# Transcriptomics¶

createTissueSpecificModel(model, options, funcModel, exRxnRemove, optionalParams)[source]

Creates draft tissue specific model from mRNA expression data

Usage

tissueModel = createTissueSpecificModel(model, options)

Input

• model – model strusture
options: structure field containing method specific
informations
.solver: Use either ‘GIMME’,’iMAT’,’INIT’,’MBA’,
‘mCADRE’,’fastCore’

.additionalparam: see NOTE section below

Optional inputs

• funcModel – 1 - Build a functional model having only reactions that can carry a flux (using a consistency check), 0 - skip this step (Default = 0)
• exRxnRemove – Names of exchange reactions to remove (Default = [])
optionalParams Additional paramaters for the consistency
check. Will only be used if funcModel = 1 Is a structure with possible fields of epsilon (numeric, min nonzero mass), modeFlag (return flux mode, 0/1), and method (‘fastcc’,’dc’)

Output

• tissueModel – extracted model

NOTES: This section describes the additional parameter fields that need to be set in ‘options’ structure depending on the solver used. Some of these are optional (marked by an ‘*’), if not defined, they will be set at their default values.

for iMAT
options.expressionRxns reaction expression, expression data corresponding to model.rxns.
Note : If no gene-expression data are available for the reactions, set the value to -1
options.threshold_lb lower bound of expression threshold, reactions with
expression below this value are “non-expressed”
options.threshold_ub upper bound of expression threshold, reactions with
expression above this value are “expressed”
options.tol* minimum flux threshold for “expressed” reactions
(default 1e-8)
options.core* cell with reaction names (strings) that are manually put in
the high confidence set (default - no core reactions)

options.logfile* name of the file to save the MILP log (defaut - ‘MILPlog’) options.runtime* maximum solve time for the MILP (default - 7200s) options.epsilon* small value to consider when modeling

flux (default 1)
for GIMME
options.expressionRxns reaction expression, expression data corresponding to model.rxns.
Note : If no gene-expression data are available for the reactions, set the value to -1

options.threshold expression threshold, reactions below this are minimized options.obj_frac* minimum fraction of the model objective function

(default - 0.9)
for INIT
options.weights column with positive (high expression) and negative
(low expression) weights for each reaction
options.tol* minimum flux threshold for “expressed” reactions
(default - 1e-8)

options.logfile* name of the file to save the MILP log (defaut - ‘MILPlog’)

options.runtime* maximum solve time for the MILP (default - 7200s) options.epsilon* small value to consider when modeling

flux (default 1)
for MBA

options.medium_set list of reaction names with medium confidence options.high_set list of reaction names with high confidence options.tol* minimum flux threshold for “expressed” reactions

(default - 1e-8)
for mCADRE
options.ubiquityScore ubiquity scores, vector of the size of ‘model.rxns’
quantifying how often a gene is expressed accross samples.
options.confidenceScores literature-based evidence for generic model,
vector of the size of ‘model.rxns’
options.protectedRxns* cell array with reactions names that are manually added to
the core reaction set (default- no reactions)
options.checkFunctionality* Boolean variable that determine if the model should be able
to produce the metabolites associated with the protectedRxns
0: don’t use functionality check (default value) 1: include functionality check
options.eta* tradeoff between removing core and zero-expression
reactions (default - 1/3)
options.tol* minimum flux threshold for “expressed” reactions
(default - 1e-8)
for fastCore
options.core indices of reactions in cobra model that are part of the
core set of reactions
options.epsilon* smallest flux value that is considered
nonzero (default 1e-4)

options.printLevel* 0 = silent, 1 = summary, 2 = debug (default 0)