Effector search (analysis)

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Analysis title
Molecular-networks-Effector-search-icon.png Effector search
Provider
geneXplain GmbH
Class
EffectorKeyNodes
Plugin
biouml.plugins.keynodes (Master regulator node analysis plugin)

Description

Find genes or proteins regulated by the input set of genes.

Parameters:

  • Molecules collection – Input the collection of molecules/genes
  • Weighting column (expert) – Column to replace weights in search graph
  • Limit input size (expert) – Limit size of input list
  • Input size (expert) – Size of input list
  • Max radius – Maximal search radius
  • Score cutoff – Molecules with Score lower than specified will be excluded from the result
  • Search collection – Collection containing reactions
  • Custom search collection – Path to the custom search collection
  • Relation sign – Consider only specified type of relation chain between molecules.
  • Species – Species to which analysis should be confined
  • Calculate FDR – If true, analysis will calculate False Discovery Rate
  • FDR cutoff – Molecules with FDR higher than specified will be excluded from the result
  • Z-score cutoff – Molecules with Z-score lower than specified will be excluded from the result
  • Penalty (expert) – Penalty value for false positives
  • Decorators – Decorators
  • Normalize multi-forms (expert) – Normalize weights of multiple forms
  • Output name – Output name.
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