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Table 1 List of all features

From: Machine learning based analyses on metabolic networks supports high-throughput knockout screens

Short form

Explanation

 

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)

  1. athe optimized features, bfeatures from gene expression