Comparative transcriptomics analysis pipeline for the meta-analysis of phylogenetically divergent datasets (CoRMAP)

Area of Science:

• Genomics
• Bioinformatics
• Transcriptomics

Background:

• RNA-Seq is widely used to measure gene transcription levels across various biological contexts.
• Technical variations in RNA-Seq studies hinder comparative analysis and meta-analyses.
• Extracting comparable gene expression data from diverse RNA-Seq experiments is challenging.

Purpose of the Study:

• To introduce a meta-analysis tool, Comparative RNA-Seq Metadata Analysis Pipeline (CoRMAP), for standardized gene expression comparison.
• To enable the retrieval and comparison of gene expression data from disparate RNA-Seq studies.
• To facilitate cross-species gene expression analysis without reliance on reference genomes.

Main Methods:

• CoRMAP utilizes de novo assembly and standardized gene expression tools.
• Ortholog identification is performed using the OrthoMCL algorithm for accurate gene comparisons.
• Orthogroup assignments ensure reliable comparison of gene expression levels across experiments and species.

Main Results:

• CoRMAP was demonstrated on two mouse brain transcriptomes with differing sequencing and analysis methods.
• The tool successfully retrieved and compared gene expression data from distinct studies.
• Performance comparison with a functional mapping tool was conducted.

Conclusions:

• CoRMAP offers a framework for meta-analysis of RNA-Seq data from diverse taxonomic groups.
• The method standardizes assembly and analysis for gene expression level retrieval and comparison.
• CoRMAP's independence from reference genomes allows direct comparison across a wide range of organisms.