Download Additional file 3. Universally and Exclusively Enriched Functions in

Additional file 3. Universally and Exclusively Enriched Functions in Modules from
Specific Networks
Universally and Exclusively Enriched Functions in Modules from Specific Networks
Using Annotations for Proteins
GO BP terms that are universally enriched in the total network and five tissue-specific
subnetworks:
GO:0006096
GO:0015031
GO:0008152
GO:0009408
GO:0006606
GO:0006014
GO:0007264
GO:0006810
GO:0044267
GO:0016192
GO:0006635
GO:0009058
GO:0006544
GO:0006457
GO:0006413
GO:0019344
GO:0006412
GO:0055114
GO:0006511
GO:0006633
GO:0010388
GO:0006563
GO:0006886
GO:0006508
GO:0009742
GO:0006888
glycolysis
protein transport
metabolic process
response to heat
protein import into nucleus
D-ribose metabolic process
small GTPase mediated signal transduction
transport
cellular protein metabolic process
vesicle-mediated transport
fatty acid beta-oxidation
biosynthetic process
glycine metabolic process
protein folding
translational initiation
cysteine biosynthetic process
translation
oxidation reduction
ubiquitin-dependent protein catabolic process
fatty acid biosynthetic process
cullin deneddylation
L-serine metabolic process
intracellular protein transport
proteolysis
brassinosteroid mediated signaling
ER to Golgi vesicle-mediated transport
Enriched GO BP terms in the total network but not in any subnetworks:
GO:0019760
GO:0006334
GO:0008150
GO:0045038
GO:0006790
GO:0006396
GO:0009958
glucosinolate metabolic process
nucleosome assembly
biological_process
protein import into chloroplast thylakoid membrane
sulfur metabolic process
RNA processing
positive gravitropism
GO:0006874 cellular calcium ion homeostasis
GO:0022900 electron transport chain
GO:0009638 phototropism
GO:0048437 floral organ development
GO:0006349 genetic imprinting
GO:0009736 cytokinin mediated signaling
GO:0006821 chloride transport
GO:0007031 peroxisome organization
GO:0008272 sulfate transport
GO:0019722 calcium-mediated signaling
GO:0016226 iron-sulfur cluster assembly
GO:0045449 regulation of transcription
GO:0009617 response to bacterium
GO:0000160 two-component signal transduction system (phosphorelay)
GO:0009294 DNA mediated transformation
GO:0006839 mitochondrial transport
GO:0007165 signal transduction
GO:0051726 regulation of cell cycle
GO:0010017 red or far red light signaling pathway
GO:0006298 mismatch repair
GO:0009626 plant-type hypersensitive response
GO:0010216 maintenance of DNA methylation
GO:0006352 transcription initiation
GO:0010332 response to gamma radiation
GO:0006828 manganese ion transport
GO:0010020 chloroplast fission
GO:0006617 "SRP-dependent cotranslational protein targeting to membrane, signal
sequence recognition"
GO:0000724 double-strand break repair via homologous recombination
GO:0006367 transcription initiation from RNA polymerase II promoter
GO:0006355 "regulation of transcription, DNA-dependent"
GO:0009960 endosperm development
GO:0007018 microtubule-based movement
GO:0006875 cellular metal ion homeostasis
GO:0009934 regulation of meristem organization
Root-specific enriched GO BP terms in roots network:
GO:0009116
GO:0010387
GO:0006519
GO:0019430
GO:0010107
GO:0006749
GO:0009620
nucleoside metabolic process
signalosome assembly
cellular amino acid and derivative metabolic process
removal of superoxide radicals
potassium ion import
glutathione metabolic process
response to fungus
GO:0006464
GO:0000338
GO:0019509
GO:0000910
GO:0016481
GO:0009407
GO:0006896
GO:0015914
GO:0015992
GO:0006751
GO:0006086
protein modification process
protein deneddylation
methionine salvage
cytokinesis
negative regulation of transcription
toxin catabolic process
Golgi to vacuole transport
phospholipid transport
proton transport
glutathione catabolic process
acetyl-CoA biosynthetic process from pyruvate
