CoRMAP

CoRMAP performs standardized meta-analysis of RNA-Seq gene expression datasets to enable cross-species comparative transcriptomic studies using de novo assembly and orthogroup assignments.

Key Features:

• Standardized Analysis Framework: Provides a framework that applies de novo assembly and standardized gene expression tools to ensure consistency and comparability across datasets.
• Orthogroup Assignments: Implements OrthoMCL to assign orthologous groups for accurate cross-species gene expression comparisons.
• Reference Genome Independence: Operates without reliance on reference genomes, enabling analyses across diverse and divergent taxonomic groups.
• Comparative Analysis Capability: Retrieves and compares gene expression levels from published RNA-Seq datasets to support large-scale comparative studies of transcriptional processes.

Scientific Applications:

• Cross-species transcriptomics: Comparative analysis of gene expression profiles across multiple species using orthogroup-based comparisons.
• Meta-analysis of RNA-Seq data: Harmonization and meta-analysis of datasets from different tissues, experimental conditions, and sequencing technologies.
• Method demonstration: Validation and demonstration using two mouse brain transcriptomes collected at different times with varying sequencing technologies and analysis methods.

Methodology:

Extraction of RNA-Seq data, standardized de novo assembly of transcripts without reference genomes, orthogroup assignment using OrthoMCL, and application of standardized tools for expression analysis.