VitisNet: Molecular Networks for Grapevine

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1 Metabolism

1.1 Carbohydrate metabolism
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VVID Network name
#genes #proteins #mets
10010 Glycolysis
223 29 28
10020 Citrate cycle
79 18 21
10030 Pentose phosphate
89 17 21
10040 Pentose/glucuronate interconversion
62 11 14
10051 Fructose and mannose metabolism
117 20 20
10052 Galactose metabolism
176 16 27
10053 Ascorbate and aldarate metabolism
53 9 9
10500 Starch and sucrose metabolism
373 47 34
10530 Aminosugars metabolism
108 8 10
10520 Nucleotide sugars metabolism
72 16 18
10620 Pyruvate metabolism
230 28 19
10630 Glyoxylate and dicarboxylate metabolism
88 18 19
10640 Propanoate metabolism
71 11 12
10650 Butanoate metabolism
88 18 19
10562 Inositol phosphate metabolism
70 18 20

1.2 Energy metabolism
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VVID Network name
#genes #proteins #mets
10190 Oxidative phosphorylation
383 105 7
10195 Photosynthesis
223 52
10196 Photosynthesis antenna proteins
38 11
10710 Carbon fixation
182 21 20
10720 Reductive carboxylate cycle
44 10 14
10680 Methane metabolism
133 10 11
10910 Nitrogen metabolism
117 23 19
10920 Sulfur metabolism
48 13 12

1.3 Lipid Metabolism
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VVID Network name
#genes #proteins #mets
10061 Fatty acid biosynthesis
86 13 36
10062 Fatty acid elongation in mitochondria
29 7 29
10071 Fatty acid metabolism
111 30 40
10072 Synthesis/degradation of ketone bodies
20 3 4
10100 Biosynthesis of steroids
150 49 76
10140 C21-Steroid hormone metabolism
18 6 14
10561 Glycerolipid metabolism
159 19 18
10564 Glycerophospholipid metabolism
150 34 32
10565 Ether lipid metabolism
53 13 9
10600 Sphingolipid metabolism
77 13 15
10592 Alpha-linolenic acid metabolism
106 21 29
11040 Biosynthesis of unsaturated fatty acids
54 20 27

1.4 Nucleotide metabolism
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VVID Network name
#genes #proteins #mets
10230 Purine metabolism
154 49 62
10240 Pyrimidine metabolism
113 39 46

1.5 Amino Acid metabolism
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VVID Network name
#genes #proteins #mets
10251 Glutamate metabolism
97 28 25
10252 Alanine and aspartate metabolism
117 24 24
10260 Glycine serine and threonine metabolism
116 31 38
10271 Methionine metabolism
135 32 47
10272 Cysteine metabolism
84 17 25
10280 Val. leu. and ile degradation
92 20 34
10290 Val. leu. and ile biosynthesis
73 14 26
10300 Lysine biosynthesis
85 52 22
10330 Arginine and proline metabolism
65 17 23
10340 Histidine metabolism
65 18 19
10350 Tyrosine metabolism
165 27 39
10360 Phenylalanine metabolism
224 17 14
10380 Tryptophan metabolism
19 6 7
10400 Phenylalanine tyrosine and tryptophan biosynthesis
159 30 35
10220 Urea cycle and metabolism of amino groups
134 33 41

1.6 Other amino acids metabolism
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VVID Network name
#genes #proteins #mets
10410 Beta-alanine metabolism
59 13 13
10450 Selenoamino acid metabolism
82 15 17
10460 Cyanoamino acid metabolism
39 8 16
10480 Glutathione metabolism
159 37 16

1.7 Glycan biosynthesis and metabolism
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VVID Network name
#genes #proteins #mets
10510 N-Glycan biosynthesis
56 23 22
10511 N-Glycan degradation
780 8
10540 Lipopolysaccharides biosynthesis
11 10 13
10550 Peptidoglycan biosynthesis
20 3 10
10563 GPI-anchor biosynthesis
22 12 14
10602 Glycosphingolipid biosynthesis
17 7 16
11030 Glycan structures-biosynthesis1
101 26 48

