Supplementary table 1: Database list
|
miRNA Sequence and Annotation Resource |
|||||
|
Resource |
Organism |
Main feature |
Unique features |
URL |
Reference |
|
miRBase |
Any |
miRNA sequences and annotations |
Stem loop structure and deep sequencing Search miRNAs by genomic location Search of miRNA clusters Search of homolog miRNAs in other species
|
[1] |
|
|
CoGemiR |
Animals |
Comparative genomic analysis of miRNAs |
Pre-miRNA and mature sequence Expression data in different tissues Tissue specificity
|
\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>CoGemiR: a comparative genomics microRNA database</title><secondary-title>BMC Genomics</secondary-title><alt-title>BMC genomics</alt-title></titles><periodical><full-title>BMC Genomics</full-title><abbr-1>BMC genomics</abbr-1></periodical><alt-periodical><full-title>BMC Genomics</full-title><abbr-1>BMC genomics</abbr-1></alt-periodical><pages>457</pages><volume>9</volume><keywords><keyword>Animals</keyword><keyword>Computational Biology</keyword><keyword>Database Management Systems</keyword><keyword>*Databases, Nucleic Acid</keyword><keyword>*Genomics</keyword><keyword>MicroRNAs/*genetics</keyword><keyword>Sequence Analysis, RNA</keyword><keyword>*User-Computer Interface</keyword></keywords><dates><year>2008</year></dates><isbn>1471-2164 (Electronic)
1471-2164 (Linking)</isbn><accession-num>18837977</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/18837977</url></related-urls></urls><custom2>2567348</custom2><electronic-resource-num>10.1186/1471-2164-9-457</electronic-resource-num></record></Cite></EndNote>[2] |
|
|
microRNAviewer |
Any |
Conservation of miRNAs in species |
miRNA alignment and finding mismatches miRNA genomic location
|
\n This email address is being protected from spambots. You need JavaScript enabled to view it. .</auth-address><titles><title>miRviewer: a multispecies microRNA homologous viewer</title><secondary-title>BMC Res Notes</secondary-title><alt-title>BMC research notes</alt-title></titles><periodical><full-title>BMC Res Notes</full-title><abbr-1>BMC research notes</abbr-1></periodical><alt-periodical><full-title>BMC Res Notes</full-title><abbr-1>BMC research notes</abbr-1></alt-periodical><pages>92</pages><volume>5</volume><dates><year>2012</year></dates><isbn>1756-0500 (Electronic)
1756-0500 (Linking)</isbn><accession-num>22330228</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/22330228</url></related-urls></urls><custom2>3292992</custom2><electronic-resource-num>10.1186/1756-0500-5-92</electronic-resource-num></record></Cite></EndNote>[3] |
|
|
miRiadne |
Human |
miRNA annotation |
A tool for re-annotating miRNA name lists or datasets
|
http://www.miriadne.org/ |
[4] |
|
miRNAfe |
Any |
RNA sequences features |
A tool for RNA sequences features extraction |
http://fich.unl.edu.ar/sinc/blog/web-demo/mirnafe/ |
\n This email address is being protected from spambots. You need JavaScript enabled to view it. .
Research Center for Signals, Systems and Computational Intelligence, sinc(i), FICH-UNL, CONICET, Ciudad Universitaria UNL, 3000 Santa Fe, Argentina.
Instituto de Investigaciones en Microbiologia y Parasitologia Medica (UBA), CONICET, Paraguay 2155, piso 13, 1121, Buenos Aires, Argentina.</auth-address><titles><title>miRNAfe: A comprehensive tool for feature extraction in microRNA prediction</title><secondary-title>Biosystems</secondary-title><alt-title>Bio Systems</alt-title></titles><periodical><full-title>Biosystems</full-title><abbr-1>Bio Systems</abbr-1></periodical><alt-periodical><full-title>Biosystems</full-title><abbr-1>Bio Systems</abbr-1></alt-periodical><pages>1-5</pages><volume>138</volume><dates><year>2015</year><pub-dates><date>Dec</date></pub-dates></dates><isbn>1872-8324 (Electronic)
0303-2647 (Linking)</isbn><accession-num>26499212</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/26499212</url></related-urls></urls><electronic-resource-num>10.1016/j.biosystems.2015.10.003</electronic-resource-num></record></Cite></EndNote>[5] |
|
mirNEST |
Any |
miRNA sequence with integrative approach |
Collection of animal, plant and virus microRNAs miRNA prediction based on EST data Integration with 13 resources include miRNA expression, polymorphisms and targets
|
http://rhesus.amu.edu.pl/mirnest/copy/ |
[6] |
|
miROrtho |
Any |
Conservation of miRNAs in species |
Genomic location both known and predicted miRNAs Ortholog multiple alignments RNA secondary structure conservation |
[7] |
|
|
mirvar |
Human |
Genetic variations in microRNAs |
Genetic variants of miRNAs and its functional results |
[8] |
|
|
mirpub |
Any |
Search for publications related to microRNAs |
Information about the correlation of microRNAs to any diseases, tissues and genes |
http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=mirpub |
[9] |
|
miTRATA |
Any |
3′ modifications of microRNAs |
Analysis of 3′ modifications of microRNAs Including the loss or gain of nucleotides relative to the canonical sequence
|
https://wasabi.ddpsc.org/~apps/ta/ |
