Table 5 Optimal regulation coefficient λ.

From: Integration of large-scale data for extraction of integrated Arabidopsis root cell-type specific models

  

decoupled

coupled

xylem

 

0.15

 

phloem

 

0.15

0.14

pericycle

 

0.15

 

elongation zone

 

0.12

 

maturation zone

 

0.10

0.12

meristematic zone

 

0.13

 

meristematic zone

 

0.13

 

elongation zone

stele

0.15

0.15

maturation zone

 

0.13

 

meristematic zone

 

0.13

 

elongation zone

endodermis

0.14

0.15

maturation zone

 

0.15

 

meristematic zone

 

0.07

 

elongation zone

cortex &endodermis

0.14

0.15

maturation zone

 

0.15

 

meristematic zone

 

0.13

 

elongation zone

epidermis

0.14

0.15

maturation zone

 

0.15

 

meristematic zone

 

0.14

 

elongation zone

lat root cap

0.14

0.15

maturation zone

 

0.07

 
  1. The underlying principle of RegrEx12 is the LASSO approach45, in which a regularization term can be controlled by the coefficient \(\lambda \). In RegrEx, it also controlled the number of reactions that were extracted from the initial genome-scale model. From a series of \(\lambda \) ranging between 0 and 0.15 with a step size of 0.01 an optimal value was given when the Pearson correlation between the predicted flux values and the transcriptomics data was maximum. For all three scenarios Li 1, Li 2 and Birnbaum this was checked for the (de)coupled models.
Back to article page