The Bio-Analytic Resource for Plant Biology

Welcome to the Bio-Analytic Resource - the BAR! Below are user-friendly web-based tools for working with functional genomics and other data. Most are designed with the plant (mainly Arabidopsis) researcher in mind, but a couple of them can be useful to the wider research community, e.g. Mouse eFP Browser and Human eFP Browser or BlastDigester. Click on the icon to read the partner paper to a given tool. Mouse-over a given link for further information.

Gene Expression and Protein Tools

 Expression AnglerPoplar Expression Angler
 Sample Angler    
 e-Northerns w. Expression Browser,  Poplar Expression Browser    
 Arabidopsis eFP Browser, Cell eFP Browser  
 Other Dicot eFPs: Poplar,  M. truncatula,  Soybean,  Potato,  Tomato,
    E. salsugineum,  Grape
 Monocot eFPs: Maize,  Rice,  Barley,  Triticale    
 Arabidopsis Seed Coat eFP Browser
 Expressolog Tree Viewer  
 Arabidopsis Interactions Viewer  
 Rice Interactions Viewer  
 Classification SuperViewer  
 _at to AGI converter    
 ePlant (link to PLoS ONE version)  
 Arabidopsis Translatome eFP Browser    
 Arabidopsis Spatio-Temporal Root Stress eFP Browser    

Molecular Markers and Mapping Tools

 Next Generation Mapping

Other Genomic Tools

 ClustalW with MView Output
 Heatmapper Plus
 Duplicate Remover
 Venn Selector
 Venn SuperSelector
 Random ID list generator

Click the printer icon for printing tips. Further information on the above tools is available by clicking the Help icon to the BAR help page on any page. For Arabidopsis queries, the following annotation and lookup tables are used:

  BAR Version 14-05
The MapMan data used by Classification SuperViewer is updated to Ath_AGI_LOCUS_TAIR10_Aug2012.txt. [most recent version as of 4 June 2013].
Promomer data sets are updated to TAIR10. [most recent version as of 4 June 2013].
Arabidopsis Annotation from TAIR, called TAIR10_pep_20101209, which is merged with Gene Aliases from TAIR, called gene_aliases.20120207.txt. [most recent versions as of 21 September 2012]
Arabidopsis GO Classification from TAIR, ATH_GO_GOSLIM.20120925.txt. [most recent version as of September 25, 2012].
Affymetrix probe set identifier to AGI number lookup table from TAIR dated 20 December 2010. It was called affy_ATH1_array_elements-2010-12-20.txt. [most recent version as of 21 September 2012]
Predicted protein-protein interactions from Dr. Matt Geisler and colleagues at Southern Illinois University. Interactome 2.0 [most recent version as of 10 February 2009]
Literature-documented PPIs from TairProteinInteraction.20090527, and IntAct Arabidopsis Interactions as of 5 May 2010. Another source is AMPv3 membrane protein interactome data from the Frommer lab, and Pascal Braun et al.'s Arabidopsis Interactome.
Documented and predicted subcellular localizations from Dr. A. Harvey Millar and colleagues at the University of Western Australia. SUBA2.0 [updated March 2009]
Documented and predicted protein structures in ePlant are respectively from PDB and Dr. Lawrence Kelley at Imperial College, London, in the UK, computed using his Phyre algorithm [updated 19 November 2009]
Poplar annotations and lookup from Chung-Jui Tsai, University of Georgia, AffyAnnotationV3_102707mtu.csv [updated October 2007]

Maintained by Nicholas J. Provart, last updated 2 June 2015. Visit the Provart Lab website! The BAR has been funded in part by Centre for the Analysis of Genome Evolution and Function, grants from the Canada Foundation for Innovation to NJP, and from Genome Canada to NJP and the Arabidopsis Research Group at the Department of Cell and Systems Biology, University of Toronto.