Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments.
Alternative splicing, polyadenylation of pre-messenger RNA molecules and differential promoter usage can produce a variety of transcript isoforms whose respective expression levels are regulated in time and space, thus contributing specific biological functions. However, the repertoire of mammalian alternative transcripts and their regulation are still poorly understood. Second-generation sequencing is now opening unprecedented routes to address the analysis of entire transcriptomes. Here, we developed methods that allow the prediction and quantification of alternative isoforms derived solely from exon expression levels in RNA-Seq data. These are based on an explicit statistical model and enable the prediction of alternative isoforms within or between conditions using any known gene annotation, as well as the relative quantification of known transcript structures. Applying these methods to a human RNA-Seq dataset, we validated a significant fraction of the predictions by RT-PCR. Data further showed that these predictions correlated well with information originating from junction reads. A direct comparison with exon arrays indicated improved performances of RNA-Seq over microarrays in the prediction of skipped exons. Altogether, the set of methods presented here comprehensively addresses multiple aspects of alternative isoform analysis. The software is available as an open-source R-package called Solas at http://cmb.molgen.mpg.de/2ndGenerationSequencing/Solas/.
Richard
Hugues
H
Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestr 73, 14195 Berlin, Germany. hugues.richard@molgen.mpg.de
Schulz
Marcel H
MH
Sultan
Marc
M
Nürnberger
Asja
A
Schrinner
Sabine
S
Balzereit
Daniela
D
Dagand
Emilie
E
Rasche
Axel
A
Lehrach
Hans
H
Vingron
Martin
M
Haas
Stefan A
SA
Yaspo
Marie-Laure
ML
D017398:Alternative Splicing; D002460:Cell Line; D003198:Computer Simulation; D005091:Exons; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D006801:Humans; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis; D020033:Protein Isoforms / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA
D020033:Protein Isoforms