Name
Title | ||
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Workshop: Using a transcript catalog and paired-end RNA-Seq data to identify differential alternative splicing |
Abstract | ||
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Alternative splicing is one of the major contributors to transcript and protein diversity in many higher eukaryotes including humans, but so far the extent and impact of alternative splicing in plants has not been thoroughly investigated [1]. The purpose of our NSF-Eager grant is to use high-throughput RNA sequencing of the transcriptome to assess the role of alternative splicing in the host-pathogen interaction between Arabidopsis thaliana and Pseudomonas syringae. Although previous studies have demonstrated that alternative splicing plays an important role for individual genes during this interaction [2, 3], our whole-genome approach will investigate thousands of potential splicing events simultaneously. Our method employs a linear models framework to estimate the ratios of known isoforms in a given sample, taking into account the non-uniformity of RNA-Sequencing reads along the targeted transcripts [4]. Recently, we have adapted our method in order to accommodate paired-end sequencing technology. Briefly, we map reads to a transcript catalog (TAIR 10 gene models), partition the reads according to their compatibility with these models, identify reads that are informative for isoform quantification, and then use a linear model to estimate isoform expression ratios for each gene. Our results provide a first approximation of the extent of pathogen-induced alternative splicing and so far indicate evidence for a wide variety of novel alternative transcripts. In addition, the set of differentially spliced genes appears to be independent of the set of differentially expressed genes, providing new evidence for a hidden layer of regulation in the transcriptome [5]. Hence, the set of differentially spliced genes provides a promising set of candidate genes that researchers may have previously overlooked by focusing solely on differential gene expression. |
Year | DOI | Venue |
|---|---|---|
2011 | 10.1109/ICCABS.2011.5729924 | Computational Advances in Bio and Medical Sciences |
Keywords | Field | DocType |
novel alternative transcript,gene model,transcript catalog,promising set,differential alternative splicing,individual gene,potential splicing event,differentially spliced gene,differential gene expression,pathogen-induced alternative splicing,paired-end rna-seq data,candidate gene,alternative splicing,transcriptome,immune system,linear model,splicing,genetics,genomics,macromolecules,microorganisms,gene expression,high throughput,molecular biophysics | Gene,Candidate gene,RNA-Seq,Biology,Transcriptome,Gene expression,Alternative splicing,Genomics,RNA splicing,Bioinformatics,Genetics | Conference |
ISBN | Citations | PageRank |
978-1-61284-851-8 | 0 | 0.34 |
References | Authors | |
1 | 4 | |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Brian E. Howard | 1 | 26 | 4.24 |
| Xiaoping Tan | 2 | 0 | 0.34 |
| Paola Veronese | 3 | 0 | 0.68 |
| Steffen Heber | 4 | 219 | 22.88 |