Enriched GO BP terms in roots network but not total network:
GO:0009116
GO:0007021
GO:0009051
GO:0009821
GO:0010387
GO:0006519
GO:0006006
GO:0006749
GO:0006486
GO:0009620
GO:0010623
GO:0042546
GO:0019509
GO:0006378
GO:0045454
GO:0051605
GO:0006090
GO:0031087
GO:0000910
GO:0016481
GO:0006414
GO:0015865
GO:0042819
GO:0015992
GO:0006995
GO:0006751
GO:0008295
GO:0042732
GO:0006086
nucleoside metabolic process
tubulin complex assembly
"pentose-phosphate shunt, oxidative branch"
alkaloid biosynthetic process
signalosome assembly
cellular amino acid and derivative metabolic process
glucose metabolic process
glutathione metabolic process
protein amino acid glycosylation
response to fungus
developmental programmed cell death
cell wall biogenesis
methionine salvage
mRNA polyadenylation
cell redox homeostasis
protein maturation by peptide bond cleavage
pyruvate metabolic process
deadenylation-independent decapping of nuclear-transcribed mRNA
cytokinesis
negative regulation of transcription
translational elongation
purine nucleotide transport
vitamin B6 biosynthetic process
proton transport
cellular response to nitrogen starvation
glutathione catabolic process
spermidine biosynthetic process
D-xylose metabolic process
acetyl-CoA biosynthetic process from pyruvate
Leaf-specific enriched GO BP terms in leaves network:
GO:0006423
GO:0007033
GO:0042325
GO:0006529
GO:0006535
GO:0009767
GO:0009793
GO:0010143
cysteinyl-tRNA aminoacylation
vacuole organization
regulation of phosphorylation
asparagine biosynthetic process
cysteine biosynthetic process from serine
photosynthetic electron transport chain
embryonic development ending in seed dormancy
cutin biosynthetic process
Enriched GO BP terms in leaves network but not total network:
GO:0045037
GO:0006423
GO:0009821
GO:0031998
GO:0009744
GO:0007033
GO:0015979
GO:0042325
GO:0000302
GO:0006535
GO:0009793
GO:0048366
GO:0006879
GO:0006378
GO:0045454
GO:0055072
GO:0006826
GO:0006090
GO:0008361
GO:0010039
GO:0010540
GO:0019253
GO:0006510
GO:0006744
GO:0006414
GO:0015865
GO:0042819
GO:0043481
GO:0006995
GO:0008295
protein import into chloroplast stroma
cysteinyl-tRNA aminoacylation
alkaloid biosynthetic process
regulation of fatty acid beta-oxidation
response to sucrose stimulus
vacuole organization
photosynthesis
regulation of phosphorylation
response to reactive oxygen species
cysteine biosynthetic process from serine
embryonic development ending in seed dormancy
leaf development
cellular iron ion homeostasis
mRNA polyadenylation
cell redox homeostasis
iron ion homeostasis
iron ion transport
pyruvate metabolic process
regulation of cell size
response to iron ion
basipetal auxin transport
reductive pentose-phosphate cycle
ATP-dependent proteolysis
ubiquinone biosynthetic process
translational elongation
purine nucleotide transport
vitamin B6 biosynthetic process
anthocyanin accumulation in tissues in response to UV light
cellular response to nitrogen starvation
spermidine biosynthetic process
Flower-specific enriched GO BP terms in flowers network:
GO:0010267
GO:0007067
GO:0009910
GO:0006499
GO:0030422
GO:0009723
GO:0006306
GO:0009750
GO:0043087
GO:0006913
GO:0009738
GO:0000085
GO:0006221
GO:0006468
GO:0009218
GO:0009616
GO:0045900
GO:0006470
GO:0019761
GO:0006890
GO:0010617
GO:0040007
"RNA interference, production of ta-siRNAs"
mitosis
negative regulation of flower development
N-terminal protein myristoylation
"RNA interference, production of siRNA"
response to ethylene stimulus
DNA methylation
response to fructose stimulus
regulation of GTPase activity
nucleocytoplasmic transport
abscisic acid mediated signaling
G2 phase of mitotic cell cycle
pyrimidine nucleotide biosynthetic process
protein amino acid phosphorylation
pyrimidine ribonucleotide metabolic process
virus induced gene silencing
negative regulation of translational elongation
