Characterizing Reactions using MINVAL

In minval: MINimal VALidation for Stoichiometric Reactions

knitr::opts_chunk$set(collapse = TRUE, dev = "png", fig.width = 7, fig.height = 5, message = FALSE, warning = FALSE)

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)

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

• Arrows symbols must be given in the form '=>' or '<=>' (Inverse arrow symbols '<=' or other types as: '-->', '<==>', '->' will not be parsed and will lead to errors.)
• Arrow symbols and plus signs (+) must be surrounded by a space character.
• Stoichiometric coefficients must be surrounded by a space character and not by parentheses.
• Each metabolite must have only one stoichiometric coefficient, substituents must be joined to metabolite name by a hyphen (-) symbol.
• Exchange reactions must have only one metabolite before arrow symbol.
• Compartments must be given between square brackets ([compartment]) joined at the end of metabolite name.

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

Computed values can be easy plotted as follows:

compartmentNames <- c(c = "Cytosol", 
                      e = "Extracellular", 
                      g = "Golgi apparatus", 
                      l = "Lysosome", 
                      m = "Mitochondria", 
                      n = "Nucleus", 
                      r = "Endoplasmic reticulum",
                      x = "Peroxisome"
                      )

Type of Reactions

Metabolic models generally includes three types of reactions:

• Compartmentalized reactions: Reactions in where all involved metabolites (all reactants and products) were assigned to the same compartment. e.g. h[m] + nadph[m] + o2[m] + 25hvitd2[m] => h2o[m] + nadp[m] + 1a25dhvitd2[m]
• Transport reactions: Reactions in where the involved metabolites (reactants or products) were assigned to two or more compartments. e.g. 2 hco3[e] + na1[e] <=> 2 hco3[c] + na1[c]
• Exchange reactions: Reaction used to import or release metabolites to the boundary. e.g. acetone[e] <=>

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
    )

minval documentation built on May 9, 2022, 5:07 p.m.