LivestockExp

LivestockExp aggregates and uniformly processes 43,710 RNA-seq samples from livestock animals and related species across six orders to enable comparative analysis of gene expression and alternative splicing.

Key Features:

• Extensive Dataset: Contains 43,710 uniformly processed RNA-seq samples from livestock animals and related species spanning six orders.
• Advanced Querying Functions: Provides robust querying to search and retrieve gene expression and alternative splicing data.
• Differential/Specific Expression Analysis: Performs differential expression and species-specific expression analyses to identify genes with altered transcriptional levels.
• Co-expression Network Analysis: Constructs gene co-expression networks to investigate regulatory relationships and gene interactions.
• Cross-species Gene Expression Conservation Analysis: Analyzes conservation of gene expression across species to assess evolutionary patterns.
• Data Integration and Co-analysis: Supports re-analysis of public RNA-seq datasets and co-analysis with user-provided datasets.
• Visualization Tools: Produces visualizations to interpret gene expression and alternative splicing results.
• External Database Links: Integrates links to external databases for extended annotation and cross-referencing.

Scientific Applications:

• Genetic Improvement: Identifies expression and alternative splicing variants associated with desirable phenotypes to inform breeding and genetic improvement.
• Phenotypic Trait Analysis: Links gene expression and splicing patterns to traits such as growth rate, disease resistance, and productivity to investigate genetic bases of phenotypes.
• Comparative Genomics: Enables cross-species comparisons to identify conserved gene expression patterns and derive evolutionary insights.

Methodology:

Uniform processing of 43,710 RNA-seq samples; differential and species-specific expression analysis; co-expression network construction; cross-species gene expression conservation analysis; re-analysis and co-analysis of public and user-provided RNA-seq datasets.