Essential Resources for miRNA Functional Studies: Additional Readings

Central repository for published miRNA sequences and annotations

Manually curated.
Provides detailed evidence summary

Manually curated.
Detailed evidence summary
Display validated targets along with prediction results from multiple target predictors

Comprehensive breakdown of validated target functions (including disease, pathway, tissue, etc.)

Automated extraction of miRNA-gene associations from literatures
Search by GO based on the extracted miRNA-gene pairs

One of the most traditional predictors, decent performance, high false negatives.

The first predictor to take into consideration the binding site accessibility

One of the most traditional predictors, decent performance, similar algorithm to TargetScan

Data-driven predictor, do not consider conservation, good to predict non-conservative miRNAs.
Precompiled prediction results from 3'UTR, 5'UTR and CDS.

Manually curated miRNA-Disease association database.
Search by disease, miRNA, or validated targets from literature or TarBase.

Manually curated miRNA-disease database

Allow quick and easy interpretation of the involvement of a series of genes in biological processes.
Search by miRNAs only.

FAME (Functional Assignment of MicroRNAs via Enrichment) developed its own statistics to evaluate GO or pathway terms enriched by miRNA predicted targets (TargetScan)

Automated extraction of miRNA-gene associations from literatures
Search by GO based on the extracted miRNA-gene pairs

Maps SNPs (Ensembl) in three miRNA-related groups
miRNA targets, pre-miRNAs, miRNA silencing machinery members

Manually curated TF-miRNA association database.

miRNA-Transcription factor association prediction tool.

miRNA expression database and analysis tool for microarray experiments.

Annotating and discovering small (microRNAs, siRNAs, piRNAs...), long ncRNAs (lncRNAs) and circular RNAs (circRNAs) from next generation sequencing data

Command line program for miRNA discovery

Web tool for miRNA expression profile and discovery analysis

Profiling of small RNAs and its sequence variants in single or multi-species high-throughput experiments

GeneSet2MiRNA searches for single miRNA, or multiple miRNAs (cooperative model) that target a significant subsets of input by at least 4 target predictors.