Table 3.
Top-ranking predicted co-regulations
| Gene 1 | Gene 2 | DPbits | Jaccard, % | Hypersig | Mutual info | Annotated regulon | Co-expression | Similar function |
|---|---|---|---|---|---|---|---|---|
| LEU2 | LEU1 | 10.2 | 16.2 | 22.7 | 0.00203 | LEU3 | ||
| RNR1 | RAD27 | 10.0 | 12.2 | 12.3 | 0.00129 | DNA replication and repair | ||
| RNR1 | CDC21 | 9.9 | 9.8 | 4.6 | 0.00077 | MBP1 | ||
| SWI4 | RNR1 | 9.6 | 4.9 | 1.5 | 0.00035 | SWI6 | ||
| RNR1 | CDC6 | 9.3 | 3.9 | 2.3 | 0.00029 | MBP1 | ||
| LEU1 | BAT1 | 9.3 | 11.5 | 13.1 | 0.00135 | 1 | Branched amino acid metabolism | |
| RNR1 | RAD53 | 9.2 | 13.7 | 9.9 | 0.00114 | SWI6 | ||
| YKR075C | HXT3 | 9.2 | 4.9 | 6.0 | 0.00085 | Regulated by glucose | ||
| ZRT2 | ZPS1 | 9.2 | 27.1 | 25.5 | 0.00221 | ZAP1 | ||
| YKR075C | HXT2 | 9.2 | 11.0 | 29.4 | 0.00246 | MIG1 | ||
| GAL10 | GAL1 | 9.1 | 39.7 | 53.2 | 0.00413 | GAL4 | 1 | |
| SST2 | FUS1 | 9.0 | 14.7 | 5.7 | 0.00085 | MOT3 | 1 | |
| RNR1 | CLB5 | 8.9 | 1.7 | 4.0 | 0.00017 | SWI6 | ||
| PCK1 | FBP1 | 8.8 | 5.8 | 8.2 | 0.00100 | CAT8 | 1 | |
| RAD27 | CDC21 | 8.7 | 7.4 | 1.8 | 0.00058 | 1 | DNA replication and repair | |
| SWI4 | RAD27 | 8.7 | 4.8 | 1.6 | 0.00035 | DNA replication and cell cycle regulation | ||
| FTR1 | FIT2 | 8.7 | 4.2 | 2.8 | 0.00063 | Iron transport and homeostasis | ||
| HIS7 | ARG3 | 8.6 | 5.9 | 0.3 | 0.00047 | GNC4 | ||
| RNR1 | ABF1 | 8.6 | 6.4 | 2.8 | 0.00064 | DNA replication and repair | ||
| TPO1 | LEU1 | 8.6 | 3.2 | 1.4 | 0.00035 | |||
| LEU1 | ILV5 | 8.6 | 5.7 | 3.2 | 0.00066 | LEU3 | ||
| MEP2 | DUR1,2 | 8.6 | 23.8 | 7.2 | 0.00095 | GLN3 | ||
| ZRT3 | ZRT2 | 8.6 | 10.9 | 5.5 | 0.00083 | ZAP1 | ||
| MEP2 | DAL1 | 8.6 | 4.5 | 1.3 | 0.00037 | GLN3 | ||
| DAL4 | DAL1 | 8.5 | 23.6 | 38.3 | 0.00309 | GLN3 | ||
| GAL2 | GAL1 | 8.5 | 4.1 | 1.2 | 0.00036 | GAL4 | ||
| SWI4 | CDC21 | 8.5 | 25.0 | 10.0 | 0.00115 | SWI6 | ||
| RAD27 | CDC6 | 8.5 | 6.5 | 1.7 | 0.00056 | DNA replication and repair | ||
| LEU1 | GDH1 | 8.4 | 6.2 | 9.8 | 0.00111 | LEU3 | 1 | |
| DUR1,2 | DAL1 | 8.4 | 9.4 | 6.3 | 0.00089 | GLN3 | ||
| LEU1 | ILV3 | 8.4 | 7.6 | 5.6 | 0.00083 | LEU3 | 1 | |
| MEP2 | DAL4 | 8.3 | 4.8 | 1.2 | 0.00037 | GLN3 | ||
| SWI4 | CDC6 | 8.3 | 8.0 | 1.3 | 0.00054 | SWI6 | ||
