From: Machine learning based analyses on metabolic networks supports high-throughput knockout screens
Short form | Explanation |
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Topology features: local structures | |
RUPa | Reachable/Unreachable Products (RUP): more than or equal to one product cannot be produced when blocking a reaction |
PUP | Percentage of Unreachable Products (PUP): the percentage of products which cannot be produced when blocking a reaction |
NSa | Number of Substrates (NS) |
NPa | Number of Products (NP) |
NNRa | Number of Neighbouring Reactions (NNR) |
NNNRa | Number of Neighbours of Neighbouring Reactions (NNNR) |
CCVa | Clustering Coefficient Value (CCV): clustering coefficient of a reaction |
DIRa | Directionality of a reaction (DIR) |
Topology features: deviations, choke points, load scores and damage | |
ND | Number of Deviations (ND) |
APL | Average Path Length (APL): the average path length of the deviations |
LSPa | Length of Shortest Path (LSP): the length of the shortest path of the deviations |
CP | Choke Point (CP): a reaction is a choke point or not (Rahman et al, 2006) |
LSa | Load Score (LS): load score of a reaction (Rahman et al, 2006) |
NDRa | Number of Damaged Reactions (NDR): the number of damaged reactions after blocking a reaction (Lemke et al, 2004) |
NDCa | Number of Damaged Compounds (NDC): the number of damaged compounds after blocking a reaction (Lemke et al, 2004) |
NDRDa | 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 |
NDCDa | 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 |
NDCRa | Number of Damaged Choke point Reactions (NDCR): the number of damaged choke point reactions after blocking a reaction |
NDCCa | Number of Damaged Choke point Compounds (NDCC): the number of damaged choke point compounds after blocking a reaction |
NDCRDa | 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 |
NDCCDa | 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 |
Gene expression data, genomic data and miscellaneous | |
NCGa | Number of Coding Genes (NCG): the number of coding genes for a reaction |
H10a | Homology at 10-10 (H10): the number of homologous genes with e-value cutoff 10-10 |
H7 | Homology at 10-7 (H7): the number of homologous genes with e-value cutoff 10-7 |
H5a | Homology at 10-5 (H5): the number of homologous genes with e-value cutoff 10-5 |
H3a | Homology at 10-3 (H3): the number of homologous genes with e-value cutoff 10-3 |
NRSGa,b | Number of Reactions from Same Genes (NRSG): the number of reactions derived from the same genes |
NRSEa,b | Number of Reaction having Similar Expression (NRSE): the number of reactions that have similar expression (correlation coefficient >0.8) |
MCCa,b | Maximum of Correlation Coefficients (MCC): maximum value of the correlation coefficients for all neighbouring reactions |
Flux distribution | |
BFVa | Biomass Flux Value (BFV): biomass flux value when blocking a reaction (under aerobic glucose condition) |