BAR Framework The Bio-Array Resource consists of numerous MySQL DBs. There is also associated code written in Perl, Python, Ruby, and some Java for exploring gene expression data, protein-protein interactions, subcellular localization, orthologs, and protein structure Expression data are from in-house or public DBs, such as GEO or the PDB, and are stored in a MIAME-compliant format. Details on experimental setup, genetic background (whether the material is from a mutant plant), etc. are captured. In general, we try to capture such details using standardized ontologies, such a the Boyes system for describing the age of plants, GO etc. Unfortunately not all of these ontologies are suitable for our needs (e.g. Plant Ontology for now). MinSeq may be suitable for NGS data… The BAR runs off on a Dell webserver with 2 Dual Core Xeon Processors (2.33GHz), 4 GB of RAM, and ~80 GB of redundant disk storage.
The Bio-Array Resource: e-Northerns w. Expression Browser Toufighi et al. (2005), Plant J 43(1): Experiment Identifier Experiment Category Control/Treatment Flag black=treatment, white=control Expression Levels red=higher expression level AGI IDs, My Gene Categories colouring as specified by user Functional Classification ’Barcode’ indicates GO category Cluster Tree co-expressed genes are grouped Growth Stage darker=older Tissue type e.g. green=leaf Mutant/WT Flag white=WT, blue=mutant Timecourse darker=later Protein Interactions if present
Looking at DHS3 response with the eFP Browser Data Source to choose different AtGenExpress projects and other projects, e.g. Birnbaum set. Expression Level scale red=higher expression level Expression Level distribution shows how maximum level compares with all other genes, and maximum level in any set Clickable tissues hyperlink to the NASCArrays, GEO or literature record for the sample Mode allows viewing in Absolute, Relative, and Compare modes Signal Threshold to set a maximum for colour scale Winter et al. (2007) PLoS One 2(8): e718
AtGenExpress data Browser array_element_name locus (from affy_ATH1_array_elements txt at TAIR) _at AT1G _at AT1G _at AT1G _at AT1G _at AT1G _at AT1G _at AT1G _at AT1G _at AT1G _at AT1G _at AT1G _at AT1G01130 At-TAX data from Tuebingen w. webservices
New for 2008 – cross-species expression viewing
New for 2009 – ePl : seamless viewing of km- to nm-scale data David Di Biase, Geoff Fucile, Shokoufeh Kohdabandeh, Hardeep Nahal 3DDI.orgBAR.utoronto.ca/ePlant
NGS mRNA-seq data could be displayed with BAR tools