| RNR1 | CLB6 | 8.3 | 6.3 | 1.5 | 0.00055 | DNA replication and repair | ||
| HXT3 | HXT2 | 8.3 | 5.8 | 5.2 | 0.00080 | CYC8 | ||
| PCK1 | ICL1 | 8.2 | 6.7 | 9.2 | 0.00107 | CAT8 | ||
| RAD53 | RAD27 | 8.2 | 9.1 | 4.1 | 0.00073 | DNA repair | ||
| CDC6 | CDC21 | 8.2 | 7.0 | 0.4 | 0.00043 | SWI6 | ||
| HIS1 | ARG3 | 8.2 | 7.0 | 1.5 | 0.00056 | Amino acid metabolism | ||
| PCK1 | MDH2 | 8.2 | 6.7 | 10.0 | 0.00113 | CAT8 | ||
| RNR3 | RNR1 | 8.2 | 6.2 | 10.4 | 0.00116 | TUP1 | ||
| LEU1 | ILV2 | 8.2 | 6.1 | 2.9 | 0.00064 | LEU3 | 1 | |
| RAD27 | ABF1 | 8.2 | 37.8 | 61.5 | 0.00470 | DNA replication and repair | ||
| GAL2 | GAL10 | 8.1 | 4.9 | 0.5 | 0.00042 | GAL4 | ||
| HXT4 | HXT2 | 8.1 | 6.9 | 10.2 | 0.00114 | MIG1 | ||
| ZRT2 | ZRT1 | 8.1 | 12.2 | 6.1 | 0.00087 | ZAP1 | ||
| DUR1,2 | DAL4 | 8.1 | 10.0 | 6.5 | 0.00090 | GLN3 | ||
| RAD53 | CDC21 | 8.1 | 26.3 | 7.6 | 0.00099 | MBP1 | ||
| ZRT2 | VEL1 | 8.0 | 9.1 | 3.1 | 0.00066 | ZAP1 | ||
| HXT6 | HXT2 | 8.0 | 6.7 | 6.5 | 0.00089 | Hexose transporters | ||
| SWI4 | RAD53 | 8.0 | 10.3 | 0.2 | 0.00047 | SWI6 | ||
| LEU1 | ACO1 | 8.0 | 1.8 | 4.7 | 0.00013 | |||
| LEU4 | LEU1 | 8.0 | 5.1 | 2.5 | 0.00061 | LEU3 | 1 | |
| LEU1 | BAP2 | 8.0 | 2.4 | 2.9 | 0.00025 | LEU3 | 1 | |
| PRB1 | MEP2 | 7.9 | 0.9 | 4.7 | 0.00014 | GLN3 | ||
| YKR075C | HXT4 | 7.9 | 3.8 | 2.6 | 0.00061 | MIG1 | ||
| CLB5 | CDC6 | 7.9 | 2.5 | 2.2 | 0.00030 | SWI6 | ||
| PDE2 | DED1 | 7.9 | 21.4 | 41.3 | 0.00330 | |||
| TRP3 | ARG3 | 7.9 | 6.9 | 1.4 | 0.00055 | GCN4 | ||
| CLB5 | CDC21 | 7.9 | 2.2 | 2.1 | 0.00031 | SWI6 |
Top-ranking predictions of co-regulation in Saccharomyces cerevisiae, ordered by DPbits score, completed with the alternative scores (Jaccard, hypergeometric significance and mutual information). Gene pairs regulated by a same TF (annotated regulons) are highlighted in bold. Italics indicate gene pairs that are not annotated as regulated by a common TF, but which are involved in similar functions. Note that in our quantitative evaluation, these pairs are labeled as ‘false positive’ (FP), despite their very likelihood to be co-regulated. White background corresponds to gene pairs with no evidence of co-regulation or functional relationship.