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VitisNet: Molecular Networks for Grapevine

Users can access the VitisNet (12X) files from this page in different formats. 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). Files need to be unzipped. Cytoscape sessions contain groups of processed networks that can be directly loaded and used in Cytoscape.

Click here for the tutorial

1 Metabolism

1.1 Carbohydrate metabolism Download pictures zip file Download Celldesigner zip file Download Cytoscape zip file
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 Download pictures zip file Download Celldesigner zip file Download Cytoscape zip file
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 Download pictures zip file Download Celldesigner zip file Download Cytoscape zip file
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 Download pictures zip file Download Celldesigner zip file Download Cytoscape zip file
VVID Network name #genes #proteins #mets
10230 Purine metabolism 154 49 62
10240 Pyrimidine metabolism 113 39 46

 

1.5 Amino Acid metabolism Download pictures zip file Download Celldesigner zip file Download Cytoscape zip file
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 Download pictures zip file Download Celldesigner zip file Download Cytoscape zip file
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 Download pictures zip file Download Celldesigner zip file Download Cytoscape zip file
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 Download pictures zip file Download Celldesigner zip file Download Cytoscape zip file
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 Download pictures zip file Download Celldesigner zip file Download Cytoscape zip file
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 Download pictures zip file Download Celldesigner zip file Download Cytoscape zip file
VVID Network name #genes #proteins #mets
11000 Single reactions 190 15 38

2 Genetic information processing networks

2.1 Transcription Download pictures zip file Download Celldesigner zip file Download Cytoscape zip file
VVID Network name #genes #proteins #mets
23020 RNA polymerase 96 34  
23022 Basal transcription factors 67 23  
23040 Spliceosome 280 139  
2.2 Translation Download pictures zip file Download Celldesigner zip file Download Cytoscape zip file
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 Download pictures zip file Download Celldesigner zip file Download Cytoscape zip file
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 Download pictures zip file Download Celldesigner zip file Download Cytoscape zip file
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 Download pictures zip file Download Celldesigner zip file Download Cytoscape zip file
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 Download pictures zip file Download Celldesigner zip file Download Cytoscape zip file
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 Download pictures zip file Download Celldesigner zip file Download Cytoscape zip file
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 Download pictures zip file Download Celldesigner zip file Download Cytoscape zip file
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 Download pictures zip file Download Celldesigner zip file Download Cytoscape zip file
VVID Network name #genes #proteins #mets
44810 Regulation of actin cytoskeleton 396 117 1
4.3 Cell growth and death Download pictures zip file Download Celldesigner zip file Download Cytoscape zip file
VVID Network name #genes #proteins #mets
44110 Cell cycle 358 238  
40006 Cell wall 518 62 11

5 Transport

5.1 Membrane transport Download pictures zip file Download Celldesigner zip file Download Cytoscape zip file
VVID Network name #genes #proteins #mets
52010 ABC transporters 284 93  
5.2 Hormone transport Download pictures zip file Download Celldesigner zip file Download Cytoscape zip file
VVID Network name #genes #proteins #mets
50004 Auxin transport 58 27 1
5.3 Transport system Download pictures zip file Download Celldesigner zip file Download Cytoscape zip file
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 Download pictures zip file Download Celldesigner zip file Download Cytoscape zip file
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

  Download pictures zip file Download Celldesigner zip file Download Cytoscape zip file
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  

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.

VitisNet Gene Annotation Reference file -The complete Vitis vinifera gene functional annotation and 8x to 12X sequence correspondence: Genes_annotation

Please reference: Grimplet J, J Van Hemert, P Carbonell-Bejerano, J Diaz-Riquelme, J Dickerson, A Fennell, M Pezzotti, JM Martinez-Zapater. 2012. Comparative analysis of grapevine whole-genome predictions, functional annotation, categorization and integration of the predicted gene sequences. BMC Research Notes 5:213 doi:10.1186/1756-0500-5-213

The 8X version of VitisNet can be accessed here

Cytoscape sessions

Files need to be unzip 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

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