Table 1.
Phylogenetic profiling-based function predictions that have been verified in the original or by subsequent publications. Complement: anti-correlating occurrence profiles; ibid.: verification in same publication as prediction.
| protein/gene | context | relation | function | prediction | verification |
|---|---|---|---|---|---|
| SelR | fusion/fission, gene order, co-occurrence | enzymatic activity | methionine sulphoxide reductase | Galperin & Koonin (2000); Huynen et al. (2000) | Kryukov et al. (2002) |
| Yfh1 | co-occurrence, biochemical data | process | iron–sulphur protein maturation | Huynen et al. (2001) | Muhlenhoff et al. (2002) |
| YchB | co-occurrence | metabolic pathway | terpenoid synthesis | Luttgen et al. (2000) | ibid. |
| SmpB | co-occurrence | process | trans-translation | Pellegrini et al. (1999) | Karzai et al. (1999) |
| ThyX | complement, knockout data | enzymatic activity | thymidilate synthase | Galperin & Koonin (2000) | Kuhn et al. (2002); Myllykallio et al. (2002) |
| ThiN | complement, fusion/fission | enzymatic activity | thiamine phosphate synthase | Rodionov et al. (2002) | Morett et al. (2003) |
| NrdR | co-occurrence, neighbourhood | physical interaction | regulator of nucleotide reductases | Rodionov & Gelfand (2005) | Borovok et al. (2004) |
| NM_029821 | co-occurrence, neighbourhood | metabolic pathway | 5-hydroxyisourate (HIU) hydrolase | Ramazzina et al. (2006) | Ramazzina et al. (2006); Lee et al. (2006) |
| NM_001039678 | fusion/fission, neighbourhood, co-occurrence | metabolic pathway | 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU) decarboxylase | Ramazzina et al. (2006) | ibid. |
| B17.2L | co-occurrence, homology | physical interaction | Complex I assembly factor | Gabaldon et al. (2005) | Ogilvie et al. (2005) |
| LytB | co-occurrence | metabolic pathway | DOXP/MEP pathway | Cunningham et al. (2000) | Altincicek et al. (2001a) |
| GcpE | co-occurrence | metabolic pathway | DOXP/MEP pathway | Cunningham et al. (2000) | Altincicek et al. (2001b) |
| PRP43 | integrated (including: fusion/fission, co-occurrence) | physical interaction | RNA helicase also involved in ribosome biogenesis and rRNA processing | Lee et al. (2004) | Combs et al. (2006) |
| RLI | co-occurrence, conserved co-expression | — | RNase L inhibitor involvement in ribosome assembly | Gabaldon & Huynen (2004) | Yarunin et al. (2005); Kispal et al. (2005) |
| COG1980 | co-occurrence, complement | metabolic pathway | fructose-1,6-bisphosphatase | Makarova et al. (2003) | Sato et al. (2004) |
| Msa | genotype/phenotype correlation | — | mannose-specific adhesin | Pretzer et al. (2005) | ibid. |
| BBS5 | genotype/phenotype co-occurrence | — | flagella and basal body | Li et al. (2004) | ibid. |
| SUR2 (YDR297W) | genotype/metabolite co-occurrence | metabolic pathway | fungal sphingolipid C9-methyltransferase | Ternes et al. (2006) | ibid. |
| COG1206 (=trmFO, gid) | genotype/phenotype co-occurrence | metabolic pathway | flavin-dependent tRNA:m5U-54 MTase | Urbonavicius et al. (2005) | ibid. |