Data summary & Data processing

Data summary

Beyond of adding new created small variations from the databases of NCBI dbSNP, new types of regulatory elements and more extend annotation (such as SNP related disease), significant adjustments on database structure and function have been made in this update. The concerns of rSNPBase 3.0 were extended from regulatory elements that position overlap SNPs to SNP related regulatory element-target gene (E-G) pairs. Based on the annotation of regulatory element-gene pairs, rSNPBase 3.0 supports SNP-based regulatory network analysis. A summarized data content of rSNPBase 3.0 is shown in Table 1.

Data processing

As shown in Figure 1, several types of regulatory elements were gotten from reference databases (mostly of them provide experimental supported data), their relation with genes from Ensembl (GRCh37) were analyzed with genomic proximity or by using reference databases. Genome-wide human SNPs from NCBI dbSNP (build 150) were analyzed and filtered by involved regulatory elements sets and thus connected to corresponding E-G pairs in the same time. The analysis results were stored in rSNPBase 3.0 and presented as regulatory SNP (rSNP) reports and SNP-based regulatory network.

Figure 1. Data processing and data content of rSNPBase 3.0

Reference data

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