Bio-Analytic Resource (BAR)

Bio-Analytic Resource (BAR) provides computational analyses for plant functional genomics by enabling gene expression, coexpression, promoter, protein–protein interaction, and enrichment analyses across genomes, transcriptomes, proteomes, and epigenomes with primary focus on Arabidopsis.

Key Features:

• Gene Expression and Coexpression Analysis: Performs gene expression profiling and coexpression network analysis to assess functional relationships between genes.
• Promoter Analyses: Analyzes promoter sequences to identify regulatory elements that control gene expression.
• Functional Classification Enrichment Analysis: Conducts enrichment analyses on gene sets to identify overrepresented biological functions or pathways.
• Protein-Protein Interaction Examination: Examines protein–protein interactions to elucidate cellular processes and identify potential targets for genetic manipulation or therapeutic intervention.
• Integration of Multi-source Data: Integrates data from multiple sources to provide a comprehensive view of biological systems and support hypothesis generation and cross-species applications.
• Expression Profile Definition and Gene Identification (Expression Angler): Defines specific expression profiles and identifies genes that match those profiles to aid design of reporter constructs and generation of expression markers.
• Cis-element Prediction and Exploration (Cistome): Predicts and explores cis-elements in promoters of co-expressed genes to investigate gene regulatory networks.

Scientific Applications:

• Plant functional genomics: Supports analysis of gene function and regulation in plants, with emphasis on Arabidopsis.
• Multi-omic dataset analysis: Enables examination of genomes, transcriptomes, proteomes, and epigenomes to interpret large-scale biological data.
• Hypothesis generation: Facilitates identification of regulatory relationships and candidate genes for experimental validation.
• Reporter and marker development: Aids design of reporter constructs and selection of gene expression markers based on defined expression profiles.
• Translational research: Provides analyses that can inform comparative and translational studies in species beyond Arabidopsis.
• Cellular process elucidation: Assists in elucidating cellular processes and identifying targets for genetic manipulation or therapeutic investigation.

Methodology:

Computational methods explicitly include gene expression profiling, coexpression network analysis, promoter analysis, functional enrichment analysis, protein–protein interaction analysis, integration of multi-source data, Expression Angler-based profile matching, and Cistome cis-element prediction.