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.
  News

Gene Expression and Protein Tools

• Expression Angler, Poplar Expression Angler 		   

News, June 2nd 2015


• Try out our Gene Slider tool for exploring more than 90000 conserved non-coding sequences in the Brassicaceae from Haudry et al. 2013, displayed along with putative transcription factor binding sites from the JASPAR database.
• We've developed a Grape eFP Browser based on gene expression data in Fasoli et al.'s 2012 Plant Cell paper.
• Our Expressolog Tree Viewer for exploring both sequence and expression pattern similiarity for homologs in 10 plant species now includes grape!
• The BAR will be at this year's ASPB in Minneapolis and the ICAR meeting in Paris. Drop by the Plant Bioinformatics booth in Minneapolis, or the BAR booth in Paris. We're also participating in a mini-symposium and workshops at both conferences, where we'll present on our work on contributing to the new Arabidopsis information portal at Araport.org/.
• Thanks for liking us 600 times on Facebook! If you haven't, like us on Facebook to keep up-to-date with the latest BAR and plant bioinformatics news...this might help us get funding down the road too ;-)
• 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  
• Promomer  
• Cistome    
• Arabidopsis Interactions Viewer  
• Rice Interactions Viewer  
• AGURR    
• Classification SuperViewer  
• _at to AGI converter    
• ePlant (link to PLoS ONE version)  
• MASTA    
• Arabidopsis Translatome eFP Browser    
• Arabidopsis Spatio-Temporal Root Stress eFP Browser    
• GeneMANIA    

Molecular Markers and Mapping Tools

• Next Generation Mapping 		 
• MarkerTracker    
• BlastDigester  
• CapsID  

Other Genomic Tools

• ClustalW with MView Output
• DataMetaFormatter
• Heatmapper
• 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 associomics.org 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.