Table S1. GO enrichment of the R. solanacearum proteins in the predicted PPIs.
GO term / q-valueacation transport / 2.52E-10
electron transport chain / 6.99E-06
cellular protein metabolic process / 0.00014
protein metabolic process / 0.000162
respiratory electron transport chain / 0.000264
proton transport / 0.000849
secretion by cell / 0.00191
protein secretion / 0.00191
tetracycline transport / 0.00237
carboxylic acid transport / 0.010163
energy derivation by oxidation of organic compounds / 0.0112
amino acid transport / 0.0153
programmed cell death / 0.0224
innate immune response / 0.0224
host programmed cell death induced by symbiont / 0.0224
plant-type hypersensitive response / 0.0224
oxidative phosphorylation / 0.0284
maintenance of location in cell / 0.0284
cytolysis of cells in other organism during symbiotic interaction / 0.0284
maintenance of protein location / 0.0284
killing by symbiont of host cells / 0.0284
cytoskeleton organization / 0.0284
modification by symbiont of host morphology or physiology / 0.0284
modification of structure of other organism during symbiotic interaction / 0.0284
disruption of cells of other organism during symbiotic interaction / 0.0284
chemical homeostasis / 0.0284
phosphate metabolic process / 0.0392
multidrug transport / 0.0485
lipoprotein metabolic process / 0.049
lipid modification / 0.049
cell redox homeostasis / 0.049
aThe q-value of a test measures the minimum false discovery rate. Only GO terms with a q-value less than 0.05 are listed. For more details about the calculation of q-value, see the section of Materials and Methods in the main text.
Table S2. GO enrichment of theA. thalianaproteins in the predicted PPIs.
GO term / q-valueaphosphate metabolic process / 3.58E-38
protein metabolic process / 1.42E-37
cellular protein metabolic process / 3.04E-37
biopolymer modification / 3.27E-29
cellular biopolymer metabolic process / 2.65E-28
glycolysis / 1.49E-18
alcohol catabolic process / 2.48E-15
carbohydrate catabolic process / 5.02E-13
cellular carbohydrate catabolic process / 5.02E-13
response to heat / 4.30E-12
monosaccharide metabolic process / 2.55E-09
signal transduction / 4.94E-09
response to cold / 9.16E-09
intracellular signaling cascade / 2.71E-08
cation transport / 5.34E-08
cellular macromolecule catabolic process / 5.92E-07
cytoskeleton-dependent intracellular transport / 6.38E-07
response to reactive oxygen species / 2.01E-05
carboxylic acid metabolic process / 2.01E-05
regulation of transport / 4.21E-05
hormone-mediated signaling / 0.000149
regulation of stomatal movement / 0.000211
S-adenosylmethionine metabolic process / 0.000224
regulation of transmembrane transporter activity / 0.000224
response to metal ion / 0.000233
cellular macromolecule biosynthetic process / 0.000255
biopolymer biosynthetic process / 0.000553
detection of calcium ion / 0.000595
cellular lipid metabolic process / 0.000609
cellular homeostasis / 0.00108
cellular ion homeostasis / 0.00117
regulation of protein localization / 0.00117
response to abscisic acid stimulus / 0.00129
amino acid metabolic process / 0.00233
root hair elongation / 0.00244
gravitropism / 0.00244
cellular carbohydrate metabolic process / 0.0031
lipid biosynthetic process / 0.0032
fatty acid metabolic process / 0.0038
chemical homeostasis / 0.00481
cell tip growth / 0.00557
plastid organization / 0.00588
response to salt stress / 0.00647
cellular amine metabolic process / 0.00697
auxin polar transport / 0.00752
hormone transport / 0.00863
regulation of ethylene mediated signaling pathway / 0.00916
isoprenoid biosynthetic process / 0.0121
photosynthesis, dark reaction / 0.0132
ribosome biogenesis / 0.0137
phototropism / 0.0156
cellular lipid catabolic process / 0.0169
lipid catabolic process / 0.0169
fatty acid biosynthetic process / 0.0171
intracellular protein transport / 0.0171
camalexin metabolic process / 0.0182
hydrogen peroxide metabolic process / 0.0182
response to steroid hormone stimulus / 0.0182
cotyledon development / 0.0182
negative regulation of transporter activity / 0.0202
negative regulation of transport / 0.0202
cellularization of the embryo sac / 0.0202
flower morphogenesis / 0.0202
isoprenoid metabolic process / 0.0206
cofactor biosynthetic process / 0.0233
phytoalexin biosynthetic process / 0.0236
indole phytoalexin metabolic process / 0.0236
indole phytoalexin biosynthetic process / 0.0236
superoxide metabolic process / 0.0236
response to arsenic / 0.0236
regulation of cell communication / 0.0245
pollen tube growth / 0.0263
cellular response to starvation / 0.0263
cellular response to extracellular stimulus / 0.0264
regulation of transferase activity / 0.0309
cellular response to nutrient levels / 0.0323
proximal/distal pattern formation / 0.0328
pigment accumulation in tissues / 0.0328
pigment accumulation in tissues in response to UV light / 0.0328
pigment accumulation in response to UV light / 0.0328
anthocyanin accumulation in tissues in response to UV light / 0.0328
protein import / 0.0328
phenylpropanoid metabolic process / 0.0357
anion transport / 0.0365
response to light stimulus / 0.0412
organic acid biosynthetic process / 0.0443
actomyosin structure organization / 0.0486
formation of actomyosin apparatus involved in cytokinesis / 0.0486
phragmoplast formation / 0.0486
hydrogen peroxide catabolic process / 0.0486
defense response, incompatible interaction / 0.0498
aThe q-value of a test measures the minimum false discovery rate. Only GO terms with a q-value less than 0.05 are listed. For more details about the calculation of q-value, see the section of Materials and Methods in the main text.
1