Citation:
If you have used VirtualPlant to analyze your data, please cite our manuscript using the following reference:
Katari MS, Nowicki SD, Aceituno FF, Nero D, Kelfer J, Thompson LP, Cabello JM, Davidson RS, Goldberg AP, Shasha DE, Coruzzi GM, and Gutierrez RA. VirtualPlant: A software platform to support Systems Biology research. Plant Physiol. 2010;152(2):500-515.
Major funding for the VirtualPlant project has been provided by NSF Arabidopsis 2010 grant (DBI-0445666)
Introduction
Welcome to VirtualPlant.
VirtualPlant integrates genomic data and provides visualization and analysis tools for rapid and efficient exploration of genomic data. The goal of VirtualPlant is to provide the tools to aid researchers to generate biological hypotheses.
To start using the VirtualPlant system you have to create sets or experiments in your cart. Use the Upload Data form (top menu) or browse the contents of the database using the tree on the left frame. You can analyze the sets in your cart using the functions in the cart. Use the "Analyze Sets" link in the cart window to access visualization and analysis functions
Enjoy!
Features of Virtualplant
- Gene Cart:
Import lists of genes of interest or from experimental
treatments.
- Analyze Genomic Data in a
Biological Context
- Sungear Compare two to ten gene lists easily using Sungear, a Multifactor Comparison System with GO analysis.
- BioMaps View gene lists as color-coded graphs denoting over-represented GO terms.
- Gene Networks View gene networks derived from gene lists using Cytoscape.
- Features coming soon to Virtualplant
- BioSkew
- TextArc
Note: A detailed description of these tools is outlined below.
Software Requirements
In order to use all the features in VirtualPlant, you need to have Java installed in your computer.
If you do not have Java installed, you can download either the J2SE SDK (full install) or the J2SE JRE (runtime only), both of which can be found here.
Be sure not to get the J2EE (Java 2 Enterprise Edition, as opposed to the Java 2 Standard Edition).
How to get started?
You can start using the VirtualPlant system by creating and adding gene sets to the Gene Cart. You can create gene sets in several different ways:
- Browse the contents of the database using the tree (bottom left frame) and click on the branch name to retrieve the information associated with the branch. If genes are associated with the name you clicked, there will be a small form on the page that will allow you to create a set with these genes. After creating the set, a new item will be added to the cart (top left frame)
- Use our query page to ask specific questions about the data stored in the system
- Upload gene lists of interest to you using the Upload form.
VirtualPlant features
- "Gene Cart"
- Our gene cart (top left frame) feature allows users to
manage any type of gene sets generated by uploading data or as
a result of querying the database.
- The gene cart functionality is analogous to that of a Shopping Cart in commercial websites: You can add, modify or delete items. You can also "checkout" the cart contents to perform a number of data analysis tools integrated in the system
- Gene networks
- You can identify the known molecular interactions in a set of genes using VirtualPlant.
- You can explore the networks you find using Cytoscape.
- You can query VirtualPlant and launch Cytoscape from the Gene Cart.
- You can explore the networks you find using Cytoscape.
- Sungear Multifactor Comparison System
- Sungear is a generalized Venn Diagram that can accomodate,
visualize and compare more than three datasets, the size limit
of a traditional Venn diagram. You can use this tool to
compare a large number of gene sets. Sungear runs as an applet
and can be started from the GeneCart.
- Sungear can be used to learn the biological significance of gene lists or intersections among gene lists. We have integrated Gene Names and Gene Ontology information to evaluate the significance of any intersection or selection made within Sungear rapidly.
- You can also hypothesize major trends in your data by using Sungear. The software can suggest biased GO terms (suggest over-representation) as well as identify the most "peculiar" intersections of gene sets based on the distribution of all GO terms associated with it.
- For a quick tour on How to use Sungear, follow this link: Sungear Tour (under construction)
- Sungear can be used to learn the biological significance of gene lists or intersections among gene lists. We have integrated Gene Names and Gene Ontology information to evaluate the significance of any intersection or selection made within Sungear rapidly.
- "Gene Cart"
- Our gene cart (top left frame) feature allows users to
manage any type of gene sets generated by uploading data or as
a result of querying the database.
- The gene cart functionality is analogous to that of a Shopping Cart in commercial websites: You can add, modify or delete items. You can also "checkout" the cart contents to perform a number of data analysis tools integrated in the system.
- Browsing Tree
- You can browse the contents of the VirtualPlant database using the tree on the bottom left frame
- You can query the database and create data sets to add to your gene cart using the browsing tree feature
- Supporting data
- AtGenExpress microarray data set
- Latest TAIR release of Arabidopsis expression data
- Gene ontology: We have Anatomy, temporal and Gene ontologies available for browsing.
- The MIPS functional classification scheme
- Latest TIGR Arabidopsis genome annotation