PopTargs: a database for studying population evolutionary genetics of human microRNA target sites.

Andrea Hatlen,Antonio Marco,Mohab Helmy

doi:10.1093/database/baz102

Andrea Hatlen, Antonio Marco + Show 1 more

Open Access

https://doi.org/10.1093/database/baz102

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Abstract

There is an increasing interest in the study of polymorphic variants at gene regulatory motifs, including microRNA target sites. Understanding the effects of selective forces at specific microRNA target sites, together with other factors like expression levels or evolutionary conservation, requires the joint study of multiple datasets. We have compiled information from multiple sources and compared it with predicted microRNA target sites to build a comprehensive database for the study of microRNA targets in human populations. PopTargs is a web-based tool that allows the easy extraction of multiple datasets and the joint analyses of them, including allele frequencies, ancestral status, population differentiation statistics and site conservation. The user can also compare the allele frequency spectrum between two groups of target sites and conveniently produce plots. The database can be easily expanded as new data becomes available and the raw database as well as code for creating new custom-made databases is available for downloading. We also describe a few illustrative examples.

Highlights

As genome sequencing costs continue to decrease, the interest in population genetics increases
We have developed a database which cross-links allele frequencies and other variables of evolutionary interest at predicted microRNA target sites, as well as expression and evolutionary conservation information from other sources, permitting the analysis of frequency spectrums and population differentiation at target sites
MicroRNA tissue expression information was obtained from five RNASeq datasets from Meunier et al [14] and 46 datasets cataloged in miRmine [15]

Summary

Introduction

As genome sequencing costs continue to decrease, the interest in population genetics increases. MicroRNAs are important gene regulators that target gene transcripts by partial complementarity [2] The fact that their targets can be predicted from their primary. Sequence has been exploited to study the potential impact of single-nucleotide polymorphisms at their target sites. A number of studies have reported selective pressures at these target sites by investigating the variation in populations [3,4,5,6]. A number of databases for analyzing polymorphic microRNA target sites exists We have developed a database which cross-links allele frequencies and other variables of evolutionary interest at predicted microRNA target sites, as well as expression and evolutionary conservation information from other sources, permitting the analysis of frequency spectrums and population differentiation at target sites

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