Analyze promoters (TRANSFAC(R)) (workflow) - Revision history

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;Workflow title
:Analyze promoters (TRANSFAC(R))
;Provider
:[[GeneXplain GmbH]]
== Workflow overview ==
[[File:Analyze-promoters-TRANSFAC-R-workflow-overview.png|400px]]
== Description ==
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.

At the first step, the input table is converted into a table with Ensembl Gene IDs.

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, as they are annotated in Ensembl.

Site search is done with the help of the TRANSFAC® library of the positional weight matrices, PWMs, namely with the profile vertebrate_non_redundant_minSUM.

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 (as they are published in PMID: 19534766)

The result of this step is a list of PWMs the hits of which are overrepresented in Yes set versus No set.

Next, the list of PWMs is converted into a table of transcription factors. Two tables are produced, with Ensembl Gene IDs and with Entrez IDs.

Finally, both tables with transcription factors are annotated with additional information, gene description and gene symbols.

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.

This workflow is available together with a valid TRANSFAC® license.

== Parameters ==
;Input gene set
;Species
;Results folder

[[Category:Workflows]]
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← Older revision		Revision as of 04:09, 19 April 2013
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 [[File:Analyze-promoters-TRANSFAC-R-workflow-overview.png|400px]]
 == Description ==
-This workflow is designed to search for putative transcription factor binding sites, TFBS, on the promoters of an input gene set.
+This workflow is designed to search for putative transcription factor binding sites  (TFBS) in 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.
-At the first step, the input table is converted into a table with Ensembl Gene IDs.
+At the first 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, as they are annotated in Ensembl.
-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, as they are annotated in Ensembl.
+Site search is done with the help of the TRANSFAC® library of the positional weight matrices (PWMs), namely with the default profile (matrix collection) vertebrate_non_redundant_minSUM. 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 (as they are published in PMID: 19534766)
-Site search is done with the help of the TRANSFAC® library of the  positional weight matrices, PWMs, namely with the profile vertebrate_non_redundant_minSUM.
+The result of this step is a list of transcription factor binding sites, which are overrepresented in Yes set versus No set.
-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 (as they are published in PMID: 19534766)
+Next, the list of PWMs is converted into a table of corresponding transcription factors and are annotated with additional information (gene description and gene symbols).
-The result of this step is a list of PWMs the hits of which are overrepresented in Yes set versus No set.
+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 their sites. As well as the final table with transcription factors, that are potentially regulating the genes in the Yes set.
-−
-Next, the list of PWMs is converted into a table of transcription factors. Two tables are produced, with Ensembl Gene IDs and with Entrez IDs.
-−
-Finally,  both tables with transcription factors are annotated with additional information, gene description and gene symbols.
-−
-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.
 This workflow is available together with a valid TRANSFAC® license.

@@ Line 29: / Line 29: @@
 == Parameters ==
-;Input gene set
+;Input gene set (Yes set)
 ;Species
 ;Results folder

@@ Line 2: / Line 2: @@
 :Analyze promoters (TRANSFAC(R))
 ;Provider
-:[[GeneXplain GmbH]]
+:[[geneXplain GmbH]]
 == Workflow overview ==
 [[File:Analyze-promoters-TRANSFAC-R-workflow-overview.png|400px]]