Effector search (analysis)

Analysis title

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.