[10] |
|
PNRD |
Plant |
miRNA and ncRNA basic information |
Including literature mining, experimental targets, predicted targets, miRNA-ncRNA interaction, miRNA expression
|
http://structuralbiology.cau.edu.cn/PNRD/ |
\n This email address is being protected from spambots. You need JavaScript enabled to view it. .</auth-address><titles><title>PNRD: a plant non-coding RNA database</title><secondary-title>Nucleic Acids Res</secondary-title><alt-title>Nucleic acids research</alt-title></titles><periodical><full-title>Nucleic Acids Res</full-title><abbr-1>Nucleic acids research</abbr-1></periodical><alt-periodical><full-title>Nucleic Acids Res</full-title><abbr-1>Nucleic acids research</abbr-1></alt-periodical><pages>D982-9</pages><volume>43</volume><number>Database issue</number><keywords><keyword>*Databases, Nucleic Acid</keyword><keyword>Genomics</keyword><keyword>Internet</keyword><keyword>MicroRNAs/metabolism</keyword><keyword>RNA, Plant/chemistry/genetics/*metabolism</keyword><keyword>RNA, Untranslated/chemistry/genetics/*metabolism</keyword><keyword>Transcriptome</keyword></keywords><dates><year>2015</year><pub-dates><date>Jan</date></pub-dates></dates><isbn>1362-4962 (Electronic)
0305-1048 (Linking)</isbn><accession-num>25398903</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/25398903</url></related-urls></urls><custom2>4383960</custom2><electronic-resource-num>10.1093/nar/gku1162</electronic-resource-num></record></Cite></EndNote>[11] |
|
VIRmiRNA |
Virus |
Experimentally validated viral miRNAs |
Including VIRmiRNA, VIRmiRtar and AVIRmir subdatabases VIRmiRNA includes 1308 experimentally validated miRNA sequences with their isomiRs encoded by 44 viruses in viral miRNA |
http://crdd.osdd.net/servers/virmirna/ |
[12] |
|
WMD3 |
Plant |
Automated design of artificial plant microRNAs |
Platform requires only selection of favorite candidates according to a small set of criteria |
http://wmd3.weigelworld.org/cgi-bin/webapp.cgi?page= Home;project=stdwmd |
[13] |
|
Resources for Prediction of miRNA in A Sequence |
|||||
|
Resource |
Organism |
Main feature |
Unique features |
URL |
Reference |
|
CID-miRNA |
Human |
Identification of miRNAs in a sequence
|
Identification is based on secondary structure filtering systems |
[14] |
|
|
deepSOM |
Animal Plant |
Identification of miRNAs in a sequence |
Machine learning tool for novel miRNA precursor prediction in genome-wide data
|
http://fich.unl.edu.ar/sinc/blog/web-demo/deepsom/ |
[15] |
|
MapMI |
Any |
Recognition of miRNAs in a sequence |
Recognition is based on mapping validated miRNAs in one species to their most likely orthologous in other species
|
[16] |
|
|
MatureBayes |
Human Mouse |
Finding a mature miRNA in sequence |
Finding mature miRNA within a miRNA precursor Identification is based on the sequence and secondary structures |
[17] |
|
|
microPred |
Human |
Identification of a pre-miRNA in sequence |
Human pre-miRNA prediction with high sensitivity and specificity |
http://www.cs.ox.ac.uk/people/manohara.rukshan.batuwita/microPred.htm |
\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>microPred: effective classification of pre-miRNAs for human miRNA gene prediction</title><secondary-title>Bioinformatics</secondary-title><alt-title>Bioinformatics</alt-title></titles><periodical><full-title>Bioinformatics</full-title><abbr-1>Bioinformatics</abbr-1></periodical><alt-periodical><full-title>Bioinformatics</full-title><abbr-1>Bioinformatics</abbr-1></alt-periodical><pages>989-95</pages><volume>25</volume><number>8</number><keywords><keyword>Animals</keyword><keyword>Base Sequence</keyword><keyword>Computational Biology/*methods</keyword><keyword>Databases, Genetic</keyword><keyword>Humans</keyword><keyword>MicroRNAs/chemistry/*classification/*genetics</keyword><keyword>Molecular Sequence Data</keyword><keyword>Nucleic Acid Conformation</keyword><keyword>RNA Precursors/chemistry/*classification/*genetics</keyword><keyword>Sequence Analysis, RNA/methods</keyword><keyword>*Software</keyword></keywords><dates><year>2009</year><pub-dates><date>Apr 15</date></pub-dates></dates><isbn>1367-4811 (Electronic)
1367-4803 (Linking)</isbn><accession-num>19233894</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/19233894</url></related-urls></urls><electronic-resource-num>10.1093/bioinformatics/btp107</electronic-resource-num></record></Cite></EndNote>[18] |
|
Micro-pro SVM |
Human |
Recognition of miRNAs in a sequence |
Recognition of miRNA based on Drosha cleavage sites on a sequence |
https://demo1.interagon.com/miRNA/cgi-bin/MicroprocessorSVM.cgi |
[19] |
|
MiPred |
Human |
Recognition of miRNAs in a sequence |
Distinguish the real pre-miRNAs from other hairpin sequences with similar stem-loops |
http://www.bioinf.seu.edu.cn/miRNA/ |
[20] |
|
Mir-abela |
Human Mouse Rat
|
Identification of clustered microRNAs |
Discovery of novel miRNAs based on the theory that many miRNAs occur in clusters |
[21] |
|
|
Miralign |
Animal Plant |
