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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