Find master regulators in networks (GeneWays)

Created: 2013-11-13 16:39:26      Last updated: 2015-04-17 13:36:06

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 Entrez Gene IDs.
At the next step the Entrez genes are annotated with additional information, gene description and gene symbols.
The annotated gene table is subjected to master regulator search in the GeneWays 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.

What is the geneXplain type?

The geneXplain platform is an online toolbox for a broad range of bioinformatic and systems biology applications. It is developed by geneXplain GmbH. The technology behind the geneXplain platform is BioUML (, which has been built, improved and supported for many years at the Institute of Systems Biology in Novosibirsk. The individual workflows (geneXplain type), or Bricks, are unified under a standardized interface.
To run the workflows you just need to register for a free account here:

You get a password from BioStore to login the platform. It is open for everyone.

After clicking the workflow link (bottom) you can immediately enter the platform and execute the workflow via simple drag and drop of uploaded data files in your project.

Workflow_Find master regulators in networks (GeneWays)

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