Difference between revisions of "Score based FBC table builder (analysis)"

Revision as of 19:00, 13 February 2017

Analysis title

Score based FBC table builder

Provider

Institute of Systems Biology

Class

ScoreBasedFbcTableBuilder

Plugin

biouml.plugins.fbc (Flux Balance)

Description

This analysis constructs FBC data table using data about enzymes (reaction modifiers) from the specified tables.

Parameters:

• Diagram – Path to diagram
• Enzymes table – Path to table with enzymes
• Max column – Name of the column with values for flux upper bound
• Normalize bounds – Shows if bounds should be normalized
• Score column – Name of the column with score from table with enzymes
• Is score correlation (expert) – Shows if enzymes score is correlation
• Objective function table – Table with objective function values
• Objective column – Name of the column with values of objective function
• Output table – Path to output table with FBA data table

Method description:

This analysis constructs FBC data table for Flux Balance Constraint analysis. Such table contains information about fluxes (reactions): lower and upper bound, objective function coefficients. Unlike Building Flux Balance DataTable analysis, this one constructs FBC data table using data about enzymes (reaction modifiers) from the specified tables. So if one want to use, e.g., enzymes expression or other data about enzymes as in [1], [2], this analysis is recommended.

Upper bound

Upper bound of reaction is constructed in a following way. If Enzymes table or Max column is not specified '1.0' is selected as upper bound. Else we select values from Max column for all enzymes which are reaction modifiers and choose the smallest in absolute value. If no enzymes were found, then the smallest absolute value from Max column will be used.

Lower bound

Lower bound will be '-upperBound' for reversible reaction and '0.0' for irreversible.

Objective function coefficient

Three different ways can be used to obtain objective function coefficient. For this purpose 4 parameters are used: Enzymes table, Score column, Objective function table and Objective column, and must be specified at least one: Objective function table or (Enzymes table and Score column).

1. Objective function table is not specified. In this case Enzymes table and Score column must be specified. Coefficient is evaluated in the same way as upper bound, but will be selected the max value from Score column for all enzymes which are reaction modifiers.
2. Enzymes table or Score column is not specified. For all reactions, which name is in IDs of Objective function table table, coefficient will be equal value from Objective column (if this parameter is specified) and '1.0' (if not). And '0.0' for others.
3. Objective function table, Enzymes table and Score column are specified. In this case coefficient will be equal to multiplication of the values obtained by items 1. and 2.

References:

1. Caroline Colijn, Aaron Brandes, Jeremy Zucker, Desmond S. Lun, Brian Weiner, Maha R. Farhat, Tan-Yun Cheng, D. Branch Moody, Megan Murray, James E. Galagan. "Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production." PLoS Comput Biol. 2009 August; 5(8): e1000489. doi: 10.1371/journal.pcbi.1000489
2. Rasmus Agren, Sergio Bordel, Adil Mardinoglu, Natapol Pornputtapong, Intawat Nookaew, Jens Nielsen. "Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT." PLoS Comput Biol. 2012 May; 8(5): e1002518. doi: 10.1371/journal.pcbi.1002518