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. 2008;9 Suppl 1(Suppl 1):S2.
doi: 10.1186/1471-2105-9-S1-S2.

SNP@Promoter: A Database of Human SNPs (Single Nucleotide Polymorphisms) Within the Putative Promoter Regions

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Free PMC article

SNP@Promoter: A Database of Human SNPs (Single Nucleotide Polymorphisms) Within the Putative Promoter Regions

Byoung-Chul Kim et al. BMC Bioinformatics. .
Free PMC article

Abstract

Background: Analysis of single nucleotide polymorphism (SNP) is becoming a key research in genomics fields. Many functional analyses of SNPs have been carried out for coding regions and splicing sites that can alter proteins and mRNA splicing. However, SNPs in non-coding regulatory regions can also influence important biological regulation. Presently, there are few databases for SNPs in non-coding regulatory regions.

Description: We identified 488,452 human SNPs in the putative promoter regions that extended from the +5000 bp to -500 bp region of the transcription start sites. Some SNPs occurring in transcription factor (TF) binding sites were also predicted (47,832 SNP; 9.8%). The result is stored in a database: SNP@promoter. Users can search the SNP@Promoter database using three entries: 1) by SNP identifier (rs number from dbSNP), 2) by gene (gene name, gene symbol, refSeq ID), and 3) by disease term. The SNP@Promoter database provides extensive genetic information and graphical views of queried terms.

Conclusion: We present the SNP@Promoter database. It was created in order to predict functional SNPs in putative promoter regions and predicted transcription factor binding sites. SNP@Promoter will help researchers to identify functional SNPs in non-coding regions.

Figures

Figure 1
Figure 1
Flow chart for identifying SNPs in putative promoter regions. Cylinders represent databases. Rectangles are computational applications. (a) Putative promoter regions are identified in the human genome sequence. (b) Transcription binding sites are predicted in the putative promoter regions by using TransFac database. (c) SNPs are mapped. (d) Evolution conservation scores are calculated within transcription factor binding sites. (e) The disease association and functional annotation of target genes carried out by using an in-house functional annotation database.
Figure 2
Figure 2
SNP@Promoter user interface. SNP@Promoter main page. (A) Users can search using three entries: 1) an SNP identifier (rs number from dbSNP), 2) a gene (Gene name, gene symbol, refSeq ID), or 3) a disease term. (B) SNP@Promoter gene retrieval page. The SNP Information table shows identified SNPs within putative promoter region and TF biding sites. The Gene Information table shows various gene annotations including pathways (KEGG), gene ontology (GOA). The Information of Transcription Factor Binding Sites table shows a variety off TF information such as TF start position, upstream position, TF strand, match score, TF binding sequences, conservations score.
Figure 3
Figure 3
A graphic viewer of transcription regulatory region. The green bar represents a putative promoter region (5500 bp). The arrows in the green bar show a strand of transcription, orange box is transcription start region, yellow inverted triangles are SNP positions, and purple triangles are predicted transcription binding sites.

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References

    1. Collins FS, Brooks LD, Chakravarti A. A DNA polymorphism discovery resource for research on human genetic variation. Genome Res. 1998;8:1229–1231. - PubMed
    1. Brookes AJ. The essence of SNPs. Gene. 1999;234:177–186. doi: 10.1016/S0378-1119(99)00219-X. - DOI - PubMed
    1. Kang HJ, Choi KO, Kim BD, Kim S, Kim YJ. FESD: a Functional Element SNPs Database in human. Nucleic Acids Res. 2005;33:D518–522. doi: 10.1093/nar/gki082. - DOI - PMC - PubMed
    1. Chang H, Fujita T. PicSNP: a browsable catalog of nonsynonymous single nucleotide polymorphisms in the human genome. Biochem Biophys Res Commun. 2001;287:288–291. doi: 10.1006/bbrc.2001.5576. - DOI - PubMed
    1. Riva A, Kohane IS. SNPper: retrieval and analysis of human SNPs. Bioinformatics. 2002;18:1681–1685. doi: 10.1093/bioinformatics/18.12.1681. - DOI - PubMed

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