EXPath

EXPath infers plant metabolic pathways from gene expression profiles derived from microarray and RNA-seq datasets across developmental stages and conditions.

Key Features:

• Comprehensive Data Collection: Integrates over 1,881 microarray and 978 RNA-seq samples from six model plants—Arabidopsis thaliana, Oryza sativa, Zea mays, Solanum lycopersicum, Glycine max, and Medicago truncatula—covering developmental stages and conditions such as biotic stress, abiotic stress, and hormone secretion.
• Gene Correlation Networks: Constructs correlation networks from groups of genes to identify co-expressed genes and their associated metabolic pathways.
• Promoter Analysis: Investigates transcription factors on the promoters of co-expressed genes to elucidate potential regulatory relationships.
• Enrichment and Ontology Tools: Provides hierarchical figures of enriched Gene Ontology (GO) terms and performs pathways enrichment analysis using KEGG pathways.
• Analysis Functions: Supports Gene Search, Pathway Search, Differentially Expressed Genes (DEGs) Search, Pathways/GO Enrichment, and Coexpression Analysis.
• Differential Expression and Coexpression: Identifies DEGs and performs coexpression analysis to link expression changes to metabolic pathways.

Scientific Applications:

• Metabolic Pathway Inference: Infers metabolic pathways in plants from condition-specific gene expression profiles.
• Transcriptional Regulatory Mechanism Analysis: Identifies candidate transcription factors and regulatory relationships acting on promoters of co-expressed genes.
• Differential Expression Studies: Detects DEGs under biotic stress, abiotic stress, hormone-related conditions, and developmental stages.
• Comparative Transcriptomics: Enables comparative analysis of gene expression and pathway associations across six model plant species.

Methodology:

Computational methods include constructing gene correlation networks, promoter analysis to map transcription factors on promoters of co-expressed genes, hierarchical GO enrichment visualization, KEGG pathway enrichment analysis, DEGs identification, and coexpression analysis.