MISO

MISO quantifies isoform- and exon-level expression from RNA-seq cDNA fragments using a probabilistic mixture-of-isoforms model to study alternative splicing.

Key Features:

• Probabilistic mixture-of-isoforms model: Implements a probabilistic mixture-of-isoforms model to estimate expression of alternatively spliced isoforms and exons.
• mRNA fragment length modeling: Incorporates the mRNA fragment length distribution from paired-end RNA-seq to improve isoform-level expression estimates.
• Isoform and exon quantification: Estimates expression levels of isoforms and alternatively spliced exons from high-throughput RNA-seq cDNA fragments.
• Confidence estimation: Assesses statistical confidence in expression estimates.
• Differential regulation detection: Detects differentially regulated exons or isoforms.
• Experimental design guidance: Provides guidelines for designing RNA-seq experiments aimed at studying gene and isoform expression.

Scientific Applications:

• Alternative splicing analysis: Quantitative analysis of alternative splicing and isoform regulation from RNA-seq data.
• Splicing factor characterization: Has been used to implicate the RNA-binding protein hnRNP H1 in regulation of alternative cleavage and polyadenylation, corroborated by CLIP-seq analysis.
• Pre-mRNA processing insights: Provides functional insights into pre-mRNA processing and splicing dynamics.
• Experimental optimization: Informs design of RNA-seq experiments for gene- and isoform-level expression studies.

Methodology:

Uses a probabilistic mixture-of-isoforms model to infer isoform regulation from RNA-seq cDNA fragments, models mRNA fragment length distribution from paired-end RNA-seq, estimates isoform and exon expression, computes confidence measures, and detects differentially regulated exons or isoforms.