TreeExp

TreeExp estimates gene expression conservation (W) from multi-species RNA-seq data using a gamma distribution model and empirical Bayesian inference.

Key Features:

• Gamma distribution model: Employs a gamma distribution to quantify the strength of expression conservation (W) for each gene.
• Empirical Bayesian estimation: Implements an empirical Bayesian procedure to estimate W for individual genes using high-throughput RNA-seq datasets.
• estParaGamma: Estimates parameters related to the gamma distribution model.
• estParaQ: Assists in parameter estimation within the Bayesian framework.
• estParaWBayesian: Estimates W using an empirical Bayesian approach.
• Optimized data handling: Includes input formatting and normalization procedures for RNA-seq data processing.
• Pair-wise distance evaluation and expression character tree inference: Computes pair-wise distances between gene expression profiles and infers expression character trees.
• Preliminary phylogenetic network analysis: Provides preliminary phylogenetic network analyses to explore evolutionary scenarios involving gene flow or hybridization.

Scientific Applications:

• Expression conservation analysis: Quantifying gene-specific expression conservation (W) across species from RNA-seq data.
• Stabilizing selection assessment: Assessing the influence of stabilizing selection on gene expression levels using estimated W values.
• Comparative evolutionary studies: Investigating gene function, adaptation, and evolutionary trajectories via comparative expression analysis.
• Expression-based phylogenetics: Inferring expression character trees and exploring phylogenetic networks to study evolutionary relationships and events such as gene flow or hybridization.

Methodology:

Uses a gamma distribution model to represent expression conservation and an empirical Bayesian procedure to estimate W with functions estParaGamma, estParaQ, and estParaWBayesian; includes optimized input formatting and normalization, pair-wise distance computation, expression character tree inference, and preliminary phylogenetic network analysis.