Table 2.
Algorithms available for tissue specific metabolic network reconstruction.
| Algorithm | Input | Publication |
|---|---|---|
| Akesson04 | Set of inactive genes | Åkesson et al., 2004 |
| FASTCORE | Set of active reactions | Vlassis et al., 2014 |
| FASTCORMICS | Gene expression data | Pacheco et al., 2015 |
| GIMME | Gene expression data, objective function | Becker and Palsson, 2008 |
| GIM3E | Gene expression data, metabolomics data, objective function | Becker and Palsson, 2008 |
| iMAT | Gene expression data | Zur et al., 2010 |
| INIT | Gene expression data and metabolite presence data | Agren et al., 2012 |
| MBA | High, medium and low reaction sets | Jerby et al., 2010 |
| mCADRE | Gene expression data | Wang et al., 2012 |
| PRIME | Growth rates, gene expression data | Yizhak et al., 2014 |
| RegrEx | Gene expression data | Robaina Estévez and Nikoloski, 2015 |
| tINIT | Gene expression data, functions, metabolite presence | Agren et al., 2014 |
Most methods can use expression data as input but there are some that need additional inputs.