PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level
Bioinformatics Unit and 1 Hereditary Endocrine Cancer Group, Centro Nacional de Investigaciones Oncológicas (CNIO) Madrid, Spain
* To whom correspondence should be addressed. Tel: +34 912246919; Fax: +34 912246972; Email: jdopazo{at}cnio.es
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
Received February 3, 2004; Revised and Accepted April 15, 2004
We have developed a web tool, PupaSNP Finder (PupaSNP for short), for high-throughput searching for single nucleotide polymorphisms (SNPs) with potential phenotypic effect. PupaSNP takes as its input lists of genes (or generates them from chromosomal coordinates) and retrieves SNPs that could affect the conserved regions that the cellular machinery uses for the correct processing of genes (intron/exon boundaries or exonic splicing enhancers), predicted transcription factor binding sites (TFBS) and changes in amino acids in the proteins. The program uses the mapping of SNPs in the genome provided by Ensembl. Additionally, user-defined SNPs (not yet mapped in the genome) can be easily provided to the program. Also, additional functional information from Gene Ontology, OMIM and homologies in other model organisms is provided. In contrast to other programs already available, which focus only on SNPs with possible effect in the protein, PupaSNP includes SNPs with possible transcriptional effect. PupaSNP will be of significant help in studies of multifactorial disorders, where the use of functional SNPs will increase the sensitivity of identification of the genes responsible for the disease. The PupaSNP web interface is accessible through http://pupasnp.bioinfo.cnio.es.
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 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.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  G. A Reeves, D. Talavera, and J. M Thornton Genome and proteome annotation: organization, interpretation and integration J R Soc Interface, February 6, 2009; 6(31): 129 - 147. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Reumers, L. Conde, I. Medina, S. Maurer-Stroh, J. Van Durme, J. Dopazo, F. Rousseau, and J. Schymkowitz Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases Nucleic Acids Res., January 11, 2008; 36(suppl_1): D825 - D829. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Moreno-Estrada, F. Casals, A. Ramirez-Soriano, B. Oliva, F. Calafell, J. Bertranpetit, and E. Bosch Signatures of Selection in the Human Olfactory Receptor OR5I1 Gene Mol. Biol. Evol., January 1, 2008; 25(1): 144 - 154. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. A. Savage, K. Woodson, E. Walk, W. Modi, J. Liao, C. Douglass, R. N. Hoover, S. J. Chanock, and The National Osteosarcoma Etiology Study Group Analysis of Genes Critical for Growth Regulation Identifies Insulin-like Growth Factor 2 Receptor Variations with Possible Functional Significance as Risk Factors for Osteosarcoma Cancer Epidemiol. Biomarkers Prev., August 1, 2007; 16(8): 1667 - 1674. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Zhu, H. M. Tucker, K. E. Grear, J. F. Simpson, A. K. Manning, L. A. Cupples, and S. Estus A common polymorphism decreases low-density lipoprotein receptor exon 12 splicing efficiency and associates with increased cholesterol Hum. Mol. Genet., July 15, 2007; 16(14): 1765 - 1772. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Capriotti, R. Calabrese, and R. Casadio Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information Bioinformatics, November 15, 2006; 22(22): 2729 - 2734. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. L. Milne, G. Ribas, A. Gonzalez-Neira, R. Fagerholm, A. Salas, E. Gonzalez, J. Dopazo, H. Nevanlinna, M. Robledo, and J. Benitez ERCC4 Associated with Breast Cancer Risk: A Two-Stage Case-Control Study Using High-throughput Genotyping Cancer Res., October 1, 2006; 66(19): 9420 - 9427. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Barroso, R.L. Milne, L.P. Fernandez, P. Zamora, J.I. Arias, J. Benitez, and G. Ribas FANCD2 associated with sporadic breast cancer risk Carcinogenesis, September 1, 2006; 27(9): 1930 - 1937. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Montaner, J. Tarraga, J. Huerta-Cepas, J. Burguet, J. M. Vaquerizas, L. Conde, P. Minguez, J. Vera, S. Mukherjee, J. Valls, et al. Next station in microarray data analysis: GEPAS. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W486 - W491. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Conde, J. M. Vaquerizas, H. Dopazo, L. Arbiza, J. Reumers, F. Rousseau, J. Schymkowitz, and J. Dopazo PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W621 - W625. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H.-Y. Yuan, J.-J. Chiou, W.-H. Tseng, C.-H. Liu, C.-K. Liu, Y.-J. Lin, H.-H. Wang, A. Yao, Y.-T. Chen, and C.-N. Hsu FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W635 - W641. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. A. Pooley, C. S. Healey, P. L. Smith, P. D.P. Pharoah, D. Thompson, L. Tee, J. West, C. Jordan, D. F. Easton, B. A.J. Ponder, et al. Association of the progesterone receptor gene with breast cancer risk: a single-nucleotide polymorphism tagging approach. Cancer Epidemiol. Biomarkers Prev., April 1, 2006; 15(4): 675 - 682. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Xu, S. G. Gregory, E. R. Hauser, J. E. Stenger, M. A. Pericak-Vance, J. M. Vance, S. Zuchner, and M. A. Hauser SNPselector: a web tool for selecting SNPs for genetic association studies Bioinformatics, November 15, 2005; 21(22): 4181 - 4186. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Belanger, P. Beaulieu, C. Moreau, D. Labuda, T. J. Hudson, and D. Sinnett Functional promoter SNPs in cell cycle checkpoint genes Hum. Mol. Genet., September 15, 2005; 14(18): 2641 - 2648. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Conde, J. M. Vaquerizas, C. Ferrer-Costa, X. de la Cruz, M. Orozco, and J. Dopazo PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes Nucleic Acids Res., July 1, 2005; 33(suppl_2): W501 - W505. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Cavallo and A. C. R. Martin Mapping SNPs to protein sequence and structure data Bioinformatics, April 15, 2005; 21(8): 1443 - 1450. [Abstract] [Full Text] [PDF]
|
|