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 |