Correlation between metabolic flux and histone markers

Motivation

In theory, the metabolic activity of specific reactions should correspond to the abundance of methylation or acetylation. For example, lysine methyltransferase reaction flux should correspond to the abundance of methylation for various histone markers. This study is meant to show how the histone markers are correlated with metabolic fluxes of various reactions. This will tell us what metabolic reactions are important for modulating histone levels, and shed insights into how specific metabolites influence methylation and acetylation.

histone_corr.m

This code inputs the genome scale model, subcellular compartment, and parameters for the constrain_flux_regulation algorithm. The output is the correlation values associated with each histone mark-reaction pair and the p-value.

The pseudocode is as follows:

for every match between gene expression cell lines and proteomics cell lines:
  Get the genes that are up- or downregulated
  Get the genes that match with the genome-scale model
  Map the genes to reactions in the genome-scale model
  Get the growth rate associated with a specific cell line and its expression state
  
  for each reaction of interest:
    Set the substrate uptake rate for methionine to be non-limiting
    Set the objective coefficient for the reaction of interest to be proportional to epsilon2
    Get the metabolic flux of that reaction
  end
end