1.8 Cofactors and vitamin metabolism
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VVID Network name
#genes #proteins #mets
10730 Thiamine metabolism
22 12 20
10740 Riboflavin metabolism
70 13 15
10750 Vitamin B6 metabolism
19 7 13
10760 Nicotinate/nicotinamide metabolism
28 12 13
10770 Pantothenate/CoA biosynthesis
56 15 19
10780 Biotin metabolism
8 6 8
10790 Folate biosynthesis
40 17 24
10670 One carbon pool by folate
49 15 9
10860 Porphyrin and chlorophyll metabolism
75 32 39
10130 Ubiquinone biosynthesis
36 17 25

1.9 Biosynthesis of secondary metabolites
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VVID Network name
#genes #proteins #mets
10900 Terpenoid biosynthesis
192 18 24
10902 Monoterpenoid biosynthesis
217 29 42
10904 Diterpenoid biosynthesis
78 19 37
10908 Zeatin biosynthesis
61 11 20
10906 Carotenoid biosynthesis
49 22 33
10905 Brassinosteroid biosynthesis
21 7 24
10940 Phenylpropanoid biosynth.
243 25 46
10941 Flavonoid biosynthesis
190 25 52
10942 Anthocyanin biosynthesis
72 8 18
10943 Isoflavonoid biosynthesis
68 7 17
10950 Alkaloid biosynthesis I
65 17 23
10311 Penicillin/cephalosp. Biosynthesis
13 5 5
11002 Auxin biosynthesis
99 24 12
11012 Iba metabolism
21 11 5
11013 ABA biosynthesis
18 8 11
10966 Glucosinolate biosynthesis
40 10 27

1.10 Other
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VVID Network name
#genes #proteins #mets
11000 Single reactions
190 15 38

2 Genetic information processing networks

2.1 Transcription
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VVID Network name
#genes #proteins #mets
23020 RNA polymerase
96 34
23022 Basal transcription factors
67 23
23040 Spliceosome
280 139

2.2 Translation
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VVID Network name
#genes #proteins #mets
23010 Ribosome
612 131
20970 Aminoacyl-tRNA biosynth.
122 22 64
23013 RNA transport
260 92
23015 mRNA surveillance pathway
135 42
23008 Ribosome biogenesis in Eukaryotes
141 59

2.3 Folding, sorting degradation
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VVID Network name
#genes #proteins #mets
23060 Protein export
64 30
24141 Protein processing in endoplasmic reticulum
279 68
24130 SNARE interaction in vesicular transport
69 22
23050 Proteasome
75 47
24120 Ubiquitin mediated proteolysis
204 68 3

2.4 Replication and repair
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VVID Network name
#genes #proteins #mets
23030 DNA replication
82 38
23410 Base excision repair
32 21
23420 Nucleotide excision repair
72 36
23430 Mismatch repair
49 19
23440 Homologous recombination
51 19
23450 Non homologous end joining
19 8
24122 Sulfur relay system
15 7 2
23018 RNA degradation
115 48

3 Environmental information processing

3.1 Signal transduction
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VVID Network name
#genes #proteins #mets
34020 Calcium signaling pathway
152 32 22
34070 Phosphatidylinositol signaling system
83 14 17
34150 mTOR signaling pathway
32 17

3.2 Hormone signaling
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VVID Network name
#genes #proteins #mets
30001 ABA signaling
168 101 11
30003 Auxin signaling
311 149 1
30005 Brassinosteroids signaling
63 24 2
30007 Cytokinin signaling
80 74 1
30008 Ethylene signaling
275 247 3
30010 Gibberellin signaling
43 28 1
30011 Jasmonate signaling
98 71 4

3.3 Plant-specific signaling
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VVID Network name
#genes #proteins #mets
34710 Circadian rhythm
79 63
34626 Plant-pathogen interaction
360 122 7
34627 R proteins from Plant-pathogen interaction
472 11
30009 Flower development
204 188 1

4 Cellular processes

4.1 Transport and catabolism
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VVID Network name
#genes #proteins #mets
44140 Regulation of autophagy
30 16 4
44145 Phagosome
142 29
44146 Peroxisome
95 47 1

4.2 Cell motility
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VVID Network name
#genes #proteins #mets
44810 Regulation of actin cytoskeleton
396 117 1

4.3 Cell growth and death
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VVID Network name
#genes #proteins #mets
44110 Cell cycle
358 238
40006 Cell wall
518 62 11

5 Transport

5.1 Membrane transport
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VVID Network name
#genes #proteins #mets
52010 ABC transporters
284 93