Identification of miRNAs in a sequence |
Finding new miRNAs using structural similarity and sequence conservations
|
bioinfo.au.tsinghua.edu.cn/miralign |
[22] |
|
miRClassify |
Any |
Identification of miRNAs in a sequence |
A machine learning-based web server that can rapidly identify miRNA from the primary sequence
|
http://server.malab.cn/miRClassify/ |
[23] |
|
MirEval 2.0 |
Any |
Recognition of miRNAs in a sequence |
Finding new miRNAs based on secondary structure and conservation analysis
|
http://mimirna.centenary.org.au/mireval/ |
\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>Mireval: a web tool for simple microRNA prediction in genome sequences</title><secondary-title>Bioinformatics</secondary-title><alt-title>Bioinformatics</alt-title></titles><periodical><full-title>Bioinformatics</full-title><abbr-1>Bioinformatics</abbr-1></periodical><alt-periodical><full-title>Bioinformatics</full-title><abbr-1>Bioinformatics</abbr-1></alt-periodical><pages>1394-6</pages><volume>24</volume><number>11</number><keywords><keyword>*Algorithms</keyword><keyword>Base Sequence</keyword><keyword>Chromosome Mapping/*methods</keyword><keyword>*Internet</keyword><keyword>MicroRNAs/*genetics</keyword><keyword>Molecular Sequence Data</keyword><keyword>Sequence Analysis, RNA/*methods</keyword><keyword>*Software</keyword><keyword>*User-Computer Interface</keyword></keywords><dates><year>2008</year><pub-dates><date>Jun 1</date></pub-dates></dates><isbn>1367-4811 (Electronic)
1367-4803 (Linking)</isbn><accession-num>18453555</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/18453555</url></related-urls></urls><electronic-resource-num>10.1093/bioinformatics/btn137</electronic-resource-num></record></Cite></EndNote>[24] |
|
miRNA-dis |
Any |
Recognition of miRNAs in a sequence
|
MicroRNA precursor identification based on distance structure status pairs |
http://bioinformatics.hitsz.edu.cn/miRNA-dis/ |
\n This email address is being protected from spambots. You need JavaScript enabled to view it. This email address is being protected from spambots. You need JavaScript enabled to view it. This email address is being protected from spambots. You need JavaScript enabled to view it. This email address is being protected from spambots. You need JavaScript enabled to view it. This email address is being protected from spambots. You need JavaScript enabled to view it. .</auth-address><titles><title>miRNA-dis: microRNA precursor identification based on distance structure status pairs</title><secondary-title>Mol Biosyst</secondary-title><alt-title>Molecular bioSystems</alt-title></titles><periodical><full-title>Mol Biosyst</full-title><abbr-1>Molecular bioSystems</abbr-1></periodical><alt-periodical><full-title>Mol Biosyst</full-title><abbr-1>Molecular bioSystems</abbr-1></alt-periodical><pages>1194-204</pages><volume>11</volume><number>4</number><keywords><keyword>Animals</keyword><keyword>Computational Biology/*methods</keyword><keyword>Databases, Genetic</keyword><keyword>Humans</keyword><keyword>Internet</keyword><keyword>MicroRNAs/*chemistry/*genetics</keyword><keyword>RNA, Plant</keyword><keyword>RNA, Viral</keyword><keyword>*User-Computer Interface</keyword></keywords><dates><year>2015</year><pub-dates><date>Apr</date></pub-dates></dates><isbn>1742-2051 (Electronic)
1742-2051 (Linking)</isbn><accession-num>25715848</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/25715848</url></related-urls></urls><electronic-resource-num>10.1039/c5mb00050e</electronic-resource-num></record></Cite></EndNote>[25] |
|
miRNAFold |
Any |
Recognition of miRNAs in a sequence
|
Ab initio miRNA precursor prediction in genomes |
https://evryrna.ibisc.univ-evry.fr/miRNAFold/ |
\n This email address is being protected from spambots. You need JavaScript enabled to view it. .</auth-address><titles><title>miRNAFold: a web server for fast miRNA precursor prediction in genomes</title><secondary-title>Nucleic Acids Res</secondary-title><alt-title>Nucleic acids research</alt-title></titles><periodical><full-title>Nucleic Acids Res</full-title><abbr-1>Nucleic acids research</abbr-1></periodical><alt-periodical><full-title>Nucleic Acids Res</full-title><abbr-1>Nucleic acids research</abbr-1></alt-periodical><dates><year>2016</year><pub-dates><date>May 29</date></pub-dates></dates><isbn>1362-4962 (Electronic)
0305-1048 (Linking)</isbn><accession-num>27242364</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/27242364</url></related-urls></urls><electronic-resource-num>10.1093/nar/gkw459</electronic-resource-num></record></Cite></EndNote>[26] |
|
miRNAminer |
Vertebrates |
Finding homologous miRNA genes
|
Identifying conserved homolog miRNA genes Analyzing 10 vertebrates |
