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MicroRNA enrichment software tools | Non-coding RNA data analysis

Similar to the development of gene set enrichment and gene regulatory network analysis tools over a decade ago, microRNA enrichment tools are currently gaining importance.

Source text:
(Backes et al., 2016) miEAA: microRNA enrichment analysis and annotation. Nucleic Acids Res.

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GeneTrail
A web service allowing the integrated analysis of transcriptomic, miRNomic, genomic, and proteomic datasets. GeneTrail offers multiple statistical tests, a large number of predefined reference sets, as well as a comprehensive collection of biological categories and enables direct comparisons between the computed results. GeneTrail was designed to offer users a maximal amount of flexibility while keeping the common workflow accessible to non-expert users. This is achieved by offering a user friendly, well-documented web interface. In turn, scripting capabilities allow expert users to conduct fully automated large-scale analyses and the integration into third-party applications.
TAM / Tool for Annotations of MiRNAs
A method for annotations of meaningful human miRNAs categories. We first integrated miRNAs into various meaningful categories according to prior knowledge, such as miRNA family, miRNA cluster, miRNA function, miRNA associated diseases, and tissue specificity. Using TAM, given lists of miRNAs can be rapidly annotated and summarized according to the integrated miRNA categorical data. Moreover, given a list of miRNAs, TAM can be used to predict novel related miRNAs.
FAME / Functional Assignment of MicroRNAs via Enrichment
Uses computational target predictions to automatically infer the processes affected by human miRNAs. FAME addresses specific characteristics of miRNA regulation and is based on a compendium of experimentally verified miRNA-pathway and miRNA-process associations. It predicts novel miRNA-regulated pathways, refines the annotation of miRNAs for which only crude functions are known, and assigns differential functions to miRNAs with closely related sequences.
miTEA / miRNA Target Enrichment Analysis
A framework for miRNA target enrichment analysis. miTEA takes as input a ranked list of genes and then finds miRNAs of which targets are enriched in the top of the input list. miTEA uses a novel statistical analysis that takes into account the rich information available from high-throughput experiments as well as from the different miTPAs. We show how miTEA can be applied to detect miRNA activity in different experiments and shed light into miRNA activity map in healthy and cancer samples. miTEA is a web-based tool allowing the community an easy and efficient free access.
miEAA / miRNA Enrichment Analysis and Annotation tool
Offers a miRNA enrichment tool appropriate for statistical tests and miRNA/precursor categories. miEAA lets users choose between two types of enrichment analysis: over-representation analysis (ORA) or miRNA enrichment analysis (GSEA). This software is built on the established statistical framework of the gene set analysis toolkit GeneTrail. The information integrated into this tool are provided from several miRNA-specific tools and databases (miRBase, HMDD2, miRWalk, miRTarBase).
gsa4mirna
A gene set analysis (GSA)-type methodology for functionally interpreting miRNA expression data. gsa4mirna relies on the gene set analysis paradigm which extends currently used over representation methodologies. It constitutes a general framework applicable in most genomic scenarios, even when no (or too many) miRNAs are differentially expressed, hence, gsa4mirna eradicates the arbitrariness of current “ad hoc” procedures. But more importantly, gsa4mirna can encompass biologically relevant events which are neglected by others, representing a step forward in miRNA gene-regulation modeling. First, gsa4mirna accounts for cancellation effects that arise when a gene is intercepted by different sets of miRNAs within each biological condition. Second, it is able to incorporate the additive effect caused when several weak miRNA inhibitors exert their influence on the same gene.
ENViz / Enrichment Analysis and Visualization
Allows enrichment joint analysis and visualization for integrated analysis of two types of sample matched datasets and systematic annotations. ENViz is a Cytoscape plug-in that integrates data analysis via the utilization of genomic annotation databases and enrichment statistics. It processes each pivot data element through three steps: (i) addressing the correlation to each element of primary data, (ii) ranking primary data elements according the correlations and (iii) computing the statistical enrichment of annotated elements.
miRDis / microRNA Discovery
Supports the annotation and expression profiling data of known host miRNAs and the detection of novel miRNAs, other noncoding RNAs, and the exogenous miRNAs from dietary species. miRDis is a small RNA sequencing data analysis pipeline for both endogenous and exogenous miRNA detection. This web server outperforms other state-of-the-art tools in both detection and quantification of miRNA from either animal or plant sources. miRDis provides an efficient and friendly tool for making promising discoveries in miRNA cross-species transport.
miRHiC / enrichment analysis of miRNA targets in Hierarchical gene Co-expression signatures
Infers the perturbed microRNA (miRNA) regulatory networks in cancer. miRHiC includes the hierarchically organized gene co-expression information into miRNA target gene set enrichment analysis. It determines the hierarchical gene co-expression signatures by clustering differentially expressed genes based on pairwise gene co-expression correlations. This tool exploits hierarchical signatures to process miRNA regulations.
miRTar
An integrated resource for deciphering miRNA-target interaction networks, and provides a broad range of analyzing scenarios for miRNA-target interactions, including one miRNA to one gene, one miRNA to multiple genes, and others, to help biologists understand the regulation between the miRNAs and target genes. By integrating several external databases and analyzing tools, miRTar can provide further information for elucidating miRNA regulation affected by alternative splicing. Besides, miRTar can enable biologists to easily identify the biological functions and regulatory relationships between a group of known/putative miRNAs and protein coding genes.
GuruceagaEtAl2014
Allows users to perform microRNA target enrichment analysis. The approach merges both miRNA expression data, mRNA expression data, predicted miRNA target information and functional analysis of the miRNA targets. It exploits information from eight different repositories, such as PicTar 4w, PITA or MicroCosm, that can be considered separately or as a combination. The application aims to assist researchers in investigating biological and pathological causes and effects of the expression of miRNAs.
miSEA / microRNA Set Enrichment Analysis
A web-based tool for evaluating the enrichment of relevant microRNA sets from microarray and miRNA-seq experiments on paired samples, e.g. control vs. treatment: In addition to a group of previously annotated microRNA sets embedded in the system, miSEA enables users to import new microRNA sets obtained from their own research. miSEA allows users to select from a large variety of microRNA grouping categories, such as family classification, disease association, common regulation, and genome coordinates, based on their requirements. miSEA therefore provides a knowledge-driven representation scheme for microRNA experiments.
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