Difference between revisions of "ChIP-Seq - Identify TF binding sites on peaks for multiple datasets (TRANSFAC(R)) (workflow)"
m (Cosmetic changes in category formatting) |
(Automatic synchronization with BioUML) |
||
| Line 6: | Line 6: | ||
[[File:ChIP-Seq-Identify-TF-binding-sites-on-peaks-for-multiple-datasets-TRANSFAC-R-workflow-overview.png|400px]] | [[File:ChIP-Seq-Identify-TF-binding-sites-on-peaks-for-multiple-datasets-TRANSFAC-R-workflow-overview.png|400px]] | ||
== Description == | == Description == | ||
| − | This workflow is designed to search for | + | This workflow is designed to search for TFBSs on DNA sequences identified by the ChiP-Seq approach, for multiple datasets. Actually, any dataset in BED format can be submitted as input track for this workflow. |
| + | |||
| + | In the input field ''Yes tracks'', several different tracks can be simultaneously submitted. The same background dataset, No track, is used for comparison with each of the submitted Yes tracks. The default No track corresponds to far upstream regions of the house keeping genes, where no functional composite modules are expected. | ||
| + | |||
| + | 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 first Yes-track in comparison with 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 the first Yes set versus No set. | ||
| + | |||
| + | In the second step, the list of PWMs is converted into a table of genes with Ensembl IDs using ''Matrices to molecules'' analysis and further annotated with additional information, gene descriptions and gene symbols via ''Annotate table'' analysis. | ||
| + | |||
| + | The first step and the second step are then performed for the second Yes track, and so on, repeatedly in a cyclefor each of the input Yes tracks. | ||
| + | |||
| + | This workflow is available together with a valid TRANSFAC® license | ||
| + | |||
| + | |||
== Parameters == | == Parameters == | ||
Revision as of 11:49, 30 July 2013
- Workflow title
- ChIP-Seq - Identify TF binding sites on peaks for multiple datasets (TRANSFAC(R))
- Provider
- geneXplain GmbH
Workflow overview
Description
This workflow is designed to search for TFBSs on DNA sequences identified by the ChiP-Seq approach, for multiple datasets. Actually, any dataset in BED format can be submitted as input track for this workflow.
In the input field Yes tracks, several different tracks can be simultaneously submitted. The same background dataset, No track, is used for comparison with each of the submitted Yes tracks. The default No track corresponds to far upstream regions of the house keeping genes, where no functional composite modules are expected.
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 first Yes-track in comparison with 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 the first Yes set versus No set.
In the second step, the list of PWMs is converted into a table of genes with Ensembl IDs using Matrices to molecules analysis and further annotated with additional information, gene descriptions and gene symbols via Annotate table analysis.
The first step and the second step are then performed for the second Yes track, and so on, repeatedly in a cyclefor each of the input Yes tracks.
This workflow is available together with a valid TRANSFAC® license
Parameters
- Input Yes tracks
- Sequence source1
- Input No track
- Results folder
