VitisNet 12X: Molecular Networks for Grapevine

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

2 Genetic information processing networks

3 Environmental information processing

4 Cellular processes

5 Transport

6 Transcription factors

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