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F-SNP: computationally predicted functional SNPs for disease association studies.

Lee PH, Shatkay H - Nucleic Acids Res. (2007)

Bottom Line: These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level.As such, the database helps identify and focus on SNPs with potential deleterious effect to human health.Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification.

View Article: PubMed Central - PubMed

Affiliation: Computational Biology and Machine Learning Lab, School of Computing, Queen's University, Kingston, ON, Canada. lee@cs.queensu.ca

ABSTRACT
The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from 16 bioinformatics tools and databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. As such, the database helps identify and focus on SNPs with potential deleterious effect to human health. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification. A web interface enables easy navigation for obtaining information through multiple starting points and exploration routes (e.g. starting from SNP identifier, genomic region, gene or target disease). The F-SNP database is available at http://compbio.cs.queensu.ca/F-SNP/.

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Related in: MedlinePlus

Example of an F-SNP search session. (a) The initial search page is displayed, where the user selected the disease type to be Cancers, and the specific disease to be Breast cancer (Search by disease). (b) Results obtained after clicking the Submit button in panel (a), namely a list of genes associated with Breast cancer along with their associated chromosome location, known related disorders, and links to OMIM. The BRCA1 link (circled) is selected and clicked. (c) A detailed description of SNPs associated with BRCA1 is produced (demonstrating results of Search by gene). The SNP whose identifier is rs28897699 (circled)—indicated by a ‘+’ mark to have associated functional information—is selected and clicked. (d) Information about the SNP rs28897699 is presented (demonstrating results of Search by SNP ID).
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Figure 2: Example of an F-SNP search session. (a) The initial search page is displayed, where the user selected the disease type to be Cancers, and the specific disease to be Breast cancer (Search by disease). (b) Results obtained after clicking the Submit button in panel (a), namely a list of genes associated with Breast cancer along with their associated chromosome location, known related disorders, and links to OMIM. The BRCA1 link (circled) is selected and clicked. (c) A detailed description of SNPs associated with BRCA1 is produced (demonstrating results of Search by gene). The SNP whose identifier is rs28897699 (circled)—indicated by a ‘+’ mark to have associated functional information—is selected and clicked. (d) Information about the SNP rs28897699 is presented (demonstrating results of Search by SNP ID).

Mentions: The F-SNP database is available at http://compbio.cs.queensu.ca/F-SNP/. The user can search the database by SNP identifier, gene, disease or chromosomal regions. Figure 2 shows an example of results obtained from an interactive search concerned with breast cancer.Figure 2.


F-SNP: computationally predicted functional SNPs for disease association studies.

Lee PH, Shatkay H - Nucleic Acids Res. (2007)

Example of an F-SNP search session. (a) The initial search page is displayed, where the user selected the disease type to be Cancers, and the specific disease to be Breast cancer (Search by disease). (b) Results obtained after clicking the Submit button in panel (a), namely a list of genes associated with Breast cancer along with their associated chromosome location, known related disorders, and links to OMIM. The BRCA1 link (circled) is selected and clicked. (c) A detailed description of SNPs associated with BRCA1 is produced (demonstrating results of Search by gene). The SNP whose identifier is rs28897699 (circled)—indicated by a ‘+’ mark to have associated functional information—is selected and clicked. (d) Information about the SNP rs28897699 is presented (demonstrating results of Search by SNP ID).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238878&req=5

Figure 2: Example of an F-SNP search session. (a) The initial search page is displayed, where the user selected the disease type to be Cancers, and the specific disease to be Breast cancer (Search by disease). (b) Results obtained after clicking the Submit button in panel (a), namely a list of genes associated with Breast cancer along with their associated chromosome location, known related disorders, and links to OMIM. The BRCA1 link (circled) is selected and clicked. (c) A detailed description of SNPs associated with BRCA1 is produced (demonstrating results of Search by gene). The SNP whose identifier is rs28897699 (circled)—indicated by a ‘+’ mark to have associated functional information—is selected and clicked. (d) Information about the SNP rs28897699 is presented (demonstrating results of Search by SNP ID).
Mentions: The F-SNP database is available at http://compbio.cs.queensu.ca/F-SNP/. The user can search the database by SNP identifier, gene, disease or chromosomal regions. Figure 2 shows an example of results obtained from an interactive search concerned with breast cancer.Figure 2.

Bottom Line: These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level.As such, the database helps identify and focus on SNPs with potential deleterious effect to human health.Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification.

View Article: PubMed Central - PubMed

Affiliation: Computational Biology and Machine Learning Lab, School of Computing, Queen's University, Kingston, ON, Canada. lee@cs.queensu.ca

ABSTRACT
The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from 16 bioinformatics tools and databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. As such, the database helps identify and focus on SNPs with potential deleterious effect to human health. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification. A web interface enables easy navigation for obtaining information through multiple starting points and exploration routes (e.g. starting from SNP identifier, genomic region, gene or target disease). The F-SNP database is available at http://compbio.cs.queensu.ca/F-SNP/.

Show MeSH
Related in: MedlinePlus