Find longest connected chains (analysis)

Analysis title

Find longest connected chains

Provider

geneXplain GmbH

Class

LongestChainFinder

Plugin

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

Description

Goal of this analysis is to find longest chains which contains as many elements from input collection as possible. Here chain means a path which starts and ends with the elements from the input collection. In this path length between two elements from the input collection is limited by maximal search radius.

Analysis uses Dijkstra search algorithm to find all possible chains. Then short chains, or long chains which contains just a few elements from input collection are cut off using score parameter. Let N_start be a number of elements from the input collection in the chain, N_total be a total number of elements in the chain, then score is obtained using following formula:

where coef is value of score coefficient.

Parameters:

• Molecules collection – Input the collection of molecules/genes
• Limit input size (expert) – Limit size of input list
• 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
• Max depth for Dijkstra – Maximal depth which will be used in Dijkstra search algorithm
• 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
• Species – Species to which analysis should be confined
• Decorators – Decorators
• Output table – Path to the result table
• Score coefficient (expert) – Parameter which is used to evalueate score