title: Alternative Splicing Signatures in RNA-seq Data: Percent Spliced in (PSI).
abstract: Thousands of alternative exons are spliced out of messenger RNA to increase protein diversity. High-throughput sequencing of short cDNA fragments (RNA-seq) generates a genome-wide snapshot of these post-transcriptional processes. RNA-seq reads yield insights into the regulation of alternative splicing by revealing the usage of known or unknown splice sites as well as the expression level of exons. Constitutive exons are never covered by split alignments, whereas alternative exonic parts are located within highly expressed splicing junctions. The ratio between reads including or excluding exons, also known as percent spliced in index (PSI), indicates how efficiently sequences of interest are spliced into transcripts. This protocol describes a method to calculate the PSI without prior knowledge of splicing patterns. It provides a quantitative, global assessment of exon usage that can be integrated with other tools that identify differential isoform processing. Novel, complex splicing events along a genetic locus can be visualized in an exon-centric manner and compared across conditions.
authors.affiliation: Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.|National Heart Center Singapore, Singapore.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Schafer
authors.affiliation: Duke-National University of Singapore, Singapore.
authors.forename: Kui
authors.initials: K
authors.lastname: Miao
authors.affiliation: Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts.
authors.forename: Craig C
authors.initials: CC
authors.lastname: Benson
authors.affiliation: Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.|Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.|Present address: Institute of Computational Biology, Helmholtz Zentrum München, Neuerberg, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Heinig
authors.affiliation: National Heart Center Singapore, Singapore.|Duke-National University of Singapore, Singapore.|National Heart and Lung Institute, Imperial College London, London, United Kingdom.
authors.forename: Stuart A
authors.initials: SA
authors.lastname: Cook
authors.affiliation: Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.|German Center for Cardiovascular Research (partner site), Berlin, Germany.|Charité-Universitätsmedizin, Berlin, Germany.
authors.forename: Norbert
authors.initials: N
authors.lastname: Hubner
mesh_terms: D017398:Alternative Splicing; D019295:Computational Biology / Q000379:methods; D005091:Exons; D020869:Gene Expression Profiling / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D058977:Molecular Sequence Annotation; D017423:Sequence Analysis, RNA; D012984:Software; D059467:Transcriptome
keywords: PSI; RNA-seq; alternative splicing; isoform expression; percent spliced in; transcript processing