Calculate CMA regulation (analysis)

Analysis title

Calculate CMA regulation

Provider

Biosoft

Class

CalculatorOfCMARegulation

Plugin

biouml.plugins.genomeenhancer (Genome Enhancer)

Description

This method calculates regulatory scores for transcription factors (TFs) from CMA result and keynodes analysis.

The matrices from the CMA model are converted to TFs. Keynode analysis is then performed on these TFs and resulting keynodes are sorted by keynode score. Then the keynodes, which are regulated by the model, are selected and thus feed forward loops are identified.

Resulting visualization diagram contains composite modules from CMA result, signaling network to transcription factors of the composite modules and best keynodes predicted to be regulated by the model (feed forward loops).

Parameters:

• TF table – Table with transcription factors, Composite module to proteins result
• Keynodes table – Result of keynodes analysis
• Rank column – The result will be sorted by selected column in descending order and top ranking molecules will be taken
• Ensembl IDs column – Ensembl IDs column
• Number of top ranking molecules – Number of top ranking molecules
• Take lowest-ranking – Use molecules with lowest values in given column instead
• CMA score table – Path to table with CMA model scores calculated (e.g. Model visualization table from CMA result)
• Result table – Result table
• Result diagram – Result diagram