ExoPLOT

ExoPLOT analyzes alternative splicing events involving transposed elements (TEs) to quantify and visualize TE-derived exon inclusion across seven human tissues and developmental stages using RNA high-throughput sequencing data from 313 transcriptomes.

Key Features:

• Alternative Splicing Analysis: Examines alternatively spliced exons with a focus on involvement of transposed elements (TEs) across biological samples.
• Visualization and Quantification: Visualizes relative expression levels of alternative transcripts and quantifies TE-derived exon inclusion across developmental stages and tissues.
• Database Integration: Integrates a database of 1151 repeat-masked, exonized TEs from prominent transposon families alongside human consensus coding sequences (CCDS).
• Preprocessing Efficiency: Preprocesses RNA deep sequencing datasets to reduce processing times for downstream alternative splicing analyses.
• Customizable Analysis: Supports coordinate-based, customizable study of TE-derived exons and other alternative RNA isoforms.

Scientific Applications:

• Functional Insights into TEs: Assesses contributions of exonized TEs within human coding sequences (CDS) to gene function and regulation.
• Developmental and Tissue-Specific Expression: Enables study of splicing dynamics across cerebrum, cerebellum, heart, kidney, liver, ovary, and testis at pre- and postnatal developmental stages.
• Evolutionary Linkages: Investigates exonization and exaptation processes associated with TE-derived exons in the human genome.

Methodology:

Leverages RNA high-throughput sequencing data from 313 transcriptomes representing pre- and postnatal developmental stages; preprocesses RNA deep sequencing datasets; screens and quantifies TE-derived exon splicing dynamics; and maps recently described exonized sequences onto the transcriptome libraries for visualization.