Difference between revisions of "ChIP-Seq - Identify TF binding sites on peaks (TRANSFAC(R)) (workflow)"

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[[File:ChIP-Seq-Identify-TF-binding-sites-on-peaks-TRANSFAC-R-workflow-overview.png|400px]]
 
[[File:ChIP-Seq-Identify-TF-binding-sites-on-peaks-TRANSFAC-R-workflow-overview.png|400px]]
 
== Description ==
 
== Description ==
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This workflow is designed to search for TFBSs on DNA sequences identified by the ChiP-Seq approach. Actually, any dataset in BED format can be submitted as input track for this workflow.
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This workflow is designed to search for binding sites for transcription factors on DNA sequences identified by ChiP-Seq approach. Potential binding sites are identified using TRANSFAC(R) database and the results are further refined for significance.
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As input, two different tracks should be submitted, one is a dataset under study, Yes track, and another is a background dataset, No track. The default No track corresponds to far upstream regions of the house keeping genes, where no functional composite modules are expected.
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In the first step both Yes and No tracks are submitted to the ''Site search on track'' and ''Site search results optimization'' analyses to find TFBSs enriched in the Yes-track as compared with the  No-track.  The workflow uses the default profile vertebrate_non_redundant_minSUM from the TRANSFAC® library. The output of this step is a list of PWMs the hits of which are enriched in Yes set versus No set.
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Next, the list of PWMs is converted into a table of genes with Ensembl IDs using the ''Matrices to molecules'' analysis, and further annotated with additional information, gene descriptions and gene symbols via ''Annotate table'' analysis. 
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This workflow is available together with a valid TRANSFAC® license
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== Parameters ==
 
== Parameters ==

Latest revision as of 16:19, 11 December 2014

Workflow title
ChIP-Seq - Identify TF binding sites on peaks (TRANSFAC(R))
Provider
geneXplain GmbH

[edit] Workflow overview

ChIP-Seq-Identify-TF-binding-sites-on-peaks-TRANSFAC-R-workflow-overview.png

[edit] Description

This workflow is designed to search for binding sites for transcription factors on DNA sequences identified by ChiP-Seq approach. Potential binding sites are identified using TRANSFAC(R) database and the results are further refined for significance.

[edit] Parameters

Input Yes track
Sequence source
Species
Input No track
Results folder
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