Web-based tools collection for microRNA analysis

Abstract Summary

The TAmiRNA TechNote TN-04 covers five basic groups of microRNA tools: target prediction tools, databases, deep sequencing tools, data analysis tools and other web-based tools relevant to microRNA studies.

MicroRNA target prediction tools provide a computational approach to prediction of microRNA targets, sorting through the extremely large number of potential target sites that exist for any given microRNA by modelling how microRNAs target specific mRNAs using a variety of distinct approaches, based on four basic variables: seed match, conservation, free energy and site accessibility. The paper summarizes 11 online tools, including miRDB, TargetScan, PicTar, RNA-hybrid, miRIAD, DIANA-mirPath, miRTar.human, miRmap, ComiRNet and VIRmiRNA.

Given the involvement of microRNAs in gene regulation as well as disease processes, an ever-increasing number of experiments have generated an exponential flow of data scattered in thousands of articles. Many bioinformatic microRNA database tools are now available to manage the mounting data flow. The TechNote summarizes the scope of databases accessible online, both general purpose databases, such as miRBase and DIANA tools, as well as specialized databases, including miRBase Tracker, FirePlex Discovery Engine, miROrtho, miRCancer, miRWalk and omiRas.

MicroRNA deep sequencing tools measure absolute abundance and enable discovery of novel microRNAs that have eluded previous cloning and standard sequencing efforts. Public databases provide in silico predictions of microRNA gene targets by various algorithms. These include miRDeep2 and miRNAkey.

MicroRNA data analysis tools define core sets of independent features, principally Principal components analysis (PCA), microRNA heat maps and Venn diagrams, that allow expression states to be compared directly. The TechNote compares the two principal data analysis tools, ClustVis and Venny.

TAmiRNA also summarizes four other web-based tools:

• Tools4miRs – manually curated platform gathering more than 170 methods for broadly-defined miRNA analysis.
• TissueAtlas – allowing identification of tissues of origin of miRNAs, providing insights into specificity and heterogeneity of miRNAs.
• GeneCards – a searchable, integrative database providing comprehensive information on all annotated and predicted human genes from some 125 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information.
• BloodcellAtlas – A comprehensive reference dataset of detailed miRNA expression profiles from seven types of human peripheral blood cells, serum, exosomes and whole blood.

The paper also provides a tabulated overview of web-based tools and their principal features.