Difference between revisions of "Find common effectors in networks (TRANSPATH(R)) (workflow)"

Latest revision as of 13:28, 16 May 2013

Workflow title

Find common effectors in networks (TRANSPATH(R))

Provider

geneXplain GmbH

[edit] Workflow overview

[edit] Description

This workflow is designed to find effector molecules downstream 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 which is later also present in the output folder.

This table is annotated with additional information, gene description and gene symbols.

The annotated table is subjected to Effector search in TRANSPATH® network. For each potential Effector molecule, FDR, Score, and Z-score are calculated.

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

Further, the filtered effector 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 the effector 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.

[edit] Parameters

Input gene set

Species

Results folder