[ged] a paper for the journal club next week

[Likit Preeyanon]

Hi, guys

The paper is not new but it discusses a program that I'm currently using to identify alternative splicing in my RNA-Seq study.

Analysis and design of RNA sequencing experiments for identifying isoform regulation.

Abstract
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Through alternative splicing, most human genes express multiple isoforms that often differ in function. To infer isoform regulation from high-throughput sequencing of cDNA fragments (RNA-seq), we developed the mixture-of-isoforms (MISO) model, a statistical model that estimates expression of alternatively spliced exons and isoforms and assesses confidence in these estimates. Incorporation of mRNA fragment length distribution in paired-end RNA-seq greatly improved estimation of alternative-splicing levels. MISO also detects differentially regulated exons or isoforms. Application of MISO implicated the RNA splicing factor hnRNP H1 in the regulation of alternative cleavage and polyadenylation, a role that was supported by UV cross-linking-immunoprecipitation sequencing (CLIP-seq) analysis in human cells. Our results provide a probabilistic framework for RNA-seq analysis, give functional insights into pre-mRNA processing and yield guidelines for the optimal design of RNA-seq experiments for studies of gene and isoform expression.


Nature Publishing Group, 7(12), 1009–1015. doi:10.1038/nmeth.1528
Katz, Y., Wang, E. T., Airoldi, E. M., & Burge, C. B. (2010). 


See you on Monday!
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