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Table 1 Association scores used in self-rank tests on combined evidence

From: Identifying metabolic enzymes with multiple types of association evidence

Evidence type\Organism

E.coli

S.cerevisiae

Phylogenetic profile co-occurrence.

• BLAST-based dataset score

• KEGG-based dataset score

Pairwise associations were calculated using extended hypergeometric and folding corrections, on orthologs established by best bi-directional homology relationship.

Clustering of genes on the chromosome

• Gene clustering scores. Pairwise associations were calculated on 108 genomes, with KEGG-based orthology dataset

Gene co-expression

• E. coli SMD expression dataset score

• Expression of E. coli orthologs in S. cerevisiae Rosetta dataset.

• S. cerevisiae Rosetta expression dataset score

• Expression of S. cerevisiae orthologs in E. coli SMD dataset.

Protein fusion

Separate scores were calculated for different values of E threshold :

• 10-2

• 10-5

• 10-10

Separate scores were calculated for different values of E threshold :

• 10-3

• 10-5

• 10-10

Protein interactions

 

• Interaction score based on PIE dataset