Users can access from this page to VitisNet files under different formats. Files need to be unzipped. The picture files are pdf images of the Celldesigner files. Celldesigner and Cytoscape files can be loaded in the respective programs (for help, see the tutorial). Cytoscape sessions contain networks directly loaded into Cytoscape that can be directly open with Cytoscape.
Click here for the tutorial
1 Metabolism
VVID | Network name | #genes | #proteins | #mets |
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 |
VVID | Network name | #genes | #proteins | #mets |
10190 | Oxidative phosphorylation | 383 | 105 | 7 |
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 |
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 |
VVID | Network name | #genes | #proteins | #mets |
10230 | Purine metabolism | 154 | 49 | 62 |
10240 | Pyrimidine metabolism | 113 | 39 | 46 |
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 |
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 |
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 |
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 |
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 |
11013 | ABA biosynthesis | 18 | 8 | 11 |
10966 | Glucosinolate biosynthesis | 40 | 10 | 27 |
VVID | Network name | #genes | #proteins | #mets |
11000 | Single reactions | 190 | 15 | 38 |
2 Genetic information processing networks
VVID | Network name | #genes | #proteins | #mets |
23022 | Basal transcription factors | 67 | 23 | |
VVID | Network name | #genes | #proteins | #mets |
20970 | Aminoacyl-tRNA biosynth. | 122 | 22 | 64 |
23015 | mRNA surveillance pathway | 135 | 42 | |
23008 | Ribosome biogenesis in Eukaryotes | 141 | 59 | |
VVID | Network name | #genes | #proteins | #mets |
24141 | Protein processing in endoplasmic reticulum | 279 | 68 | |
24130 | SNARE interaction in vesicular transport | 69 | 22 | |
24120 | Ubiquitin mediated proteolysis | 204 | 68 | 3 |
VVID | Network name | #genes | #proteins | #mets |
23410 | Base excision repair | 32 | 21 | |
23420 | Nucleotide excision repair | 72 | 36 | |
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
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 | |
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 |
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
VVID | Network name | #genes | #proteins | #mets |
44140 | Regulation of autophagy | 30 | 16 | 4 |
VVID | Network name | #genes | #proteins | #mets |
44810 | Regulation of actin cytoskeleton | 396 | 117 | 1 |
VVID | Network name | #genes | #proteins | #mets |
5 Transport
VVID | Network name | #genes | #proteins | #mets |
52010 | ABC transporters | 284 | 93 | |
VVID | Network name | #genes | #proteins | #mets |
50004 | Auxin transport | 58 | 27 | 1 |
VVID | Network name | #genes | #proteins | #mets |
50111 | Tethering factors | 117 | 70 | |
50112 | Nuclear pore complex | 90 | 28 | |
50113 | Thylakoid targeting pathway | 71 | 15 | |
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
VVID | Network name | #genes | #proteins | #mets |
60072 | Orphans Response reg | 16 | 16 | |
60073 | Orphans zf-b box | 15 | 15 | |
60078 | Other zf-C3HC4 | 279 | 279 | |
60087 | Orphans KIP1 SANTA | 6 | 6 | |
Users of VitisNet should cite: VitisNet: “Omics” Integration through Grapevine Molecular Networks. Jérôme Grimplet, Grant R. Cramer, Julie A. Dickerson, Kathy Mathiason, John Van Hemert and Anne Y. Fennell, 2009, PLoS ONE: http://dx.plos.org/10.1371/journal.pone.0008365.
Cytoscape sessions
Files need to be unzipped before use with Cytoscape
Raw Networks:
1. Metabolism Part 1 | Part 2
2. Genetic Information Processing
3. Environmental Information Processing
4. Cellular Processes
5. Transport
6. Transcription Factors Part 1 | Part 2
Reference file
-Vitis vinifera Genome manual annotation file:
Genes_annotation
Tutorial files
-Mapping file for affymetrix microarray:
GS_to_probeset.txt
-Model for input of abundance data:
expression_berry.txt
-Cytoscape style for visualization of berry tissues data:
berrystyle.props
-Citrate Cycle (TCA cycle)
vv10020CitrateCycle.xml
Cytoscape networks with molecular abundance in berry tissues:
from Grimplet et al., 2007 and Grimplet et al., 2009
1. Metabolism Part 1 | Part 2
2. Genetic Information Processing
3. Environmental Information Processing
4. Cellular Processes
5. Transport
6. Transcription Factors Part 1 | Part 2
Contacts:
Jerome Grimplet
Anne Fennell