Characterizing Reactions using MINVAL

Daniel Osorio, Janneth Gonzalez and Andres Pinzon

Characterize Reactions

Characterize the stoichiometric reactions of a metabolic model is a required and time-consuming work. The MINVAL package includes the characterizeReactions function to characterize the stoichiometric functions and metabolites by compartment.

To load the MINVAL package just type:

library(minval)

To show the potential use of the characterizeReactions function of the MINVAL package the Human Metabolic Reconstruction (RECON 2.04) was included in a human-readable format. To load it just type:

RECON <- read.csv(system.file("extdata", "rRECON2.csv", 
                              package = "minval"))
dim(RECON)
## [1] 7441    8

The characterizeReactions function requires a set of stoichiometric reactions as input. The given stoichiometric reactions must have the following mandatory characteristics:

The characterizeReactions function: - Counts the number of reactions - Computes the relative frequency of each reaction type (transport, exchange and compartmentalized) - Computes the relative frequency of reactions by compartment - Counts the number of unique metabolites - Computes the relative frequency of metabolites by compartment

Finally the characterizeReactions function returns all these information as a labeled list. To characterize a set of stoichiometric reactions just type:

RECONcharacteristics <- characterizeReactions(reactionList = RECON$REACTION)
RECONcharacteristics
## $nReactions
## [1] 7441
## 
## $rType
## 
## Compartmentalized reaction          Exchange reaction 
##                  55.825830                   9.420777 
##         Transport reaction 
##                  34.753393 
## 
## $cReaction
## 
##         c         e         g         l         m         n         r         x 
## 24.593469  1.760516  3.628545  2.983470  9.958339  1.666443  6.208843  5.026206 
## 
## $nMetabolites
## [1] 5063
## 
## $cMetabolites
## 
##         c         e         g         l         m         n         r         x 
## 37.092633 12.680229  6.261110  5.964843 14.892356  3.258937 11.258147  8.591744

Computed values can be easy plotted as follows:

Type of Reactions

Metabolic models generally includes three types of reactions:

To plot it just type:

pie(x = RECONcharacteristics$rType, 
    main = "Reactions by Type"
    )

Reactions by Compartment

Compartmentalized reactions identified also are categorized and reported as a relative frequency to their associated compartment. To plot it just type:

pie(x = RECONcharacteristics$cReaction, 
    main = "Reactions by Compartment", 
    labels = compartmentNames
    )

Metabolites by Compartment

Metabolites are categorized and reported as a relative frequency to their associated compartment. To plot it just type:

pie(x = RECONcharacteristics$cMetabolites, 
    main = "Metabolites by Compartment", 
    labels = compartmentNames
    )