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) |