Arabidopsis eFP Browser

Arabidopsis eFP Browser
Name	Arabidopsis eFP Browser
Type	Bioinformatics tool
Discipline	Plant biology
Developer	University of Toronto
First release	2009

Arabidopsis eFP Browser

The Arabidopsis eFP Browser is a web-based visualization tool for transcriptome data focused on the model plant Arabidopsis thaliana. It synthesizes expression datasets from diverse projects into intuitive graphical outputs used by researchers at institutions such as University of Toronto, Salk Institute, Max Planck Society, Cold Spring Harbor Laboratory, and European Molecular Biology Laboratory. The browser has informed studies referenced alongside resources like TAIR, EnsemblPlants, Gene Ontology, NCBI, and ArrayExpress.

Overview

The project originated to make gene expression patterns accessible to communities working with Arabidopsis thaliana and related plant systems, aligning with broader initiatives exemplified by Human Genome Project, 1001 Genomes Project, Genome Research Limited, International Rice Informatics Consortium, and efforts at The Arabidopsis Information Resource. It aggregates spatial, temporal, and condition-specific expression profiles derived from microarray and RNA-Seq experiments curated by groups including European Bioinformatics Institute, National Center for Biotechnology Information, Wellcome Trust Sanger Institute, John Innes Centre, and Max Planck Institute of Molecular Plant Physiology.

Features and Functionality

Core functions mirror visualization paradigms used in platforms such as UCSC Genome Browser, Ensembl, IGV, Cytoscape, and Genevestigator. Users can query individual genes, gene families, or loci to produce pictographic renderings of expression across organs, developmental stages, or treatments, with options comparable to tools by Broad Institute or Stanford University laboratories. It supports cross-referencing to annotations from UniProt, TAIR, Pfam, InterPro, and network resources like STRING and BioGRID.

Data Sources and Processing

Datasets are drawn from public repositories and consortia including ArrayExpress, Gene Expression Omnibus, 1001 Genomes Project, Phytozome, SRA, and project-specific contributions from groups at Salk Institute for Biological Studies, Max Planck Society, Cold Spring Harbor Laboratory, and Carnegie Institution for Science. Processing pipelines incorporate normalization strategies and statistical models consistent with methods referenced by Anders and Huber, Robinson and Oshlack, DESeq2, and limma frameworks, while leveraging annotation schemas from Gene Ontology Consortium and identifiers standardization from NCBI and EnsemblPlants.

User Interface and Visualization

The interface uses an organ-centric pictograph approach similar in usability goals to visualization frameworks from Broad Institute and EMBL-EBI projects, presenting heatmap-style color scales on schematic depictions of plant anatomy comparable to diagrams used by Cambridge University Press publications. Interactive features allow selection of datasets curated by teams at University of California, Berkeley, Harvard University, Massachusetts Institute of Technology, and Yale University, with export options suitable for publication alongside citation practices from journals like Nature, Science, The Plant Cell, Plant Physiology, and Genome Biology.

Applications and Impact

The browser has been applied in functional genomics studies that cite methodologies and findings from groups such as Michael Bevan, Ecker Lab, Detlef Weigel, Joe Ecker, Chris Somerville, and institutions including Sainsbury Laboratory, John Innes Centre, Max Planck Institute, and Salk Institute. It has supported gene candidate selection in investigations published in Nature Genetics, Plant Cell, PNAS, Development, and The Plant Journal, and informed comparative analyses alongside resources like Phytozome, EnsemblPlants, TAIR, and Gramene.

Development and Availability

Development has involved collaborations across academic labs and bioinformatics groups at University of Toronto, University of California, European Molecular Biology Laboratory, and contributors listed in datasets from ArrayExpress and GEO. The software distribution model follows precedents set by open-science initiatives such as Open Source Initiative, GNU General Public License, and community resources like GitHub and Bitbucket, with data access patterns reflecting policies advocated by National Institutes of Health, European Commission, and Wellcome Trust.

Category:Bioinformatics Category:Plant genomics Category:Arabidopsis thaliana