Table 1.
List of all features.
| Short form | Explanation |
|---|---|
| Topology features | |
| a) Deviation | |
| RUP | Reachable/Unreachable Products (RUP): equals one if all products could be produced when blocking the reaction, otherwise zero |
| PUP | Percentage of Unreachable Products (PUP): the percentage of products which cannot be produced when blocking the reaction |
| ND | Number of Deviations (ND) |
| APL | Average Path Length (APL): the average path length of the deviations |
| LSP | Length of the Shortest Path (LSP): the length of the shortest path of the deviations |
| b) Local topology | |
| NS | Number of Substrates (NS) |
| NP | Number of Products (NP) |
| NNR | Number of Neighboring Reactions (NNR) |
| NNNR | Number of Neighbors of Neighboring Reactions (NNNR) |
| CCV | Clustering Coefficient Value (CCV): clustering coefficient of a reaction |
| DIR | Directionality of a reaction (DIR) |
| c) Choke points and load scores | |
| CP | Choke Point (CP): a reaction is a choke point or not (Rahman et al, 2006) |
| LS | Load Score (LS): load score of a reaction (Rahman et al, 2006) |
| d) Damage | |
| NDR | Number of Damaged Reactions (NDR) (Lemke et al, 2004) |
| NDC | Number of Damaged Compounds (NDC) (Lemke et al, 2004) |
| NDRD | Number of Damaged Reactions having no Deviations (NDRD): the number of damaged reactions that have no other alternative paths to be reached after blocking a reaction |
| NDCD | Number of Damaged Compounds having no Deviations (NDCD): the number of damaged compounds that have no other alternative paths to be reached after blocking a reaction |
| NDCR | Number of Damaged Choke point Reactions (NDCR) |
| NDCC | Number of Damaged Choke point Compounds (NDCC) |
| NDCRD | Number of Damaged Choke point Reactions having no Deviations (NDCRD): the number of damaged choke point reactions that have no other alternative paths to be reached after blocking a reaction |
| NDCCD | Number of Damaged Choke point Compounds having no Deviations (NDCCD): the number of damaged choke point compounds that have no other alternative paths to be reached after blocking a reaction |
| e) Centrality | |
| BW | Betweenness centrality |
| CN | Closeness centrality |
| EC | Eccentricity centrality |
| EV | Eigenvector centrality |
| Genomic and transcriptomic features | |
| f) Homologs | |
| NAR | Number of Associated Reactions (NAR): the number of reactions that base on the knocked-out gene |
| Hn | Homology at different expectation values: the number of homologous genes with e-value cutoff 10-30,10-20,10-10,10-7,10-5,10-3 (H30, H20, H10, H7, H5, H3) |
| g) Gene expression | |
| NGSE | Number of Genes having Similar Expression (NGSE): the number of genes that have similar expression (correlation coefficient >0.8) |
| MCC | Maximum of Correlation Coefficients (MCC): maximum value of the correlation coefficients for all neighboring genes |
| h) Phyletic retention | |
| PR | Phyletic Retention (PR): the number of orthologs in the other prokaryotes |
| i) Codon usage | |
| Nc | Number of codons |
| N3s | Base composition at silent sites (T3s, C3s, A3s, G3s) |
| glt | The frequency of amino acids glutamine (exemplarily) |