FLIBase

FLIBase annotates full-length spliced isoforms in human cancers and tissues by integrating long-read and short-read RNA sequencing to characterize transcriptome diversity.

Key Features:

• Integration of Long-Read and Short-Read Sequencing Data: Integrates data from 351 long-read and 12,469 short-read RNA sequencing samples to improve representation of full-length transcripts.
• Extensive Isoform Repository: Contains 983,789 full-length spliced isoforms identified from long-read sequences and supported by short-read splice junction evidence.
• Annotated and Unannotated Isoforms: Records 188,248 annotated isoforms and 795,541 unannotated isoforms to distinguish characterized transcripts from novel candidates.

Scientific Applications:

• Transcriptome and Proteome Composition Analysis: Enables analysis of transcriptome diversity and resultant proteome composition in human cells.
• Identification of Tumor-Specific RNA Transcripts: Facilitates discovery of previously unannotated and tumor-specific isoforms that can be sources of immunogenic recurrent neoantigens.
• Development of Diagnostic and Therapeutic Strategies: Supports identification of novel isoforms and tumor-specific transcripts for RNA-based diagnostic and therapeutic development across cancers.

Methodology:

Identifies full-length isoforms from long-read sequences and validates splice junctions using short-read exon-exon splice junction evidence, combining analysis of the provided long-read and short-read RNA-seq samples.