Table 4 Attributes used in the decision tree
From: Predicting co-complexed protein pairs using genomic and proteomic data integration
Attribute ID | Attribute Description |
|---|---|
I | High-throughput screens (HTS) of interaction |
I_APMS.TAP | Tandem-affinity purification (TAP) |
I_APMS.TAP.spoke | Tandem-affinity purification (TAP), "spoke" model |
I_APMS.HMS-PCI | High-throughput mass spectrometric protein complex identification (HMS-PCI) |
I_APMS.HMS-PCI.spoke | High-throughput mass spectrometric protein complex identification (HMS-PCI), "spoke" model |
I_Y2H | Yeast two-hybrid (Y2H) |
I_Y2H.Uetz | Yeast two-hybrid (Y2H), Uetz et al. |
X | Correlated mRNA expression |
X_Rst | Correlated mRNA expression, Rosetta compendium |
X_Rst.p | Positively correlated mRNA expression, Rosetta compendium |
X_Rst.p.8 | Correlated mRNA expression, Rosetta compendium, cc > 0.8 |
X_cc.p | Positively correlated mRNA expression, cell cycle dataset |
X_cc.p.7 | Correlated mRNA expression, cell cycle dataset, cc > 0.7 |
X_cc.p.8 | Correlated mRNA expression, cell cycle dataset, cc > 0.8 |
X_cc.p.9 | Correlated mRNA expression, cell cycle dataset, cc > 0.9 |
R | Same transcriptional regulator |
R_p005.ABF1 | Bound by Abf1p, p < 0.005 |
R_p005.GRF10 | Bound by Grf10p, p < 0.005 |
R_p005.HAP4 | Bound by Hap4p, p < 0.005 |
R_p005.RAP1 | Bound by Rap1p, p < 0.005 |
R_p005.RME1 | Bound by Rme1p, p < 0.005 |
R_p005.SFP1 | Bound by Sfp1p, p < 0.005 |
R_p005.SWI4 | Bound by Swi4p, p < 0.005 |
R_p005.YAP5 | Bound by Yap5p, p < 0.005 |
R_p001.FHL1 | Bound by Fhl1p, p < 0.001 |
R_p001.HAP4 | Bound by Hap4p, p < 0.001 |
R_p001.HIR2 | Bound by Hir2p, p < 0.001 |
R_p001.RAP1 | Bound by Rap1p, p < 0.001 |
R_p001.REB1 | Bound by Reb1p, p < 0.001 |
L | Same subcellular localization (high-throughput) |
L_05 | ER |
L_08 | Mitochondrial |
L_10 | Nucleus |
L_04 | Cytoplasm |
P | Same Phenotype |
P_1 | Conditional phenotypes |
P_1.1 | Heat-sensitivity |
P_1.3 | Slow-growth |
P_2 | Cell cycle defects |
P_2.4 | Other cell cycle defects |
P_4.2 | Methionine auxotrophy |
P_4.5.4 | Respiratory deficiency |
P_5 | Cell morphology and organelle mutants |
P_5.2.5 | Other budding mutants |
P_5.3 | Cell wall mutants |
P_5.6.1 | Tubulin cytoskeleton mutants |
P_5.6.1.5 | Other tubulin cytoskeleton mutants |
P_5.6.2 | Actin cytoskeleton mutants |
P_5.9 | Secretory mutants |
P_5.11 | Mitochondrial mutants |
P_5.13.2 | Other vacuolar mutants |
P_5.14 | Other cell morphology mutants |
P_8 | Nucleic acid metabolism defects |
P_8.1 | DNA repair mutants |
P_8.1.1 | UV light sensitivity |
P_8.2 | DNA replication mutants |
P_9.9 | Staurosporine sensitivity |
H | Sequence homology, E < e-6 |
H.e-12 | Sequence homology, E < e-12 |
N | Gene neighborhood |
O | Gene co-occurrence |