Table 1 |
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Association scores used in self-rank tests on combined evidence |
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Evidence type\Organism |
E.coli |
S.cerevisiae |
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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. |
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Clustering of genes on the chromosome |
• Gene clustering scores. Pairwise associations were calculated on 108 genomes, with KEGG-based orthology dataset |
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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. |
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Protein fusion |
Separate scores were calculated for different values of Ethreshold: • 10-2 • 10-5 • 10-10 |
Separate scores were calculated for different values of Ethreshold: • 10-3 • 10-5 • 10-10 |
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Protein interactions |
• Interaction score based on PIE dataset |
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Kharchenko et al. BMC Bioinformatics 2006 7:177 doi:10.1186/1471-2105-7-177 |
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