MicroRNA and microRNA target database

This microRNA database and microRNA targets databases is a compilation of databases and web portals and servers used for microRNAs and their targets. MicroRNAs (miRNAs) represent an important class of small non-coding RNAs (ncRNAs) that regulate gene expression by targeting messenger RNAs.

microRNA target gene databases

Name	Description	type	Link	References
StarBase	starBase is designed for decoding miRNA-lncRNA, miRNA-mRNA, miRNA-circRNA, miRNA-pseudogene, miRNA-sncRNA, protein-lncRNA, protein-sncRNA, protein-mRNA and protein-pseudogene interactions and ceRNA networks from 108 CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) datasets. It also provides Pan-Cancer Analysis for microRNAs, lncRNAs, circRNAs and protein-coding genes from 6000 tumor samples.	database	website
StarScan	StarScan is developed for scanning small RNA (miRNA, piRNA, siRNA) mediated RNA cleavage events in lncRNA, circRNA, mRNA and pseudo genes from degradome sequencing data.	web-based software	website
Cupid	Cupid is a method for simultaneous prediction of miRNA-target interactions and their mediated competing endogenous RNA (ceRNA) interactions. It is an integrative approach significantly improves on miRNA-target prediction accuracy as assessed by both mRNA and protein level measurements in breast cancer cell lines. Cupid is implemented in 3 steps: Step 1: re-evaluate candidate miRNA binding sites in 3’ UTRs. Step2: interactions are predicted by integrating information about selected sites and the statistical dependency between the expression profiles of miRNA and putative targets. Step 3: Cupid assesses whether inferred targets compete for predicted miRNA regulators. * Only the source code for step 3 is provided.	software (MATLAB)	website
TargetScan	Predicts biological targets of miRNAs by searching for the presence of sites that match the seed region of each miRNA. In flies and nematodes, predictions are ranked based on the probability of their evolutionary conservation. In zebrafish, predictions are ranked based on site number, site type, and site context, which includes factors that influence target-site accessibility. In mammals, the user can choose whether the predictions should be ranked based on the probability of their conservation or on site number, type, and context. In mammals and nematodes, the user can choose to extend the predictions beyond conserved sites and consider all sites.	database, webserver	website
TarBase	A comprehensive database of experimentally supported animal microRNA targets	database	website
Diana-microT	DIANA-microT 3.0 is an algorithm based on several parameters calculated individually for each microRNA and it combines conserved and non-conserved microRNA recognition elements into a final prediction score.	webserver	webserver
miRecords	an integrated resource for microRNA-target interactions.	database	website
PicTar	PicTar is Combinatorial microRNA target predictions.	database, webserver, predictions	website
PITA	PITA, incorporates the role of target-site accessibility, as determined by base-pairing interactions within the mRNA, in microRNA target recognition.	webserver, predictions	predictions
RepTar	A database of inverse miRNA target predictions, based on the RepTar algorithm that is independent of evolutionary conservation considerations and is not limited to seed pairing sites.	database	website
RNA22	The first link (predictions) provides RNA22 predictions for all protein coding transcripts in human, mouse, roundworm, and fruit fly. It allows you to visualize the predictions within a cDNA map and also find transcripts where multiple miR's of interest target. The second web-site link (custom) first finds putative microRNA binding sites in the sequence of interest, then identifies the targeted microRNA.	webserver, predictions	predictions custom
miRTarBase	The experimentally validated microRNA-target interactions database.	database	website
miRwalk	Aggregates and compare results from other miRNA-to-mRNA databases	database, webserver	[1]
MBSTAR	Multiple Instance approach for finding out true or functional microRNA binding sites.	webserver, predictions	predictions
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microRNA databases

Name	Description	type	Link	References
deepBase	deepBase is a database for annotating and discovering small and long ncRNAs (microRNAs, siRNAs, piRNAs...) from high-throughput deep sequencing data.	database	website
miRBase	miRBase database is a searchable database of published miRNA sequences and annotation.	database	website
microRNA.org	microRNA.org is a ddatabase for Experimentally observed microRNA expression patterns and predicted microRNA targets & target downregulation scores.	database	website
miRGen 2.0	miRGen 2.0: a database of microRNA genomic information and regulation	database	website
miRNAMap	miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes	database	website
PMRD	PMRD: plant microRNA database	database	website
TargetScan	TargetScan7.0 classifies microRNAs according to their level of conservation (i.e., species-specific, conserved among mammals, or broadly conserved among vertebrates) and aggregates them into families based upon their seed sequence. It also annotates conserved isomiRs using small RNA sequencing datasets.	database	website
VIRmiRNA	VIRmiRNA is the first dedicated resource on experimental viral miRNA and their targets. This resource also provides inclusive knowledge about anti-viral miRNAs known to play role in antiviral immunity of host.	Database	website

External links

• starBase database
• StarScan tool
• Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks
• miRBase database
• deepBase database
• TargetScan
• picTar
• miRecords database
• TarBase database
• Target ID Library
• miRTarBase database
• MBSTAR tool