\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>miRNAminer: a tool for homologous microRNA gene search</title><secondary-title>BMC Bioinformatics</secondary-title><alt-title>BMC bioinformatics</alt-title></titles><periodical><full-title>BMC Bioinformatics</full-title><abbr-1>BMC bioinformatics</abbr-1></periodical><alt-periodical><full-title>BMC Bioinformatics</full-title><abbr-1>BMC bioinformatics</abbr-1></alt-periodical><pages>39</pages><volume>9</volume><keywords><keyword>Animals</keyword><keyword>Base Sequence</keyword><keyword>Cattle</keyword><keyword>Databases, Genetic/trends</keyword><keyword>Dogs</keyword><keyword>Humans</keyword><keyword>Internet/trends</keyword><keyword>Mice</keyword><keyword>MicroRNAs/analysis/*genetics</keyword><keyword>Molecular Sequence Data</keyword><keyword>Opossums</keyword><keyword>Pan troglodytes</keyword><keyword>Rats</keyword><keyword>*Sequence Homology, Nucleic Acid</keyword></keywords><dates><year>2008</year></dates><isbn>1471-2105 (Electronic)
1471-2105 (Linking)</isbn><accession-num>18215311</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/18215311</url></related-urls></urls><custom2>2258288</custom2><electronic-resource-num>10.1186/1471-2105-9-39</electronic-resource-num></record></Cite></EndNote>[27] |
|
|
miRNA SVM |
Human |
Identification of miRNAs in a sequence |
Suggesting microRNAs by a classifier that predicts 5´ Drosha processing sites in hairpins that are candidate miRNAs |
[19] |
|
|
miRNAfinder & target Search |
Human Mouse Rat |
Recognition of miRNAs in a sequence |
Finding microRNA candidates in a sequence display target expression |
|
|
|
miRQuest |
Human Plant |
Recognition of miRNAs in a sequence |
miRNA prediction interface which integrates four main tools A benchmarking function to identify which one of the four integrated tools is more suitable for the species of interest
|
http://mirquest.integrativebioinformatics.me/index.php |
[28] |
|
MiRscan |
Worm |
Identification of miRNAs in a sequence
|
Prediction based on sequence conservation and structural conformation |
[29] |
|
|
PlantMiRNAPred |
Plant |
Identification of miRNAs in a sequence |
Classify real plant pre-miRNAs and pseudo hairpins |
http://nclab.hit.edu.cn/PlantMiRNAPred/ |
[30] |
|
ProMiR II |
Mammals Fly Worm |
Recognition of miRNAs in a sequence |
Conserved, non-conserved, clustered, non-clustered miRNA prediction Incorpating stem-loop filter and conservation score filter Consists of three programs: ProMiR-v, ProMiR-c and ProMiR-g
|
https://bi.snu.ac.kr/Research/ProMiR/ProMiR.html |
[31] |
|
psRobot |
Plant |
Analyze batch of plant small RNA data |
Stem-loop small RNA prediction Small RNA target prediction
|
http://omicslab.genetics.ac.cn/psRobot/ |
[32] |
|
SSCprofiler |
Human |
Identification of miRNAs in a sequence |
Predicting putative miRNA genes based on sequence, structure and conservation Scanning by entering chromosome number and start and end nucleotide |
[33] |
|
|
Vir-Mir db |
Viruses |
miRNA identification |
Prediction of viral miRNA candidate hairpins |
[34] |
|
|
miRNA Target Prediction Resources |
|||||
|
Single Resource Target Prediction |
|||||
|
Resource |
Organism |
Main feature |
Unique features |
URL |
Reference |
|
TargetScan |
Mammals Fly Worm |
miRNA target prediction |
Finding broadly conserved, conserved and poorly conserved microRNA families Showing miRNA position on gene Alignment of miRNA target site in different organisms |
[35] |
|
|
Bi-Targeting |
Human |
Viral and host miRNAs cooperatively regulate host gene expression |
Viral and host miRNAs that cooperate in gene regulation Integrate miRNA-target binding information, miRNA expression profiles and GO annotations
|
\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>Gene bi-targeting by viral and human miRNAs</title><secondary-title>BMC Bioinformatics</secondary-title><alt-title>BMC bioinformatics</alt-title></titles><periodical><full-title>BMC Bioinformatics</full-title><abbr-1>BMC bioinformatics</abbr-1></periodical><alt-periodical><full-title>BMC Bioinformatics</full-title><abbr-1>BMC bioinformatics</abbr-1></alt-periodical><pages>249</pages><volume>11</volume><keywords><keyword>*Algorithms</keyword><keyword>Gene Regulatory Networks</keyword><keyword>Herpesvirus 4, Human/genetics</keyword><keyword>Humans</keyword><keyword>MicroRNAs/*genetics</keyword><keyword>RNA Processing, Post-Transcriptional</keyword><keyword>RNA, Messenger/*genetics</keyword><keyword>RNA, Viral/*genetics</keyword></keywords><dates><year>2010</year></dates><isbn>1471-2105 (Electronic)
1471-2105 (Linking)</isbn><accession-num>20465802</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/20465802</url></related-urls></urls><custom2>3583137</custom2><electronic-resource-num>10.1186/1471-2105-11-249</electronic-resource-num></record></Cite></EndNote>[36] |
|
|
comTAR |
Plant |
miRNA target prediction |
Analyze the variations of known miRNA targets during evolution
|
http://rnabiology.ibr-conicet.gov.ar/comtar/home |
[37] |
|
DIANA-LncBase
|
Human Mouse |
miRNA targets on long non-coding RNAs |
Computationally predicted and experimentally validated results Genomic locations
|
|
|
|
DIANA-LncBase v2 |
Human Mouse |
miRNA targets on long non-coding RNAs |
Computationally predicted and experimentally validated results Genomic locations
