View source for Find master regulators in networks with context genes (TRANSPATH(R)) (workflow)

;Workflow title
:Find master regulators in networks with context genes (TRANSPATH(R))
;Provider
:[[geneXplain GmbH]]
== Workflow overview ==
[[File:Find-master-regulators-in-networks-with-context-genes-TRANSPATH-R-workflow-overview.png|400px]]
== Description ==
'''Variant of the workflow:

It helps to specify the list of the "context genes", that is any additional list of genes to direct regular search in a way to come through the molecules from this list.'''

 

This workflow is designed to find master regulatory molecules upstream of an input list of genes. Input file is any gene or protein table.

 At the first step, the input table is converted into a table with TRANSPATH® peptides.

This table is subjected to master regulator search in the TRANSPATH® network. For each potential master regulator, FDR, Score, and Z-score are calculated.

The results are filtered by Z_Score>1 and Score>0.2 to select statistically significant master regulators.

Further, the filtered regulatory molecules are converted to both Ensembl Gene IDs and a list of UniProt protein IDs.

The table with Ensembl Gene Ids is annotated with additional information, gene description and gene symbols.

Finally, the table with master regulatory molecules is sorted by Score and networks for the three top master regulators are visualized as diagrams in the hierarchical layout.

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

== Parameters ==
;Input gene set
;Species
;Context genes
;Max steps
:Select max number of steps upstream
;Results folder

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