Icongems

ICONGEMs(model, exp, genetxt, condition, threshold, alpha, numericFlag)

Algorithm to Integrate a Gene Co-expression Network and Genome-scale Metabolic Model:

This algorithm calculates the reaction flux distribution for each condition by applying quadratic programming.

USAGE:

[solICONGEMs, boundEf] = ICONGEMs(model, exp, genetxt, condition, threashold, alpha, numericFlag)

INPUTS:

model: input model (COBRA model structure) exp: expression profile corresponding to the gene names that

extract from gene expression profile file

genetxt: list of gene names that extract from gene expression profile

file

numericFlag: 1 if using Human Recon (Default = 0).

OPTIONAL INPUTS:

threshold: The value of the correlation coefficient for constructing

the co-expression network (default value: 0.9).

condition: Row vector indicating the number of conditions

corresponding to the conditions in exp (default value: 1:size(exp, 2)).

alpha: The value for the proportion of biomass (default value: 1).

OUTPUTS:

solICONGEMs: Flux distribution table corresponding to reaction flux names. boundEf: Upper bound of E-flux.

EXAMPLES:

% This could be an example that can be copied from the documentation to MATLAB: solution = ICONGEMs(model, exp, genetxt, condition, threashold, alpha, numericFlag) % without optional values: solution = ICONGEMs(model, exp, genetxt)

..Author:

-Thummarat Paklao, 01/02/2024, Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Thailand. -Apichat Suratanee, 01/02/2024, Department of Mathematics, Faculty of Applied Science, King Mongkut’s University of Technology North Bangkok. -Kitiporn Plaimas, 01/02/2024, Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Thailand.