|
[38] |
|
|
DIANA-microT V.4 |
Human Mouse |
miRNA target prediction |
Finding targets based on miRNAs, genes or miRNA and gene Link to KEGG, UniProt and iHOP present predictions of TargetScan or Pictar or verification of TarBase Conservation of target sites in different species |
http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=microtv4/index |
[39] |
|
DIANA-microT-CDS V.5 |
Human Mouse Worm Fly |
miRNA target prediction |
Finding targets of a miRNAs based on miRNAs, genes or KEGG descriptions Present predictions of TargetScan, Miranda or verification of TarBase Conservation of target sites in different species |
http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=microT_CDS/index |
[40] |
|
EIMMo |
Human Mouse Rat Fish Worm Fly |
miRNA target prediction |
Target prediction for mRNAs in subsets of transcripts or different tissue or cell type Alignment of multiple genomes in region of predated target site Link to smiRNAdb samples that expression of selected miRNA is high
|
[41] |
|
|
GUUGle |
Any |
miRNA target prediction |
Locates potential helical regions under RNA base pairing rules, which include Watson-Crick as well as G-U pairs
|
http://bibiserv.techfak.uni-bielefeld.de/guugle |
[42] |
|
HomoloMTI |
Mammals
|
Homology of miRNA target prediction |
Identifying miRNA target sites on conserved sequences among several species Integrated three resources, miRTarBase, miRBase and HomoloGene |
|
|
|
mBISON |
Human Mouse |
miRNA target prediction |
Calculates the significance of over-representation of miRNA targets in a given non-ranked gene set |
http://cbdm.mdc-berlin.de/~mgebhardt/cgi-bin/mbison/home/ |
[43] |
|
MAMI |
Human |
miRNA target prediction |
Specificity and sensitivity tuning for prediction
|
|
|
|
MicroCosm |
Any |
miRNA target prediction |
Microcosm is basically derived from miRBase resource targets Search by gene or miRNA name, GO term or keyword Alignment of multiple genomes in region of predated target site
|
http://www.ebi.ac.uk/enright-srv/microcosm/htdocs/targets/v5/ |
\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>miRBase: tools for microRNA genomics</title><secondary-title>Nucleic Acids Res</secondary-title><alt-title>Nucleic acids research</alt-title></titles><periodical><full-title>Nucleic Acids Res</full-title><abbr-1>Nucleic acids research</abbr-1></periodical><alt-periodical><full-title>Nucleic Acids Res</full-title><abbr-1>Nucleic acids research</abbr-1></alt-periodical><pages>D154-8</pages><volume>36</volume><number>Database issue</number><keywords><keyword>Animals</keyword><keyword>*Databases, Nucleic Acid</keyword><keyword>Gene Silencing</keyword><keyword>*Genomics</keyword><keyword>Humans</keyword><keyword>Internet</keyword><keyword>Mice</keyword><keyword>MicroRNAs/chemistry/*genetics</keyword><keyword>RNA, Messenger/metabolism</keyword><keyword>Software</keyword><keyword>Terminology as Topic</keyword></keywords><dates><year>2008</year><pub-dates><date>Jan</date></pub-dates></dates><isbn>1362-4962 (Electronic)
0305-1048 (Linking)</isbn><accession-num>17991681</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/17991681</url></related-urls></urls><custom2>2238936</custom2><electronic-resource-num>10.1093/nar/gkm952</electronic-resource-num></record></Cite></EndNote>[44] |
|
microInspector |
Any Plant
|
miRNA binding sites |
Finding miRNA binding sites in a target sequence Analysis a user-defined RNA sequence |
http://bioinfo1.uni-plovdiv.bg/cgi-bin/microinspector/ |
[45] |
|
microRNA.org |
Human Mouse Rat Worm Fly |
miRNA target prediction |
miRNA target prediction using miRanda algorithm Search available for mRNA or miRNA Showing miRNA-mRNA interaction |
[46] |
|
|
miRcode |
Human |
Whole transcriptome miRNA target prediction |
Target prediction for mRNA, LncRNA and pseudogene Including 5´ UTR's , coding regions and 3´ UTR's |
http://www.mircode.org |
[47] |
|
miRDB |
Human Mouse Rat Dog Chicken
|
miRNA target prediction and functional annotation |
miRNA target prediction using miRanda algorithm Search for multiple miRNAs or genes |
\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>miRDB: a microRNA target prediction and functional annotation database with a wiki interface</title><secondary-title>RNA</secondary-title><alt-title>Rna</alt-title></titles><periodical><full-title>RNA</full-title><abbr-1>Rna</abbr-1></periodical><alt-periodical><full-title>RNA</full-title><abbr-1>Rna</abbr-1></alt-periodical><pages>1012-7</pages><volume>14</volume><number>6</number><keywords><keyword>Animals</keyword><keyword>Base Sequence</keyword><keyword>*Computational Biology</keyword><keyword>*Databases, Nucleic Acid</keyword><keyword>Dogs</keyword><keyword>Humans</keyword><keyword>Mice</keyword><keyword>MicroRNAs/*physiology</keyword><keyword>Molecular Sequence Data</keyword><keyword>*Online Systems</keyword><keyword>Rats</keyword><keyword>*Software</keyword></keywords><dates><year>2008</year><pub-dates><date>Jun</date></pub-dates></dates><isbn>1469-9001 (Electronic)
