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UCbase and miRfunc

http://microrna.osu.edu/.UCbase4

Description :
Database of Ultraconserved sequences and microRNA function

microRNA.org

http://www.microrna.org/

Description :
microRNA target predictions and expression profiles

miR2Disease

http://mlg.hit.edu.cn:8080/miR2Disease

Description :
Literature-curated database for validatedly or potentially pathogenic roles of dysregulated miRNAs in human disease

miRecords

http://mirecords.umn.edu/miRecords

Description :
Experimentally validated miRNAs

miRGator

http://genome.ewha.ac.kr/miRGator/miRGator.html

Description :
microRNA target prediction, functional analysis, and gene expression data

miROrtho

http://cegg.unige.ch/mirortho

Description :
Computational prediction of animal microRNA genes

TarBase

http://www.diana.pcbi.upenn.edu/tarbase.html

Description :
Database of experimental supported microRNA targets

Vir-Mir db

http://alk.ibms.sinica.edu.tw/

Description :
Prediction of viral microRNA candidate hairpins

DIANA TarBase : Experimentally supported miRNA targets

http://www.diana.pcbi.upenn.edu/tarbase.html Tarbase is a database that provides a means of searching through a comprehensive set of experimentally supported microRNA targets in at least 8 organisms. For every target site that has gained experimental support, TarBase describes the miRNA which binds it, the binding (alignment) picture, the kind of inhibition that it induces, its single site sufficiency status, its genomic location, the types of experiments that were conducted to support it, and the paper from which all of this data was extracted. Users can also download the entire contents of the database in the form of a tar file that will be updated frequently. TarBase also allows for users to submit newly identified targets in order to keep the database updated for the microRNA research community. We kindly request that users submit any recently verified targets using the submission instructions provided at the submission page. We encourage any comments at all regarding the interface, search site, or submission site.

CrossLink

http://www-ab.informatik.uni-tuebingen.de/software/crosslink/webstart/welcome.html

Description :
Crosslink is a tool for visualizing pairwise sequence similiarity relationships determined using BLAST, Vmatch, and RNAhybrid. The nucleotide sequences and their relationships are displayed as nodes and links of a network, respectively. CrossLink can be useful for investigating potential interactions between microRNAs and their targets.

miPred

http://www.bioinf.seu.edu.cn/miRNA/

Description :
miPred (microRNA Predictor) can distinguish between real and pseudo microRNA precursors.

miRBase

http://microrna.sanger.ac.uk/

Description :
The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. The miRBase Registry continues to provide gene hunters with unique names for novel miRNA genes prior to publication of results. The miRBase Targets database is a new resource of predicted miRNA targets in animals

GenomeTraFaC

http://genometrafac.cchmc.org/

Description :
Adopting a systematic gene-centric pipeline approach, GenomeTraFaC (http://genometrafac.cchmc.org) allows genome-wide detection and characterization of compositionally similar cis-clusters that occur in gene orthologs between any two genomes for both microRNA genes as well as conventional RNA-encoding genes. Each ortholog gene pair can be scanned to visualize overall conserved sequence regions, and within these, the relative density of conserved cis-element motif clusters form graph peak structures. The results of these analyses can be mined en masse to identify most frequently represented cis-motifs in a list of genes. The system also provides a method for rapid evaluation and visualization of gene model-consistency between orthologs, and facilitates consideration of the potential impact of sequence variation in conserved non-coding regions to impact complex cis-element structures. Using the mouse and human genomes via the NCBI Reference Sequence database and the Sanger Institute miRBase, the system demonstrated the ability to identify validated transcription factor targets within promoter and distal genomic regulatory regions of both conventional and microRNA genes.

Aknowledgement :
This work was supported by grants NCI UO1 CA84291-07 (Mouse Models of Human Cancer Consortium), NIEHS ES-00-005 (Comparative Mouse Genome Centers Consortium) and NIEHS P30-ES06096 (Center for Environmental Genetics).

PolymiRTS

http://compbio.utmem.edu/miRSNP/

Description :
Polymorphism in microRNA Target Site (PolymiRTS) database is a collection of naturally occurring DNA variations in putative microRNA target sites. PolymiRTSs may affect gene expression and cause variations in complex phenotypes. The database integrates sequence polymorphism, phenotype and expression microarray data, and characterizes PolymiRTSs as potential candidates responsible for the QTL (quantitative trait locus) effects. It is a resource for studying PolymiRTSs and their implications in phenotypic variations.

References :
1. Bao L, Zhou M, Wu L, Lu L, Goldowitz D, Williams R, Cui Y. PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits. Nucleic Acids Research. 35: in press.

Cereal Small RNA Database

http://sundarlab.ucdavis.edu/smrnas/

Description :
Small RNAs (smRNAs), which include microRNAs (miRNAs), small-interfering RNAS (siRNAs) and trans-acting siRNAs (ta-siRNAs) are ~19-24 nt RNAs that are important negative regulators of nucleotide sequences involved in development, homeostasis and in the maintenance of heterochromatic states. The Cereals Small RNA Database (CSRDB) is an integrated resource for small RNAs expressed in rice and maize that includes a genome browser and a smRNA-target relational database as well as relevant bioinformatic tools. The resource currently contains a preliminary dataset of 35,454 and 68,871 mapped smRNA sequence reads for rice and maize respectively. Future updates will include smRNA data derived from different tissues and conditions. The database is accessible online at http://sundarlab.ucdavis.edu/smrnas/.

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