TABLE 3.
Methods for informing GEMs with omics data sets
| Algorithm name and reference | Brief description |
|---|---|
| None specified [124] | Transcript absent decisions from microarray data are used to eliminate network reactions |
| iMATa (integrated Metabolic Analysis Tool) [125] | Predicts a set of reaction fluxes based on microarray and proteomic data |
| GIMMEb (Gene Inactivity Moderated by Metabolism and Expression) [126] | Uses microarray data, an expression threshold, and required metabolic functions to propose allowed network reactions and penalties |
| E-Flux [127] | Alters allowed reaction flux ranges based on gene expression data |
| MBA (Model Building Algorithm) [37] | Proposes a parsimonious set of reactions that is consistent with multiple high-throughput data sources |
| IOMAc (Integrative Omics-Metabolic Analysis) [128] | Predicts reaction fluxes that are consistent with proteomics and metabolomics measurements |
| tFBA [129] | Maximizes consistency of reaction fluxes with changes in gene expression |
| MADEd (Metabolic Adjustment by Differential Expression) [130] | Uses statistical changes in metabolic gene expression to enable network reactions |
| INIT (Integrative Network Inference for Tissues) [41] | Uses the Human Protein Atlas as a primary data source to create tissue-specific models and also allows for the accumulation of network metabolites |
| GIMMEp (Gene Inactivity Moderated by Metabolism and Expression by Proteome) [34] | Expands on the original GIMME method by integrating proteomic data to identify additional required metabolic functions |
a
iMAT is available online (www.cs.technion.ac.il/~tomersh/methods.html). Versions of the iMAT algorithm are also available in the COBRA toolbox and TIGER.
b
GIMME is available in the COBRA toolbox [117] (http://opencobra.sourceforge.net/openCOBRA) as well as in TIGER.
c
IOMA is available online (http://www.cs.technion.ac.il/~tomersh/methods.html).
d
MADE is available online (http://bme.virginia.edu/csbl/downloads.php) as well as in TIGER (Toolbox for Integrating Genome-scale metabolic models, Expression data and transcriptional Regulatory networks) [131] (https://bitbucket.org/csbl/tiger/downloads).