1355-8382 (Linking)</isbn><accession-num>18426918</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/18426918</url></related-urls></urls><custom2>2390791</custom2><electronic-resource-num>10.1261/rna.965408</electronic-resource-num></record></Cite></EndNote>[48] |
|
|
MirEE |
Human Mouse Worm |
miRNA target prediction
|
miRNA target prediction using an Ab-initio module followed by a SVM module |
http://eda.polito.it/miREE/ |
\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>miREE: miRNA recognition elements ensemble</title><secondary-title>BMC Bioinformatics</secondary-title><alt-title>BMC bioinformatics</alt-title></titles><periodical><full-title>BMC Bioinformatics</full-title><abbr-1>BMC bioinformatics</abbr-1></periodical><alt-periodical><full-title>BMC Bioinformatics</full-title><abbr-1>BMC bioinformatics</abbr-1></alt-periodical><pages>454</pages><volume>12</volume><keywords><keyword>Animals</keyword><keyword>*Artificial Intelligence</keyword><keyword>Gene Expression Regulation</keyword><keyword>Humans</keyword><keyword>MicroRNAs/*genetics/metabolism</keyword><keyword>RNA, Messenger/metabolism</keyword><keyword>*Regulatory Sequences, Ribonucleic Acid</keyword><keyword>Sensitivity and Specificity</keyword><keyword>Software</keyword><keyword>Support Vector Machines</keyword></keywords><dates><year>2011</year></dates><isbn>1471-2105 (Electronic)
1471-2105 (Linking)</isbn><accession-num>22115078</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/22115078</url></related-urls></urls><custom2>3265527</custom2><electronic-resource-num>10.1186/1471-2105-12-454</electronic-resource-num></record></Cite></EndNote>[49] |
|
miRMaid |
Any |
Integrating miRNA data sources |
Integrating miRNA data sources and developing an interface for computer programming
|
\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>miRMaid: a unified programming interface for microRNA data resources</title><secondary-title>BMC Bioinformatics</secondary-title><alt-title>BMC bioinformatics</alt-title></titles><periodical><full-title>BMC Bioinformatics</full-title><abbr-1>BMC bioinformatics</abbr-1></periodical><alt-periodical><full-title>BMC Bioinformatics</full-title><abbr-1>BMC bioinformatics</abbr-1></alt-periodical><pages>29</pages><volume>11</volume><keywords><keyword>Computational Biology/*methods</keyword><keyword>Databases, Genetic</keyword><keyword>MicroRNAs/*chemistry</keyword><keyword>*Programming Languages</keyword><keyword>Sequence Analysis, RNA</keyword><keyword>*Software</keyword></keywords><dates><year>2010</year></dates><isbn>1471-2105 (Electronic)
1471-2105 (Linking)</isbn><accession-num>20074352</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/20074352</url></related-urls></urls><custom2>2831003</custom2><electronic-resource-num>10.1186/1471-2105-11-29</electronic-resource-num></record></Cite></EndNote>[50] |
|
|
miRmap |
Mammals Fish |
miRNA target prediction |
Prediction of microRNA target repression strength Including 5´ UTR's , coding regions and 3´ UTR's |
http://mirmap.ezlab.org/ |
[51] |
|
miRNA_Targets |
Fish Worm Fly |
miRNA target prediction
|
Target prediction using miRanda and RNAhybrid algorithms on mRNA 5´ UTR's , coding regions and 3´ UTR's |
http://mamsap.it.deakin.edu.au/~amitkuma/mirna_targetsnew/index.html |
[52] |
|
MirTif |
Any |
miRNA target interaction filter |
A post-processing filter for the miRNA: gene hybrids prediction of various algorithms
|
\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>MiRTif: a support vector machine-based microRNA target interaction filter</title><secondary-title>BMC Bioinformatics</secondary-title><alt-title>BMC bioinformatics</alt-title></titles><periodical><full-title>BMC Bioinformatics</full-title><abbr-1>BMC bioinformatics</abbr-1></periodical><alt-periodical><full-title>BMC Bioinformatics</full-title><abbr-1>BMC bioinformatics</abbr-1></alt-periodical><pages>S4</pages><volume>9 Suppl 12</volume><keywords><keyword>3' Untranslated Regions</keyword><keyword>Algorithms</keyword><keyword>Area Under Curve</keyword><keyword>Artificial Intelligence</keyword><keyword>Computational Biology/methods</keyword><keyword>Computer Simulation</keyword><keyword>Computers</keyword><keyword>False Positive Reactions</keyword><keyword>Humans</keyword><keyword>MicroRNAs/*genetics/metabolism</keyword><keyword>Pattern Recognition, Automated/methods</keyword><keyword>Reproducibility of Results</keyword><keyword>Sensitivity and Specificity</keyword><keyword>Sequence Analysis, RNA/methods</keyword><keyword>Software</keyword></keywords><dates><year>2008</year></dates><isbn>1471-2105 (Electronic)
1471-2105 (Linking)</isbn><accession-num>19091027</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/19091027</url></related-urls></urls><custom2>2638144</custom2><electronic-resource-num>10.1186/1471-2105-9-S12-S4</electronic-resource-num></record></Cite></EndNote>[53] |
|
|
MtiBase |
Human Mouse |
miRNA-target interactions database |
