Difference between revisions of "Identify enriched motifs in promoters (GTRD) (workflow)"

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[[File:Identify-enriched-motifs-in-promoters-GTRD-workflow-overview.png|400px]]
 
[[File:Identify-enriched-motifs-in-promoters-GTRD-workflow-overview.png|400px]]
 
== Description ==
 
== Description ==
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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.
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 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).
  
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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''.
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In the first part of the workflow, the enriched motifs are identified by the method '''analyses/Methods/Site analysis/Search for enriched TFBSs (genes)'''. 
  
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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.
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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’. 
  
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The result folder contains several files and folders including site search results, annotated transcription factors, Profile table and table with Enriched motifs.
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This filtered profile is used to run Site search on gene set on the promoters of the input gene set.
  
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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.
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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.
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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.
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== Parameters ==
 
== Parameters ==

Latest revision as of 16:34, 12 March 2019

Workflow title
Identify enriched motifs in promoters (GTRD)
Provider
geneXplain GmbH

[edit] Workflow overview

Identify-enriched-motifs-in-promoters-GTRD-workflow-overview.png

[edit] 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.

 

 

 

[edit] 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
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