Tutorial for the mirsnpscore database: SNP effects on microRNA targeting

This database provides computer-based predictions of SNP effects on microRNA-based gene regulation.

Looking for a gene:

In the "Single Search" area, select the "Gene" radio button, write the RefSeq Gene name (Ex: ADAR) or RefSeq Gene ID (Ex: NM_001111) in the first field, and click on the first "Search" button.

Looking for a miRNA:

In the "Single Search" area, select the "miRNA" radio button, write the human microRNA ID (Ex: hsa-miR-1285 or miR-1285) in the second field, and click on the first "Search" button.

Looking for a SNP:

In the "Single Search" area, select the "SNP" radio button, write the SNP ID (Ex: rs1127313) in the third field, and click on the first "Search" button.

Looking for a Gene and a miRNA:

In the "Multiple Search" area, write the RefSeq Gene name (Ex: ADAR) or RefSeq Gene ID (Ex: NM_001111) in the first field of the area, write the human microRNA ID (Ex: hsa-miR-1285 or miR-1285) in the second field of the area, and click on the second "Search" button.

Looking for a Gene and a SNP:

In the "Multiple Search" area, write the RefSeq Gene name (Ex: ADAR) or RefSeq Gene ID (Ex: NM_001111) in the first field of the area, write the SNP ID (Ex: rs1127313) in the third field of the area, and click on the second "Search" button.

Looking for a miRNA and a SNP:

In the "Multiple Search" area, write the human microRNA ID (Ex: hsa-miR-1285 or miR-1285) in the second field of the area, write the SNP ID (Ex: rs1127313) in the third field of the area, and click on the second "Search" button.

Looking for a Gene, a miRNA and a SNP:

Output example:

Gene: ADAR, the first 3 results are shown.

chr	Gene	RefGene	Strand	miRNA	DeltaS	RsId	Pos	MAF	Allele	TargetSite
1	ADAR	NM_001111	-	miR-3614-3p	0.8371	rs9616	152822357	0.267	T	GA[A]GGCUG 7mer-m8
									A
1	ADAR	NM_015841	-	miR-3614-3p	0.8368	rs9616	152822357	0.267	T	GA[A]GGCUG 7mer-m8
									A
1	ADAR	NM_001025107	-	miR-3614-3p	0.8364	rs9616	152822357	0.267	T	GA[A]GGCUG 7mer-m8
									A

Looking for the 3 first results of gene ADAR: It lies on chromosome 1, and has several refGene IDs, on the negative strand. Results are sorted by DeltaS, which is the predicted effect of the SNPs on the miRNA regulation for a given gene/miRNA pair. Here the SNP rs9616 which lies at position 152822357 on the chromosome 1 on the human assembly hg18, has a minimum allele frequency of 0.267 in the CEU Hapmap population. We do not provide which allele is the MAF allele. Here the "T" allele gives a 7mer-m8 site for the miRNA miR-3614-3, while the "A" allele disrupt this target site. The difference of score between haplotypes that have allele "T" and those that have allele "A" is about 0.837, depending on the transcript of ADAR we consider. The difference of score is not signed.