5.2 Hormone transport
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VVID Network name
#genes #proteins #mets
50004 Auxin transport
58 27 1

5.3 Transport system
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VVID Network name
#genes #proteins #mets
50110 Protein coat
229 105
50111 Tethering factors
117 70
50112 Nuclear pore complex
90 28
50113 Thylakoid targeting pathway
71 15

5.4 Transporter catalog
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VVID Network name
#genes #proteins #mets
50101 Channels and pores
451 146
50104 Group translocators
42 10
50105 Transport electron carriers
109 38
50108 Accessory factors involved in transport
172 16
50109 Incompletely characterized transport systems
383 98
50121 Porters cat 1 to 6
197 86
50122 Porters cat 7 to 17
259 50
50123 Porters cat 18 to 29
225 46
50124 Porters cat 30 to 64
170 70
50125 Porters cat 66 to 94
230 55
50131 Prim. active transp. A2-A4
223 53
50132 Prim. active transp. A5-A8
205 84
50133 Prim. active transp. A9-A18
262 99
50134 Prim. active transp. cat D1
175 46
50135 Prim. active transp. D3-E2
156 44

6 Transcription factors


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VVID Network name
#genes #proteins #mets
60001 ABI3VP1
25 25
60002 Alfin-like
8 8
60003 AP2 EREBP
158 158
60004 ARF
29 29
60005 ARID
12 12
60006 ARR-B
15 15
60007 AS2
52 51
60008 AUXIAA
31 31
60009 BBR
6 6
60010 BES1
11 11
60011 BHLH
163 163
60012 BZIP
73 73
60013 BHSH
1 1
60014 C2C2-CO
14 14
60015 C2C2-DOF
25 25
60016 C2C2-GATA
25 25
60017 C2H2
138 138
60018 C3H
93 93
60019 C2C2-YABBY
7 7
60020 CAMTA
8 8
60021 CCAAT
35 35
60022 CPP
7 7
60023 CSD
4 4
60024 DBP
7 7
60025 DDT
10 10
60026 E2F-DP
8 8
60027 EIL
5 5
60028 FHA
23 23
60029 G2-like
43 43
60030 GeBP
8 8
60031 GIF
4 4
60032 GRAS
53 53
60033 GRF
14 14
60034 HB
102 102
60035 HMG
18 18
60036 HRT
1 1
60037 HSF
22 22
60038 Jumonji
29 29
60039 LFY
1 1
60040 LIM
12 12
60041 LUG
9 9
60042 MADS
81 81
60043 MBF1
6 6
60044 MYB
179 179
60045 MYBrelated
71 71
60046 NAC
86 86
60047 PBF-2-like
2 2
60048 PHD
81 81
60049 PLATZ
12 12
60050 PseudoARR-B
9 9
60051 RB
2 2
60052 RWP-RK
12 12
60053 S1Fa-like
3 3
60054 SAP
1 1
60055 SBP
23 23
60056 SET PCG
64 64
60057 Sigma70-like
6 6
60058 SNF2
47 47
60059 SRS
5 5
60060 TAZ
8 7
60061 TCP
21 21
60062 Trihelix
37 37
60063 TUB
17 17
60064 ULT
1 1
60065 VOZ
2 2
60066 WRKY
69 69
60067 zf-MYND
4 4
60068 zf-HD
18 18
60069 ZIM
14 14
60070 Orphans CCT
8 8
60071 Orphans FAR-RED
71 71
60072 Orphans Response reg
16 16
60073 Orphans zf-b box
15 15
60074 Orphans zf-SWIM
8 8
60075 Other BSD
12 12
60076 Other GTF
7 7
60077 Other zf-AN1
15 15
60078 Other zf-C3HC4
279 279
60079 Other zf-DHHC
25 25
60080 Other zf
39 39
60081 COAP15
2 2
60082 GNAT
36 36
60083 IWS1
1 1
60084 MED
2 2
60085 MTERF
39 39
60086 OFP
17 17
60087 Orphans KIP1 SANTA
6 6
60088 Orphans WRC
1 1
60089 Other Nozzle
1 1
60090 RCD1
2 2
60091 SOH1
1 1
60092 SWIB
16 16
60093 TRAF
34 34
60094 SWI SNF SWI3
2 2
60095 Orphans PAH
4 4