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 8The 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
## $nReactions
## [1] 7441
##
## $rType
##
## Compartmentalized reaction Exchange reaction
## 55.825830 9.420777
## Transport reaction
## 34.753393
##
## $cReaction
##
## c e g l m n r
## 24.593469 1.760516 3.628545 2.983470 9.958339 1.666443 6.208843
## x
## 5.026206
##
## $nMetabolites
## [1] 5063
##
## $cMetabolites
##
## c e g l m n r
## 37.092633 12.680229 6.261110 5.964843 14.892356 3.258937 11.258147
## x
## 8.591744Computed values can be easy plotted as follows:
Type of Reactions
Metabolic models generally includes three types of reactions:
- Compartmentalized reactions: Reactions in where all involved metabolites (all reactants and products) were assigned to the same compartment. e.g.
h[m] + nadph[m] + o2[m] + 25hvitd2[m] => h2o[m] + nadp[m] + 1a25dhvitd2[m] - Transport reactions: Reactions in where the involved metabolites (reactants or products) were assigned to two or more compartments. e.g.
2 hco3[e] + na1[e] <=> 2 hco3[c] + na1[c] - Exchange reactions: Reaction used to import or release metabolites to the boundary. e.g.
acetone[e] <=>
To plot it just type:
pie(x = RECONcharacteristics$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
)