Cortexa: a comprehensive resource for studying gene expression and alternative splicing in the murine brain

Area of Science:

• Neuroscience
• Bioinformatics
• Genomics

Background:

• Gene expression and alternative splicing are crucial for brain development and cell identity.
• Understanding their functional implications, particularly alternative splicing, remains challenging.
• Experimental neuroscientists often need bioinformatics support for analyzing splicing data.

Purpose of the Study:

• To provide a user-friendly web portal for analyzing mouse brain RNA-sequencing data.
• To facilitate the visualization and comparison of gene expression and alternative splicing patterns.
• To support researchers in integrating and analyzing their own splicing datasets.

Main Methods:

• Development of Cortexa, a web portal integrating mouse cerebral cortex and hippocampus RNA-sequencing datasets.
• Incorporation of SplicePCA tool for user data integration and comparison with neocortical splicing patterns.
• Standardization and provision of downloadable gene expression and alternative splicing datasets.

Main Results:

• Cortexa offers visualization of gene expression and alternative splicing patterns.
• SplicePCA enables comparison of user datasets with cell-specific or developmental splicing patterns.
• All data is downloadable for downstream analysis, reducing preprocessing needs.

Conclusions:

• Cortexa serves as a valuable resource for studying gene expression and alternative splicing in the mouse brain.
• The portal simplifies the analysis of complex RNA-sequencing data for neuroscientists.
• Accessible at https://cortexa-rna.com/, Cortexa promotes further research into brain regulatory processes.