Table 3.
List of cancer metabolic modeling studies.
| Ref. | Cancer | Purpose | Method | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Drug design Predict drug targets Explore Cancer biology Explain Warburg effect Patient classification | Integration | Model | Analysis | Constraints | Objective | ||||||||
| (145) | Breast | x | x | Lee-12 | HMR 1 | FBA, Comparative, Topological | Transcriptome, Fluxomic | Data Correlation | |||||
| (146) | Colorectal | x | x | tINIT | Human1 | TFA, TFVA, pTFVA | Thermodynamic, Transcriptome, Biomass | Biomass | |||||
| (147) | Eye | x | x | iMAT | Recon 2 | Gap filling, FBA, FVA, Knockout | Transcriptome | Biomass, Tasks | |||||
| (148) | Head and Neck | x | x | Upper bound | Recon 2 | FBA, Sampling, Knockout | Thermodynamics, Enzyme kinetics, Transcriptome, Metabolome | ATP, NADPH | |||||
| (149) | Liver | x | x | iMAT-like | Recon 1 | Comparative, FBA, Sampling | Transcriptome | Data Similarity | |||||
| (150) | Multiple | x | x | tINIT | HMR 2 | Comparative, Knockout | Transcriptome | Tasks | |||||
| (151) | Multiple | x | x | tINIT | HMR 2 | FBA, Knockout | Transcriptome | Biomass, Tasks | |||||
| (140) | Generic | x | x | Small-scale | FBA, DFBA, FVA, Knockout, Sampling | Biomass | |||||||
| (152) | Kidney | x | x | tINIT | iCancer-Core | FBA, Knockout | Transcriptome | Biomass | |||||
| (153) | Brain | x | tINIT | HMR 2 | Comparative, FBA, Knockout | Transcriptome | Biomass, Tasks | ||||||
| (105) | Breast, Lung, Multiple | x | Upper bound | HMR 1 | FBA, Sampling, Knockout | Transcriptome | Biomass | ||||||
| (139) | Generic | x | MBA | Recon 1 | FBA, Knockout | Transcriptome | Biomass | ||||||
| (154) | Kidney | x | MBA | Recon 1 | FBA, Knockout | Transcriptome | Biomass | ||||||
| (54) | Liver | x | tINIT | HMR 2 | Comparative, FBA, Knockout | Proteome | Biomass, Tasks | ||||||
| (155) | Liver | x | tINIT | HMR 2 | FBA, Knockout, Topological | Transcriptome | Biomass, Tasks | ||||||
| (156) | Multiple | x | iMAT | Recon 1 | FBA, ML, Topological | Transcriptome | Data Similarity | ||||||
| (102) | Multiple | x | GIMME | Recon 2 | FBA, Sampling, Knockout | Mutations, Transcriptome | Biomass | ||||||
| (157) | Prostate | x | tINIT | iCancer-Core | FBA, Knockout, Sampling | Transcriptome, Proteome | Biomass, Tasks | ||||||
| (158) | Breast, Kidney, Liver, Prostate | x | x | KEGG | Network Propagation, Knockout, ML | Transcriptome | |||||||
| (159) | Colorectal | x | x | tINIT | HMR 2 | Comparative | Transcriptome | ||||||
| (160) | Multiple | x | x | Recon 2 | Regulatory, Topological, ML | Transcriptome, Metabolome | |||||||
| (111) | Multiple | x | x | mCADRE | Recon 1 | Comparative | Transcriptome | Tasks, Biomass | |||||
| (103) | Multiple, Brain, Lung, Breast, Leukemia, Prostate | x | x | tINIT | Recon 3D | Comparative, Knockout, ML | Mutations, Protein Structures | Biomass | |||||
| (161) | Prostate | x | x | iMAT | Recon 2 | FBA, FVA | Transcriptome | Data Similarity | |||||
| (162) | Kidney, Prostate | x | INIT | HMR 1 | Knockout | Proteome, Fluxomic | Biomass | ||||||
| (108) | Multiple | x | INIT | HMR 1 | Comparative | Proteome | |||||||
| (163) | Multiple | x | Topological | ||||||||||
| (164) | Generic | x | x | C2M2N | FBA | Biosynthesis, Biomass | |||||||
| (165) | Breast, Colorectal | x | x | Recon 2 | FVA, ML | Metabolome | Metabolite Change | ||||||
| (166) | Liver | x | x | tINIT | HMR 2 | Comparative | Transcriptome, Proteome | Biomass, Tasks | |||||
| (167) | Brain | x | GIMME, MADE | iMS570 | pFBA, Sampling | Transcriptome | Biomass | ||||||
| (168) | Breast | x | E-Flux | Recon2 | FBA | Proteome | Biomass | ||||||
| (169) | Colorectal | x | Recon 2.2 | Comparative | Transcriptome | ||||||||
| (170) | Colorectal | x | CORDA | Recon 2.2 | FBA, FVA, Topological | Proteome | Biomass, ATP | ||||||
| (130) | Generic | x | HMRcore | popFBA, Sampling | Loopless | Biomass | |||||||
| (171) | Kidney | x | Recon 1 | pFBA | Flux measurements | Biomass | |||||||
| (172) | Kidney | x | INIT | HMR 1 | Comparative | Proteome | |||||||
| (173) | Liver | x | tINIT | HMR 2 | Comparative, Gap filling, Regulatory, FBA | Transcriptome, Metabolome | Biomass | ||||||
| (174) | Lung | x | 13C flux analysis | Flux measurements, Labeling measurements | |||||||||
| (141) | Lung | x | Central Carbon, Recon 2 | Elementary modes, Structural fluxes, pFBA | Protein efficiency | Biomass, Biosynthesis | |||||||
| (131) | Lung, Breast | x | E-Flux | HMRcore | scFBA | scRNA-seq, metabolomics | Biomass | ||||||
| (175) | Lung, Prostate | x | E-Flux | Recon 1 | FVA | Transcriptome | Biomass | ||||||
| (176) | Multiple | x | tINIT | HMR 2 | Comparative | Transcriptome | |||||||
| (104) | Prostate | x | IMAT, GIMME, Gonçalves, MADE | HMR 2 | FBA | Transcriptome | Data Similarity | ||||||
| (177) | Generic | x | Recon 1 | FBA, FVA, Sampling | Protein efficiency, Enzyme kinetics | Biomass | |||||||
| (178) | Generic | x | ATP | FBA | Protein efficiency | ATP | |||||||
| (179) | Generic | x | ATP, BiGG | FBA | Protein efficiency | ATP, Nutrient cost | |||||||
| (180) | Liver | x | MADE | Recon 2 | Comparative | Transcriptome | Data Similarity | ||||||
| (106) | Liver | x | Upper bound | Recon 3D | FBA, FVA | Transcriptome, Nutrient availability | Biomass | ||||||
| (181) | Liver | x | Bounds | Recon 2 | FBA | Protein efficiency, Transcriptome | ATP | ||||||
| (182) | Multiple | x | E-Flux | Recon 1 | FBA | Transcriptome | Biomass | ||||||