Skip Navigation

Nucleic Acids Research 2004 32(20):6104-6110; doi:10.1093/nar/gkh937
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (288K) Freely available
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 (15)
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Silva, A. P. M.
Right arrow Articles by Camargo, A. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Silva, A. P. M.
Right arrow Articles by Camargo, A. A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 23 November 2004

Nucleic Acids Research, Vol. 32 No. 20 © Oxford University Press 2004; all rights reserved

The impact of SNPs on the interpretation of SAGE and MPSS experimental data

Ana Paula M. Silva, Jorge E. S. De Souza1,2, Pedro A. F. Galante1,3, Gregory J. Riggins4, Sandro J. De Souza1 and Anamaria A. Camargo*

Laboratory of Molecular Biology and Genomics and 1 Laboratory of Computational Biology, Ludwig Institute for Cancer Research, 01509-010, São Paulo, SP, Brazil, 2 Interunit in Bioinformatics and 3 Department of Biochemistry, University of São Paulo, 05508-900, São Paulo, SP, Brazil and 4 John Hopkins University School of Medicine, 21224, Baltimore, MD, USA

* To whom correspondence should be addressed at Rua Prof. Antonio Prudente 109, 4th floor, 01509-010 São Paulo, SP, Brazil. Tel: +55 11 3388 3248; Fax: +55 11 3207 7001; Email: anamaria{at}compbio.ludwig.org.br

Received August 5, 2004; Revised September 24, 2004; Accepted October 25, 2004

Serial Analysis of Gene Expression (SAGE) and Massively Parallel Signature Sequencing (MPSS) are powerful techniques for gene expression analysis. A crucial step in analyzing SAGE and MPSS data is the assignment of experimentally obtained tags to a known transcript. However, tag to transcript assignment is not a straightforward process since alternative tags for a given transcript can also be experimentally obtained. Here, we have evaluated the impact of Single Nucleotide Polymorphisms (SNPs) on the generation of alternative SAGE and MPSS tags. This was achieved through the construction of a reference database of SNP-associated alternative tags, which has been integrated with SAGE Genie. A total of 2020 SNP-associated alternative tags were catalogued in our reference database and at least one SNP-associated alternative tag was observed for ~8.6% of all known human genes. A significant fraction (61.9%) of these alternative tags matched a list of experimentally obtained tags, validating their existence. In addition, the origin of four out of five SNP-associated alternative MPSS tags was experimentally confirmed through the use of the GLGI-MPSS protocol (Generation of Long cDNA fragments for Gene Identification). The availability of our SNP-associated alternative tag database will certainly improve the interpretation of SAGE and MPSS experiments.


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
 Proc. Natl. Acad. Sci. USAHome page
J. C. Roach, K. D. Smith, K. L. Strobe, S. M. Nissen, C. D. Haudenschild, D. Zhou, T. J. Vasicek, G. A. Held, G. A. Stolovitzky, L. E. Hood, et al.
Transcription factor expression in lipopolysaccharide-activated peripheral-blood-derived mononuclear cells
PNAS, October 9, 2007; 104(41): 16245 - 16250.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
E. Rivals, A. Boureux, M. Lejeune, F. Ottones, O. Pecharroman Perez, J. Tarhio, F. Pierrat, F. Ruffle, T. Commes, and J. Marti
Transcriptome annotation using tandem SAGE tags
Nucleic Acids Res., September 27, 2007; 35(17): e108 - e108.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
P. A. F. Galante, J. Trimarchi, C. L. Cepko, S. J. de Souza, L. Ohno-Machado, and W. P. Kuo
Automatic correspondence of tags and genes (ACTG): a tool for the analysis of SAGE, MPSS and SBS data
Bioinformatics, April 1, 2007; 23(7): 903 - 905.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Physiol. Lung Cell. Mol. Physiol.Home page
J. B. Vos, N. A. Datson, K. F. Rabe, and P. S. Hiemstra
Exploring host-pathogen interactions at the epithelial surface: application of transcriptomics in lung biology
Am J Physiol Lung Cell Mol Physiol, February 1, 2007; 292(2): L367 - L377.
[Abstract] [Full Text] [PDF]

Home page
 Stem CellsHome page
M. Richards, S.-P. Tan, W.-K. Chan, and A. Bongso
Reverse Serial Analysis of Gene Expression (SAGE) Characterization of Orphan SAGE Tags from Human Embryonic Stem Cells Identifies the Presence of Novel Transcripts and Antisense Transcription of Key Pluripotency Genes
Stem Cells, May 1, 2006; 24(5): 1162 - 1173.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Fedurco, A. Romieu, S. Williams, I. Lawrence, and G. Turcatti
BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies
Nucleic Acids Res., February 9, 2006; 34(3): e22 - e22.
[Abstract] [Full Text] [PDF]

Home page
 Physiol. GenomicsHome page
J. B. Vos, M. A. van Sterkenburg, K. F. Rabe, J. Schalkwijk, P. S. Hiemstra, and N. A. Datson
Transcriptional response of bronchial epithelial cells to Pseudomonas aeruginosa: identification of early mediators of host defense
Physiol Genomics, May 11, 2005; 21(3): 324 - 336.
[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.