Identify CDS-located and 5'UTR-located miRNA binding sites Systematically evaluate miRNA regulatory effects on mRNA stability and translation |
http://mtibase.sysu.edu.cn/index.php |
[54] |
|
MultiMiTar |
Any |
miRNA target prediction |
Target prediction with multi-objective feature selection |
http://www.isical.ac.in/~bioinfo_miu/multimitar.htm |
[55] |
|
NBmiRTar |
Any |
miRNA target prediction |
Target prediction based on NbmiRTar algorithm |
[56] |
|
|
Patrocles |
Vertebrates |
Polymorphisms affect gene regulation |
DNA polymorphisms predicted to affect miRNA-gene control |
[57] |
|
|
PicTar |
Vertebrate Nematode Fly |
miRNA target prediction |
Target prediction based on PicTar algorithm Multiple sequence alignment in region of predated target site |
[58] |
|
|
P-TAREF |
Plant |
miRNA target prediction |
Refines the process of microRNA target identification through incorporation of local interaction information
|
http://scbb.ihbt.res.in/new/p-taref/form1.html |
[59] |
|
repTar |
Human Mouse
|
miRNA target prediction |
Target prediction in human, mouse and several cellular targets of viral miRNAs |
[60] |
|
|
RNA22 v2 |
Human Mouse Fly Worm |
miRNA target prediction |
Identifying microRNA binding sites and their corresponding heteroduplexes Access pre-computed rna22 target predictions for multiple species |
http://cm.jefferson.edu/rna22/Precomputed/ |
[61] |
|
STarMir |
Human Mouse Worm
|
miRNA binding sites |
Finding miRNA binding sites in a target sequence Analysis a user-defined RNA sequence |
http://sfold.wadsworth.org/cgi-bin/starmir.pl |
\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>Sfold web server for statistical folding and rational design of nucleic acids</title><secondary-title>Nucleic Acids Res</secondary-title><alt-title>Nucleic acids research</alt-title></titles><periodical><full-title>Nucleic Acids Res</full-title><abbr-1>Nucleic acids research</abbr-1></periodical><alt-periodical><full-title>Nucleic Acids Res</full-title><abbr-1>Nucleic acids research</abbr-1></alt-periodical><pages>W135-41</pages><volume>32</volume><number>Web Server issue</number><keywords><keyword>Algorithms</keyword><keyword>Computational Biology</keyword><keyword>Internet</keyword><keyword>Models, Statistical</keyword><keyword>Nucleic Acid Conformation</keyword><keyword>Oligonucleotides, Antisense/chemistry</keyword><keyword>RNA/*chemistry</keyword><keyword>RNA Stability</keyword><keyword>RNA, Catalytic/chemistry</keyword><keyword>RNA, Small Interfering/chemistry</keyword><keyword>*Software</keyword><keyword>User-Computer Interface</keyword></keywords><dates><year>2004</year><pub-dates><date>Jul 1</date></pub-dates></dates><isbn>1362-4962 (Electronic)
0305-1048 (Linking)</isbn><accession-num>15215366</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/15215366</url></related-urls></urls><custom2>441587</custom2><electronic-resource-num>10.1093/nar/gkh449</electronic-resource-num></record></Cite></EndNote>[62] |
|
TargetMiner |
Human Mouse Fly
|
miRNA target prediction |
Target prediction with systematic identification of negative examples |
http://www.isical.ac.in/~bioinfo_miu/targetminer20.htm |
\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples</title><secondary-title>Bioinformatics</secondary-title><alt-title>Bioinformatics</alt-title></titles><periodical><full-title>Bioinformatics</full-title><abbr-1>Bioinformatics</abbr-1></periodical><alt-periodical><full-title>Bioinformatics</full-title><abbr-1>Bioinformatics</abbr-1></alt-periodical><pages>2625-31</pages><volume>25</volume><number>20</number><keywords><keyword>Animals</keyword><keyword>Artificial Intelligence</keyword><keyword>Computational Biology/*methods</keyword><keyword>Databases, Nucleic Acid</keyword><keyword>Humans</keyword><keyword>Internet</keyword><keyword>MicroRNAs/*chemistry</keyword><keyword>RNA, Messenger/chemistry</keyword><keyword>Sequence Analysis, RNA</keyword><keyword>*Software</keyword></keywords><dates><year>2009</year><pub-dates><date>Oct 15</date></pub-dates></dates><isbn>1367-4811 (Electronic)
1367-4803 (Linking)</isbn><accession-num>19692556</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/19692556</url></related-urls></urls><electronic-resource-num>10.1093/bioinformatics/btp503</electronic-resource-num></record></Cite></EndNote>[63] |
|
TargetRank |
Human Mouse |
miRNA target prediction |
Targeting by endogenous and exogenous microRNAs and siRNAs |
[64] |
|
|
TargetRNA2 |
Bacteria |
sRNA target prediction |
Identifies mRNA targets of sRNA regulatory action in bacteria |
http://cs.wellesley.edu/~btjaden/TargetRNA2/ |
