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INTRODUCTION |
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| F-SNP database provides integrated information about the functional effects of SNPs obtained from 16 bioinformatics tools and databases. The functional effects are predicted and indicated at the splicing, transcriptional, translational, and post-translational level. As such, the F-SNP database helps identify and focus on SNPs with potential pathological effect to human health. |
Decision Procedure for Functinoal SNP Assessment | |
| Each SNP is examined for deleterious effects with respect to each functional category (i.e., protein coding, splicing regulation, transcriptional regulation, and post-translation – as shown in the top part of the figure). For each category a series of tests is executed to determine whether the SNP has a functional impact. First the type (coding, intronic etc.) of the genomic region is identified, using data from dbSNP [17] and Ensembl [6]. Once this is determined, other tests are performed. For example, to assess if a SNP has a deleterious effect on protein coding, it first must be located on a coding region. Ensembl [6] is used to examine if this is a Nonsense mutation, in which case the SNP is considered to be deleterious. Otherwise – if the SNP is a Missense mutation, it is further tested by five different tools (PolyPhen [1], SIFT [2], SNPeffect [3], SNPs3D [4], LS-SNP [5]) to check if the non-synonymous substitution is deleterious. A majority vote between these tools concludes the process, and identifies the SNP as either having a potentially deleterious functional impact (denoted functional in the figure) or not. |
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. (Demonstrates results of Search by SNP ID). |
