Arboretum

Arboretum infers coexpressed gene modules across multiple species and reconstructs their evolutionary trajectories by integrating gene expression profiles with species and gene phylogenies.

Key Features:

• Integration of Multi-Species Data: Combines expression profiles from multiple species within a phylogenetic framework to enable cross-species comparisons.
• Phylogenetic Contextualization: Incorporates both species and gene phylogenies to place expression patterns in evolutionary context.
• Inference of Coexpressed Gene Modules: Identifies clusters of coexpressed genes (modules) in extant species.
• Evolutionary History Reconstruction: Reconstructs the evolutionary history of gene modules to trace ancestral regulatory networks and adaptations.
• Conservation and Divergence Analysis: Computes novel measures to quantify conservation and divergence in gene regulatory modules, including changes in gene content and expression such as module expansion.

Scientific Applications:

• Studying Evolutionary Responses: Applied to transcriptional responses of eight species of Ascomycota fungi to heat shock, revealing substantial conservation and divergence primarily via module expansion.
• Reconstructing Ancestral Modules: Reconstructs ancestral environmental stress response (ESR) modules to investigate evolution of regulatory networks.
• Comparative Analysis of Stress Responses: Compares responses across conditions (for example, heat shock versus glucose depletion) to characterize evolutionary divergence in gene regulation.

Methodology:

Arboretum employs a scalable computational approach that leverages phylogenetic information to align expression data across species, identify conserved coexpression patterns, and assess evolutionary changes using novel metrics; explicitly it integrates gene expression profiles with phylogenetic trees, detects clusters of coexpressed genes using advanced statistical techniques, and applies metrics to quantify conservation and divergence in gene regulatory modules.