Find master regulators for multiple gene sets (TRANSPATH(R)) (workflow)

Workflow title

Find master regulators for multiple gene sets (TRANSPATH(R))

Provider

geneXplain GmbH

Workflow overview

Description

This workflow is designed to find master regulatory molecules upstream of an input list of genes. The Input is a folder containing several gene or protein tables, and these tables are taken automatically by the workflow, one input table after another, in a cycle.

At the first step, one of the input tables from the input folder is converted into TRANSPATH® peptides.

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

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

At the next step, 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 for all input tables.

The same steps are repeated for the next input table, and several cycles are performed automatically corresponding to the number of tables in the input folder.

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

Parameters

Input folder

Input the folder containing differentially expressed genes

Species

Results folder