protein amino acid dephosphorylation
glucosinolate biosynthetic process
"retrograde vesicle-mediated transport, Golgi to ER"
circadian regulation of calcium ion oscillation
growth
Flower-specific enriched GO BP terms not in roots/leaves network:
GO:0006268
GO:0010267
GO:0007067
GO:0009910
GO:0044237
GO:0045941
GO:0006499
GO:0030422
GO:0006979
GO:0009723
GO:0009168
GO:0006397
GO:0006306
GO:0009750
GO:0009850
GO:0043087
GO:0006913
GO:0009738
DNA unwinding during replication
"RNA interference, production of ta-siRNAs"
mitosis
negative regulation of flower development
cellular metabolic process
positive regulation of transcription
N-terminal protein myristoylation
"RNA interference, production of siRNA"
response to oxidative stress
response to ethylene stimulus
purine ribonucleoside monophosphate biosynthetic process
mRNA processing
DNA methylation
response to fructose stimulus
auxin metabolic process
regulation of GTPase activity
nucleocytoplasmic transport
abscisic acid mediated signaling
GO:0006013
GO:0000085
GO:0006221
GO:0016126
GO:0006468
GO:0006270
GO:0009081
GO:0009218
GO:0009067
GO:0009616
GO:0006099
GO:0008283
GO:0045900
GO:0009809
GO:0006470
GO:0009411
GO:0019761
GO:0019243
GO:0006890
GO:0006446
GO:0010617
GO:0040007
mannose metabolic process
G2 phase of mitotic cell cycle
pyrimidine nucleotide biosynthetic process
sterol biosynthetic process
protein amino acid phosphorylation
DNA replication initiation
branched chain family amino acid metabolic process
pyrimidine ribonucleotide metabolic process
aspartate family amino acid biosynthetic process
virus induced gene silencing
tricarboxylic acid cycle
cell proliferation
negative regulation of translational elongation
lignin biosynthetic process
protein amino acid dephosphorylation
response to UV
glucosinolate biosynthetic process
methylglyoxal catabolic process to D-lactate
"retrograde vesicle-mediated transport, Golgi to ER"
regulation of translational initiation
circadian regulation of calcium ion oscillation
growth
Enriched GO BP terms in flowers network but not total network:
GO:0010267
GO:0009821
GO:0006006
GO:0045941
GO:0030422
GO:0006486
GO:0009723
GO:0010623
GO:0009168
GO:0006306
GO:0009750
GO:0000085
GO:0006090
GO:0031087
GO:0008361
GO:0010540
GO:0009616
GO:0006744
GO:0006099
GO:0019243
"RNA interference, production of ta-siRNAs"
alkaloid biosynthetic process
glucose metabolic process
positive regulation of transcription
"RNA interference, production of siRNA"
protein amino acid glycosylation
response to ethylene stimulus
developmental programmed cell death
purine ribonucleoside monophosphate biosynthetic process
DNA methylation
response to fructose stimulus
G2 phase of mitotic cell cycle
pyruvate metabolic process
deadenylation-independent decapping of nuclear-transcribed mRNA
regulation of cell size
basipetal auxin transport
virus induced gene silencing
ubiquinone biosynthetic process
tricarboxylic acid cycle
methylglyoxal catabolic process to D-lactate
GO:0043481 anthocyanin accumulation in tissues in response to UV light
GO:0040007 growth
Silique-specific enriched GO BP terms in siliques network:
GO:0008654
GO:0006595
GO:0009186
GO:0006970
GO:0006891
GO:0019762
GO:0006301
GO:0030149
GO:0010204
GO:0009624
GO:0008652
GO:0051276
GO:0007049
phospholipid biosynthetic process
polyamine metabolic process
deoxyribonucleoside diphosphate metabolic process
response to osmotic stress
intra-Golgi vesicle-mediated transport
glucosinolate catabolic process
postreplication repair
sphingolipid catabolic process
"defense response signaling pathway, resistance gene-independent"
response to nematode
cellular amino acid biosynthetic process
chromosome organization
cell cycle
Silique-specific enriched GO BP terms not in roots/leaves network:
GO:0006268
GO:0008654
GO:0044237
GO:0006595
GO:0009186
GO:0006970
GO:0006891
GO:0019762
