Skip Navigation

Nucleic Acids Research 2005 33(14):4612-4617; doi:10.1093/nar/gki771
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (2734K) Freely available
Right arrow Screen PDF (360K) Freely available
Right arrow Supplementary Material
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (4)
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Eisenberg, E.
Right arrow Articles by Levanon, E. Y.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Eisenberg, E.
Right arrow Articles by Levanon, E. Y.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 12 August 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

Identification of RNA editing sites in the SNP database

Eli Eisenberg1, Konstantin Adamsky2, Lital Cohen2, Ninette Amariglio2, Abraham Hirshberg3, Gideon Rechavi2 and Erez Y. Levanon2,4,*

1School of Physics and Astronomy, Raymond and Beverly Sackler Faculty of Exact Sciences, TAU Tel Aviv 69978, Israel 2Department of Pediatric Hemato-Oncology, Safra Children's Hospital, Sheba Medical Center and Sackler School of Medicine, Tel Aviv University Tel Aviv 69978, Israel 3Department of Oral Pathology, School of Dental Medicine, Tel Aviv University Tel Aviv 69978, Israel 4Compugen Ltd 72 Pinchas Rosen Street, Tel Aviv 69512, Israel

*To whom correspondence should be addressed. Tel: +972 3 765 8503; Fax: +972 3 765 8555; Email: erez{at}compugen.co.il

Received July 7, 2005. Revised July 29, 2005. Accepted July 29, 2005.

The relationship between human inherited genomic variations and phenotypic differences has been the focus of much research effort in recent years. These studies benefit from millions of single-nucleotide polymorphism (SNP) records available in public databases, such as dbSNP. The importance of identifying false dbSNP records increases with the growing role played by SNPs in linkage analysis for disease traits. In particular, the emerging understanding of the abundance of DNA and RNA editing calls for a careful distinction between inherited SNPs and somatic DNA and RNA modifications. In order to demonstrate that some of the SNP database records are actually somatic modification, we focus on one type of these modifications, namely A-to-I RNA editing, and present evidence for hundreds of dbSNP records that are actually editing sites. We provide a list of 102 RNA editing sites previously annotated in dbSNP database as SNPs, and experimentally validate seven of these. Interestingly, we show how dbSNP can serve as a starting point to look for new editing sites. Our results, for this particular type of RNA editing, demonstrate the need for a careful analysis of SNP databases in light of the increasing recognition of the significance of somatic sequence modifications.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 RNAHome page
W. M. Gommans, N. E. Tatalias, C. P. Sie, D. Dupuis, N. Vendetti, L. Smith, R. Kaushal, and S. Maas
Screening of human SNP database identifies recoding sites of A-to-I RNA editing
RNA, October 1, 2008; 14(10): 2074 - 2085.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
D. J. Sugarbaker, W. G. Richards, G. J. Gordon, L. Dong, A. De Rienzo, G. Maulik, J. N. Glickman, L. R. Chirieac, M.-L. Hartman, B. E. Taillon, et al.
Transcriptome sequencing of malignant pleural mesothelioma tumors
PNAS, March 4, 2008; 105(9): 3521 - 3526.
[Abstract] [Full Text] [PDF]

Home page
 Brief Funct Genomic ProteomicHome page
E. Y. Levanon and E. Eisenberg
Algorithmic approaches for identification of RNA editing sites
Brief Funct Genomic Proteomic, March 1, 2006; 5(1): 43 - 45.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.