Animal IsomiR and MiRNA Expression Explorer (AIMEE) is an open-source, Shiny-based browser that facilitates miRNA data exploration, visualization, and the export of raw and normalized data for additional downstream analyses. AIMEE utilizes expression matrices generated by the Framework for Analysis and Refinement of miRNAs (FarmiR) pipeline and associated sample metadata as input for multiple visualization and analysis modules. These include...
- Quality control and processing attrition
- Interrogating expression of Ref-miRs/isomiRs of interest
- Target prediction tables with Gene Ontology (GO) over-representation analysis
- Assessing inter- or intra-tissue Ref-miR/isomiR rank aggregation and tissue-specificity
AIMEE contains the largest collection of processed equine miRNA expression data from 461 samples across 61 presumed healthy tissue types. Data was sourced from small RNA-seq generated as part of FarmiR/AIMEE development (primary), the equine Functional Annotation of Animal Genomes (FAANG) project, and other public sources (public).
The primary, FAANG, and public data processed with FarmiR and accessible via AIMEE, provide valuable information about the critical roles miRNAs play in tissue-specific regulatory functions contributing to equine production and health.
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Mapping the way forward for equine research
Dr. Jonah Cullen, a postdoctoral researcher, embarks on a groundbreaking project funded by the USDA. With a $218,000 grant, he pioneers the development of pengenome and pantranscripitome graphs for horses. These tools, a first for the species, promise to revolutionize equine genetics, offering a comprehensive understanding of genetic diversity and expression. Cullen's work, aided by advanced computational methods, opens new frontiers in equine genetic research.