GO:0009168
GO:0006013
GO:0006301
GO:0030149
GO:0016126
GO:0010204
GO:0006270
GO:0009624
GO:0009081
GO:0008652
GO:0009067
GO:0008283
GO:0009809
GO:0009411
GO:0051276
DNA unwinding during replication
phospholipid biosynthetic process
cellular metabolic process
polyamine metabolic process
deoxyribonucleoside diphosphate metabolic process
response to osmotic stress
intra-Golgi vesicle-mediated transport
glucosinolate catabolic process
purine ribonucleoside monophosphate biosynthetic process
mannose metabolic process
postreplication repair
sphingolipid catabolic process
sterol biosynthetic process
"defense response signaling pathway, resistance gene-independent"
DNA replication initiation
response to nematode
branched chain family amino acid metabolic process
cellular amino acid biosynthetic process
aspartate family amino acid biosynthetic process
cell proliferation
lignin biosynthetic process
response to UV
chromosome organization
GO:0019243 methylglyoxal catabolic process to D-lactate
GO:0006446 regulation of translational initiation
GO:0007049 cell cycle
Enriched GO BP terms in siliques network but not total network:
GO:0007021
GO:0009051
GO:0008654
GO:0009821
GO:0006595
GO:0006006
GO:0031998
GO:0009744
GO:0009186
GO:0006486
GO:0006970
GO:0019762
GO:0009168
GO:0042546
GO:0006879
GO:0006378
GO:0055072
GO:0006826
GO:0051605
GO:0006301
GO:0030149
GO:0010204
GO:0006090
GO:0031087
GO:0009624
GO:0010039
GO:0019253
GO:0008652
GO:0006414
GO:0015865
GO:0042819
GO:0019243
GO:0006995
GO:0042732
tubulin complex assembly
"pentose-phosphate shunt, oxidative branch"
phospholipid biosynthetic process
alkaloid biosynthetic process
polyamine metabolic process
glucose metabolic process
regulation of fatty acid beta-oxidation
response to sucrose stimulus
deoxyribonucleoside diphosphate metabolic process
protein amino acid glycosylation
response to osmotic stress
glucosinolate catabolic process
purine ribonucleoside monophosphate biosynthetic process
cell wall biogenesis
cellular iron ion homeostasis
mRNA polyadenylation
iron ion homeostasis
iron ion transport
protein maturation by peptide bond cleavage
postreplication repair
sphingolipid catabolic process
"defense response signaling pathway, resistance gene-independent"
pyruvate metabolic process
deadenylation-independent decapping of nuclear-transcribed mRNA
response to nematode
response to iron ion
reductive pentose-phosphate cycle
cellular amino acid biosynthetic process
translational elongation
purine nucleotide transport
vitamin B6 biosynthetic process
methylglyoxal catabolic process to D-lactate
cellular response to nitrogen starvation
D-xylose metabolic process
Seed-specific enriched GO BP terms in seeds network:
GO:0009061 anaerobic respiration
GO:0030036
GO:0010188
GO:0006950
GO:0001676
actin cytoskeleton organization
response to microbial phytotoxin
response to stress
long-chain fatty acid metabolic process
Seed-specific enriched GO BP terms not in roots/leaves network:
GO:0009061
GO:0030036
GO:0045941
GO:0006979
GO:0006397
GO:0009850
GO:0006013
GO:0010188
GO:0006950
GO:0006099
GO:0001676
GO:0006446
anaerobic respiration
actin cytoskeleton organization
positive regulation of transcription
response to oxidative stress
mRNA processing
auxin metabolic process
mannose metabolic process
response to microbial phytotoxin
response to stress
tricarboxylic acid cycle
long-chain fatty acid metabolic process
regulation of translational initiation
Enriched GO BP terms in seeds network but not total network:
GO:0045037
GO:0009821
GO:0009061
GO:0006006
GO:0030036
GO:0045941
GO:0015979
GO:0000302
GO:0048366
GO:0006879
GO:0055072
GO:0006826
GO:0010039
GO:0006510
GO:0006950
GO:0006414
GO:0015865
GO:0006099
GO:0008295
protein import into chloroplast stroma
alkaloid biosynthetic process
anaerobic respiration
glucose metabolic process
