PlantGenIE.org

PlantGenIE.org enables exploration and analysis of large-scale plant genomics and transcriptomics datasets to support comparative genomics, gene expression and coexpression network studies in species including Populus (including Populus tremula), conifers, and Arabidopsis thaliana.

Key Features:

• Genome Browsers: Visual navigation of genomic sequences for Populus, conifers, and Arabidopsis thaliana.
• Gene List Annotation: Annotation of gene lists providing functional insights and contextual information.
• BLAST Homology Searches: BLAST searches to identify homologous sequences for comparative analyses.
• Gene Information Pages: Detailed pages presenting individual gene expression profiles and functional annotations.
• Expression Networks and Visualization Tools: Visualization and analysis of gene expression networks and coexpression relationships.
• Community Annotation via WebApollo Integration: Support for community-driven genome annotation updates through WebApollo.
• RNA-Seq Expression Atlas for Populus tremula: Integration of a genome-wide RNA-Seq expression atlas for Populus tremula into the expression tools.
• ComPlEx Resource Integration: Updated ComPlEx resource for comparative plant expression analyses and studies of coexpression network conservation.

Scientific Applications:

• Comparative Genomics: Homology searches and comparative expression analyses to study evolutionary relationships and functional conservation among plant species.
• Gene Expression Studies: Use of the RNA-Seq atlas and expression network visualizations to investigate gene regulation and expression patterns across conditions and developmental stages.
• Community Collaboration: WebApollo-enabled collaborative genome annotation to improve annotation accuracy and coverage.

Methodology:

Computational methods explicitly include BLAST homology searches, an RNA-Seq expression atlas for Populus tremula, gene expression and coexpression network visualization, integration of the ComPlEx comparative expression resource, and WebApollo-based community annotation.