The user may prioritize specific genes by providing gene symbols and prioritization scores as input to SPOT. This information is represented by the ‘User Gene’ node. Similarly, the user may prioritize genomic regions and single SNPs in the ‘User Region’ and ‘User Special SNP’ nodes, respectively. When a gene is specified two different ways, or when two user-specified regions overlap, SPOT will combine the prioritization scores according to the user-specified option ‘Multiple Query Method’, which may be maximum (the default), minimum, sum or average. When a SNP is in an evolutionary conserved region (ECR) with fractional conservation P (0 ≤ P ≤ 1), the corresponding ECR node contributes F*P to the overall score where F is a factor currently set to 0.75. We used ECRBase for data on human/mouse ECRs (11).