actin cytoskeleton organization
positive regulation of transcription
photosynthesis
response to reactive oxygen species
leaf development
cellular iron ion homeostasis
iron ion homeostasis
iron ion transport
response to iron ion
ATP-dependent proteolysis
response to stress
translational elongation
purine nucleotide transport
tricarboxylic acid cycle
spermidine biosynthetic process
Universally and Exclusively Enriched Functions in Modules from Specific Networks
Using Annotations for Protein Interacting Pairs
GO BP terms that are universally enriched in every network:
GO:0006096
GO:0009821
GO:0015031
GO:0008152
GO:0009408
GO:0006606
GO:0009970
GO:0007264
GO:0005975
GO:0006810
GO:0042147
GO:0030163
GO:0015986
GO:0044267
GO:0009086
GO:0006414
GO:0016192
GO:0006099
GO:0006635
GO:0009058
GO:0006544
GO:0006457
GO:0007165
GO:0006413
GO:0046686
GO:0019344
GO:0006412
GO:0055114
GO:0006511
GO:0006633
GO:0010388
GO:0006563
GO:0006556
GO:0006886
GO:0006508
GO:0009640
GO:0009742
GO:0006995
GO:0006888
glycolysis
alkaloid biosynthetic process
protein transport
metabolic process
response to heat
protein import into nucleus
cellular response to sulfate starvation
small GTPase mediated signal transduction
carbohydrate metabolic process
transport
"retrograde transport, endosome to Golgi"
protein catabolic process
ATP synthesis coupled proton transport
cellular protein metabolic process
methionine biosynthetic process
translational elongation
vesicle-mediated transport
tricarboxylic acid cycle
fatty acid beta-oxidation
biosynthetic process
glycine metabolic process
protein folding
signal transduction
translational initiation
response to cadmium ion
cysteine biosynthetic process
translation
oxidation reduction
ubiquitin-dependent protein catabolic process
fatty acid biosynthetic process
cullin deneddylation
L-serine metabolic process
S-adenosylmethionine biosynthetic process
intracellular protein transport
proteolysis
photomorphogenesis
brassinosteroid mediated signaling
cellular response to nitrogen starvation
ER to Golgi vesicle-mediated transport
Enriched GO BP terms in the total network but not in any subnetworks:
GO:0006289 nucleotide-excision repair
GO:0009451 RNA modification
GO:0030148 sphingolipid biosynthetic process
GO:0006334 nucleosome assembly
GO:0048364 root development
GO:0006817 phosphate transport
GO:0006790 sulfur metabolic process
GO:0006396 RNA processing
GO:0006121 "mitochondrial electron transport, succinate to ubiquinone"
GO:0007169 transmembrane receptor protein tyrosine kinase signaling pathway
GO:0006874 cellular calcium ion homeostasis
GO:0006464 protein modification process
GO:0009638 phototropism
GO:0030001 metal ion transport
GO:0009736 cytokinin mediated signaling
GO:0006301 postreplication repair
GO:0008272 sulfate transport
GO:0008380 RNA splicing
GO:0009966 regulation of signal transduction
GO:0045449 regulation of transcription
GO:0009617 response to bacterium
GO:0051726 regulation of cell cycle
GO:0006891 intra-Golgi vesicle-mediated transport
GO:0006298 mismatch repair
GO:0010216 maintenance of DNA methylation
GO:0007015 actin filament organization
GO:0006828 manganese ion transport
GO:0010020 chloroplast fission
GO:0006730 one-carbon compound metabolic process
GO:0006617 "SRP-dependent cotranslational protein targeting to membrane, signal
sequence recognition"
GO:0006367 transcription initiation from RNA polymerase II promoter
GO:0006510 ATP-dependent proteolysis
GO:0009616 virus induced gene silencing
GO:0006355 "regulation of transcription, DNA-dependent"
GO:0010224 response to UV-B
GO:0010617 circadian regulation of calcium ion oscillation
GO:0006875 cellular metal ion homeostasis
Root-specific enriched GO BP terms in roots network:
GO:0006519 cellular amino acid and derivative metabolic process
GO:0019509 methionine salvage
GO:0015914 phospholipid transport
