TarMiR1.0 is an integrated database that holds pre-computed microRNA target lists from nine commonly used miRNA target prediction servers along with target lists from the only server that provides a list of experimentally validated targets. The primary aim of TarMiR 1.0 is to allow users to search and retrieve information from the pre-computed miRNA target lists in a customizable and comprehensive manner.
Users can retrieve targets of miRNA/s from TarMiR 1.0 in three different ways – (1) As individual, ranked lists derived from all or a selection of servers or 2) As a comprehensive list that contains the non-redundant list of miRNA targets from across selected servers or 3) As a filtered list that contains only targets shared by user selected servers. It is also possible to restrict the output list from each server by specifying the percentile cut-off for top-targets for any miRNA. Conversely, TarMiR 1.0 can also accept a gene or transcript name as input and return a list of miRNAs that are predicted to target it. Additionally, lists of miRNAs and mRNAs (that can be the set of differentially expressed miRNAs & mRNAs from an expression profiling experiment) can be compared in TarMiR 1.0 to map corresponding miRNA-mRNA target pairs. For all functionalities, the option of specifying percentile cut-off and server choice is available. TarMiR 1.0 accepts gene/transcript/miRNAs names in almost all the commonly used formats.
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Computational microRNA target prediction with high sensitivity and specificity remains a challenging task. At least a dozen different miRNA target prediction algorithms exist, the majority being implemented in the form of online web-resources. Several of these algorithms provide the option of selecting parameters that either increase specificity of prediction or its sensitivity. Mainly owing to the different approaches toward miRNA target prediction used by the different servers, consensus prediction of targets across servers is seldom obtained. Here, we have compiled pre-computed lists of miRNA targets from nine commonly used public, target prediction servers -TargetScan, PicTar, DIANA Micro-T, EIMMo, EMBL, Miranda, miBRIDGE, Microcosm, PITA and data from TarBase, which contains experimentally validated miRNA-targets.
We gratefully acknowledge all authors and curators of TargetScan, PicTar, DIANA Micro- T, EIMMo, EMBL, Miranda, miBRIDGE, Microcosm, PITA and TarBase for making their data freely available. Our interests in making TarMiR 1.0 are purely academic.
