembl genes is a list of transcription factors linked to the enriched motifs.

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