NDLI: Workshop: Using a transcript catalog and paired-end RNA-Seq data to identify differential alternative splicing

Content Provider	IEEE Xplore Digital Library
Author	Howard, B.E. Xiaoping Tan Veronese, P. Heber, S.
Copyright Year	2011
Description	Author affiliation: Bioinformatics Research Center, North Carolina State University, Raleigh, 27606, USA (Howard, B.E.; Heber, S.) \|\| Department of Plant Pathology, North Carolina State University, Raleigh, 27606, USA (Xiaoping Tan; Veronese, P.)
Abstract	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.
Starting Page	270
Ending Page	270
File Size	106588
Page Count	1
File Format	PDF
ISBN	9781612848518
e-ISBN	9781612848525
DOI	10.1109/ICCABS.2011.5729924
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2011-02-03
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Splicing USA Councils Adaptation model Focusing Catalogs Immune system Diseases
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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