GO:0015992 proton transport
GO:0009845 seed germination
Enriched GO BP terms in roots network but not total network:
GO:0009116
GO:0007021
GO:0009156
GO:0007033
GO:0008333
GO:0009165
GO:0006378
GO:0045454
GO:0015865
GO:0044249
GO:0050832
GO:0016036
GO:0009845
nucleoside metabolic process
tubulin complex assembly
ribonucleoside monophosphate biosynthetic process
vacuole organization
endosome to lysosome transport
nucleotide biosynthetic process
mRNA polyadenylation
cell redox homeostasis
purine nucleotide transport
cellular biosynthetic process
defense response to fungus
cellular response to phosphate starvation
seed germination
Leaf-specific enriched GO BP terms in leaves network:
GO:0009733
GO:0006529
GO:0006535
GO:0019253
response to auxin stimulus
asparagine biosynthetic process
cysteine biosynthetic process from serine
reductive pentose-phosphate cycle
Enriched GO BP terms in leaves network but not total network:
GO:0000103
GO:0009744
GO:0007033
GO:0009733
GO:0000302
GO:0006529
GO:0048366
GO:0006378
GO:0045454
GO:0009098
GO:0055072
GO:0019253
GO:0009416
GO:0015865
sulfate assimilation
response to sucrose stimulus
vacuole organization
response to auxin stimulus
response to reactive oxygen species
asparagine biosynthetic process
leaf development
mRNA polyadenylation
cell redox homeostasis
leucine biosynthetic process
iron ion homeostasis
reductive pentose-phosphate cycle
response to light stimulus
purine nucleotide transport
GO:0016036 cellular response to phosphate starvation
Flower-specific enriched GO BP terms in flowers network:
GO:0030048
GO:0010267
GO:0009910
GO:0006499
GO:0006397
GO:0006306
GO:0009750
GO:0009850
GO:0009738
GO:0006221
GO:0006468
GO:0007010
GO:0016575
GO:0009218
GO:0019761
GO:0006751
actin filament-based movement
"RNA interference, production of ta-siRNAs"
negative regulation of flower development
N-terminal protein myristoylation
mRNA processing
DNA methylation
response to fructose stimulus
auxin metabolic process
abscisic acid mediated signaling
pyrimidine nucleotide biosynthetic process
protein amino acid phosphorylation
cytoskeleton organization
histone deacetylation
pyrimidine ribonucleotide metabolic process
glucosinolate biosynthetic process
glutathione catabolic process
Flower-specific enriched GO BP terms not in roots/leaves network:
GO:0030048
GO:0006268
GO:0010267
GO:0009910
GO:0044237
GO:0045941
GO:0006499
GO:0006979
GO:0009723
GO:0006397
GO:0006306
GO:0009750
GO:0009850
GO:0042938
GO:0009738
GO:0006013
GO:0006221
GO:0006468
GO:0006270
GO:0007010
GO:0009081
actin filament-based movement
DNA unwinding during replication
"RNA interference, production of ta-siRNAs"
negative regulation of flower development
cellular metabolic process
positive regulation of transcription
N-terminal protein myristoylation
response to oxidative stress
response to ethylene stimulus
mRNA processing
DNA methylation
response to fructose stimulus
auxin metabolic process
dipeptide transport
abscisic acid mediated signaling
mannose metabolic process
pyrimidine nucleotide biosynthetic process
protein amino acid phosphorylation
DNA replication initiation
cytoskeleton organization
branched chain family amino acid metabolic process
GO:0000059
GO:0016575
GO:0009218
GO:0009396
GO:0008283
GO:0009809
GO:0009411
GO:0019761
GO:0019243
GO:0006751
"protein import into nucleus, docking"
histone deacetylation
pyrimidine ribonucleotide metabolic process
folic acid and derivative biosynthetic process
cell proliferation
lignin biosynthetic process
response to UV
glucosinolate biosynthetic process
methylglyoxal catabolic process to D-lactate
glutathione catabolic process
Enriched GO BP terms in flowers network but not total network:
GO:0030048
GO:0007021
GO:0007033
GO:0006397
GO:0006306
GO:0009750
GO:0009098
GO:0016575
GO:0050832
GO:0016036
GO:0019243
actin filament-based movement
