Jinjiang's WebWatcher on Biology (7) - MicroRNA Target Prediction

MicroRNA target prediction
More than 17000 microRNAs are available from the current edition of miRBase (version 16). It is a challenge ahead to identify the targets of all these small RNAs.
A number of algorithms have been developed to be used for the microRNA target prediction (http://www.exiqon.com/microrna-target-prediction).

MicroRNA target gene databases
Name	Description
targetScan	targetScan is Search for predicted microRNA targets in animals
StarBase	starBase is a database for exploring microRNA-target interaction maps from Argonaute (Ago) CLIP-Seq (HITS-CLIP) and degradome sequencing (Degradome-Seq, PARE) data.
TarBase	A comprehensive database of experimentally supported animal microRNA targets
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.
miRecords	an integrated resource for microRNA-target interactions.
PicTar	PicTar is Combinatorial microRNA target predictions.
PITA	PITA, incorporates the role of target-site accessibility, as determined by base-pairing interactions within the mRNA, in microRNA target recognition.
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.
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.
MicroRNA database
Name	Description
miRBase	miRBase database is a searchable database of published miRNA sequences and annotation.
deepBase	deepBase is a database for annotating and discovering small and long ncRNAs (microRNAs, siRNAs, piRNAs...) from high-throughput deep sequencing data.
microRNA.org	microRNA.org is a ddatabase for Experimentally observed microRNA expression patterns and predicted microRNA targets & target downregulation scores.
miRGen 2.0	miRGen 2.0: a database of microRNA genomic information and regulation
miRNAMap	miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes
PMRD	PMRD: plant microRNA database

 

Method	Type of Method	Ref	Method Availability	Data availability	Resource
Stark et. al	Complementary	(Stark et. al., 2003)	Online search	Yes	http://www.russell.embl.de/miRNAs
miRanda	Complementary	(John et al., 2004)	Download	Yes	http://www.microrna.org
miRanda MiRBase	Complementary	(Enright et al., 2003)	Online search	Yes	http://microrna.sanger.ac.uk
miRWalk	-	-	Online search	Yes	http://www.umm.uni-heidelberg.de/apps/zmf/mirwalk/index.html
Target Scan	Seed Complementary	(Lewis et al., 2005)	Online search	Yes	http://www.targetscan.org
DIANA microT	Thermodynamics	(Kirakidou et al., 2004)	Download	Yes	http://diana.cslab.ece.ntua.gr/
PicTar	Thermodynamics	(Krek et al., 2005)	N/A	Yes	http://pictar.mdc-berlin.de/
RNAHybrid	Thermodynamics & Statistical model	(Rehmsmeier et al., 2004)	Download	Yes	http://bibiserv.techfak.uni-bielefeld.de/rnahybrid
miRGen++	Baynesian Inference	(Huang et al., 2007b)	Mathlab Code	Yes	http://www.psi.toronto.edu/genmir
MiTarget	Support Vector Machine	(Kim et al. 2006)	Online search	Yes	http://cbit.snu.ac.kr/~miTarget
MiRtaget2	Support Vector Machine	(Wang and El Naqa, 2008)	Online search	Yes	http://mirdb.org
TarBase	Experimentally Validated Targets	(Sethupathy et al., 2006)	N/A	Yes	http://diana.cslab.ece.ntua.gr/tarbase/