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What is Poptargs? [version 2.0]

PopTargs is a tool for studying the population genetics of human miRNA target sites. It is based on a mySQL database made up of all SNPs (single nucleotide polymorphisms) found in human miRNA target sites.

Animal miRNAs have seed regions which are 6-8nt long and have perfect complementarity to their target region in the 3'UTRs of genes (see Bartel 2009 for the types of seed regions). Therefore, SNPs in these regions would disrupt the targeting (Review on SNPs in miRNA target sites: MoszyƄska et al. 2017).

How do I use this site?

There are four ways to access the data, which are located in the tabs above:

Search: You can find here polymorphic target sites for scpecific microRNAs or genes. the table can be browsed or downloaded for downstream analysis.

User lists: There are text-input boxes where you can compare a list of miRNAs against another list (or all others) for a specific group of genes of your choice. Or, separately, two lists of genes for a list of miRNAs. The data has two output options: a pdf of the site frequency spectrum plots (target allele frequency and derived allele frequency) or a text file with the background data.

Browse: You can select which tissues, populations, and/or conservation statuses they are interested in. Again there are two output options: a pdf of the plots or a text file of the data.

Downloads: On the downloads page you can download all the data from the database for private use. It is available in MySQL form as a .sql file or each table in the database can be downloadsd individually in .txt format.

Where is the data from?

To find miRNA target sites both targets and near targets of all human miRNA in 3'UTR of the genome were found, (using the software seedVicious), then only the sites that had polymorphisms that made the site a target and not were kept (ex: a near target with a SNP that does not turn it into a target would not be kept).

Along with the gene ID, miRNA name (as listed in
miRBase), and SNP ID, the database includes the ancestral allele (based on classification from dbSNP), target allele, and allele frequency (also from dbSNP), all of which can be used for population genetics studies.

References:

Hatlen A., Helmy M, Marco A. PopTargs: A database for studying population evolutionary genetics of human microRNA target sites (Under review).