tubulin complex assembly
vacuole organization
mRNA processing
DNA methylation
response to fructose stimulus
leucine biosynthetic process
histone deacetylation
defense response to fungus
cellular response to phosphate starvation
methylglyoxal catabolic process to D-lactate
Silique-specific enriched GO BP terms in siliques network:
GO:0006839
GO:0008654
GO:0006623
GO:0006021
GO:0016126
GO:0031087
GO:0009624
GO:0009067
GO:0051276
mitochondrial transport
phospholipid biosynthetic process
protein targeting to vacuole
inositol biosynthetic process
sterol biosynthetic process
deadenylation-independent decapping of nuclear-transcribed mRNA
response to nematode
aspartate family amino acid biosynthetic process
chromosome organization
Silique-specific enriched GO BP terms not in roots/leaves network:
GO:0006268
GO:0006839
GO:0008654
GO:0006623
DNA unwinding during replication
mitochondrial transport
phospholipid biosynthetic process
protein targeting to vacuole
GO:0044237
GO:0042938
GO:0006021
GO:0006013
GO:0016126
GO:0031087
GO:0006270
GO:0009624
GO:0009081
GO:0009067
GO:0009396
GO:0008283
GO:0009809
GO:0009411
GO:0019243
GO:0051276
cellular metabolic process
dipeptide transport
inositol biosynthetic process
mannose metabolic process
sterol biosynthetic process
deadenylation-independent decapping of nuclear-transcribed mRNA
DNA replication initiation
response to nematode
branched chain family amino acid metabolic process
aspartate family amino acid biosynthetic process
folic acid and derivative biosynthetic process
cell proliferation
lignin biosynthetic process
response to UV
methylglyoxal catabolic process to D-lactate
chromosome organization
Enriched GO BP terms in siliques network but not total network:
GO:0000103
GO:0009116
GO:0008654
GO:0006623
GO:0009156
GO:0009744
GO:0007033
GO:0008333
GO:0009165
GO:0006378
GO:0006021
GO:0009624
GO:0009067
GO:0015865
GO:0044249
GO:0050832
GO:0016036
GO:0019243
sulfate assimilation
nucleoside metabolic process
phospholipid biosynthetic process
protein targeting to vacuole
ribonucleoside monophosphate biosynthetic process
response to sucrose stimulus
vacuole organization
endosome to lysosome transport
nucleotide biosynthetic process
mRNA polyadenylation
inositol biosynthetic process
response to nematode
aspartate family amino acid biosynthetic process
purine nucleotide transport
cellular biosynthetic process
defense response to fungus
cellular response to phosphate starvation
methylglyoxal catabolic process to D-lactate
Seed-specific enriched GO BP terms in seeds network:
GO:0030036
GO:0006139
GO:0010188
GO:0008295
actin cytoskeleton organization
"nucleobase, nucleoside, nucleotide and nucleic acid metabolic process"
response to microbial phytotoxin
spermidine biosynthetic process
Seed-specific enriched GO BP terms not in roots/leaves network:
GO:0030036
GO:0045941
GO:0006979
GO:0009723
GO:0042938
GO:0006013
GO:0006139
GO:0010188
GO:0000059
GO:0008295
actin cytoskeleton organization
positive regulation of transcription
response to oxidative stress
response to ethylene stimulus
dipeptide transport
mannose metabolic process
"nucleobase, nucleoside, nucleotide and nucleic acid metabolic process"
response to microbial phytotoxin
"protein import into nucleus, docking"
spermidine biosynthetic process
Enriched GO BP terms in seeds network but not total network:
GO:0030036
GO:0007033
GO:0000302
GO:0008333
GO:0048366
GO:0055072
GO:0006139
GO:0009416
GO:0015865
GO:0016036
GO:0008295
actin cytoskeleton organization
vacuole organization
response to reactive oxygen species
endosome to lysosome transport
leaf development
iron ion homeostasis
"nucleobase, nucleoside, nucleotide and nucleic acid metabolic process"
response to light stimulus
purine nucleotide transport
cellular response to phosphate starvation
spermidine biosynthetic process