Cluster by shortest path (analysis)

Analysis title

Cluster by shortest path

Provider

geneXplain GmbH

Class

ShortestPathClustering

Plugin

biouml.plugins.keynodes (Master regulator node analysis plugin)

Description

This analysis allows you to make a cluster of genes/molecules upstream or downstream or both by taking reactions and all intermediate molecules using shortest paths from a specified search collection.

Parameters:

• Molecules collection – Input the collection of molecules/genes
• Input size (expert) – Size of input list
• Search direction – Direction to perform search in (either upstream, downstream reactions or both directions)
• Max radius – Maximal search radius
• Display intermediate molecules – Output the diagram with the direct reactions and all intermediate molecules
• Search collection – Collection containing reactions
• Custom search collection – Path to the custom search collection
• Species – Species to which analysis should be confined
• Output name – Output name.