\n This email address is being protected from spambots. You need JavaScript enabled to view it. .</auth-address><titles><title>TargetRNA2: identifying targets of small regulatory RNAs in bacteria</title><secondary-title>Nucleic Acids Res</secondary-title><alt-title>Nucleic acids research</alt-title></titles><periodical><full-title>Nucleic Acids Res</full-title><abbr-1>Nucleic acids research</abbr-1></periodical><alt-periodical><full-title>Nucleic Acids Res</full-title><abbr-1>Nucleic acids research</abbr-1></alt-periodical><pages>W124-9</pages><volume>42</volume><number>Web Server issue</number><keywords><keyword>Escherichia coli/genetics</keyword><keyword>Internet</keyword><keyword>Nucleic Acid Conformation</keyword><keyword>RNA, Bacterial/*chemistry/metabolism</keyword><keyword>RNA, Messenger/*chemistry/metabolism</keyword><keyword>RNA, Small Untranslated/*chemistry/metabolism</keyword><keyword>Sequence Analysis, RNA</keyword><keyword>*Software</keyword></keywords><dates><year>2014</year><pub-dates><date>Jul</date></pub-dates></dates><isbn>1362-4962 (Electronic)
0305-1048 (Linking)</isbn><accession-num>24753424</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/24753424</url></related-urls></urls><custom2>4086111</custom2><electronic-resource-num>10.1093/nar/gku317</electronic-resource-num></record></Cite></EndNote>[65] |
|
TargetSpy |
Human Mouse Rat Chicken Fly |
miRNA target prediction |
Target prediction based on scores without demanding a seed match |
http://webclu.bio.wzw.tum.de/targetspy/index.php?down=true |
[66] |
|
VIRmiRNA |
Virus |
miRNA target prediction |
Including VIRmiRNA, VIRmiRtar and AVIRmir subdatabases VIRmiRtar contains 7283 target genes of viral miRNAs AVIRmir includes 542 antiviral miRNAs encoded by the host against 24 viruses |
http://crdd.osdd.net/servers/virmirna/ |
[12] |
|
Vita |
Human Mouse Rat Chicken Virus |
miRNA target prediction |
Prediction of host miRNA targets in viruses |
[67] |
|
|
miRNA Target Prediction Resources |
|||||
|
User Defined Sequence Resources |
|||||
|
Resource |
Organism |
Main feature |
Unique features |
URL |
Reference |
|
RNAhybrid |
Human Worm Fly |
Hybridization of two RNA sequence |
Searching the minimum free energy hybridization of two desired RNA sequences |
[68] |
|
|
IntaRNA |
Any |
Interaction prediction for your own sequence |
Prediction of interactions between two RNA molecules |
http://rna.informatik.uni-freiburg.de/IntaRNA/Input.jsp |
\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions</title><secondary-title>Bioinformatics</secondary-title><alt-title>Bioinformatics</alt-title></titles><periodical><full-title>Bioinformatics</full-title><abbr-1>Bioinformatics</abbr-1></periodical><alt-periodical><full-title>Bioinformatics</full-title><abbr-1>Bioinformatics</abbr-1></alt-periodical><pages>2849-56</pages><volume>24</volume><number>24</number><keywords><keyword>Computational Biology/*methods</keyword><keyword>Escherichia coli/genetics/metabolism</keyword><keyword>RNA, Bacterial/*chemistry</keyword><keyword>RNA, Messenger/chemistry</keyword><keyword>RNA, Untranslated/*chemistry</keyword><keyword>*Software</keyword></keywords><dates><year>2008</year><pub-dates><date>Dec 15</date></pub-dates></dates><isbn>1367-4811 (Electronic)
1367-4803 (Linking)</isbn><accession-num>18940824</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/18940824</url></related-urls></urls><custom2>2639303</custom2><electronic-resource-num>10.1093/bioinformatics/btn544</electronic-resource-num></record></Cite></EndNote>[69] |
|
miRNA_Targets |
Any |
Interaction prediction for your own sequence |
Interaction prediction of a desired sequence and known miRNAs Target prediction using miRanda and RNAhybrid algorithms on mRNA 5´ UTR's , coding regions and 3´ UTR's
|
http://mamsap.it.deakin.edu.au/~amitkuma/mirna_targetsnew/index.html |
[52] |
|
MIRZA |
Any |
Interaction prediction for your own sequence |
A biophysical miRNA-mRNA interaction model based on Argonaute 2 cross-linking and immunoprecipitation data |
http://www.clipz.unibas.ch/index.php?r=tools/sub/mirza
|
[70] |
|
MR-microT |
Human Mouse Fly
|
Interaction prediction for your own sequence |
Provides near-real time predictions for custom miRNA sequences |
http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=mrmicrot/index |
\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>Functional microRNA targets in protein coding sequences</title><secondary-title>Bioinformatics</secondary-title><alt-title>Bioinformatics</alt-title></titles><periodical><full-title>Bioinformatics</full-title><abbr-1>Bioinformatics</abbr-1></periodical><alt-periodical><full-title>Bioinformatics</full-title><abbr-1>Bioinformatics</abbr-1></alt-periodical><pages>771-6</pages><volume>28</volume><number>6</number><keywords><keyword>*3' Untranslated Regions</keyword><keyword>Algorithms</keyword><keyword>Animals</keyword><keyword>Humans</keyword><keyword>MicroRNAs/chemistry/genetics/*metabolism</keyword><keyword>*Open Reading Frames</keyword><keyword>*Regulatory Sequences, Ribonucleic Acid</keyword></keywords><dates><year>2012</year><pub-dates><date>Mar 15</date></pub-dates></dates><isbn>1367-4811 (Electronic)
1367-4803 (Linking)</isbn><accession-num>22285563</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/22285563</url></related-urls></urls><electronic-resource-num>10.1093/bioinformatics/bts043</electronic-resource-num></record></Cite></EndNote>[71] |
|
PITA |
Human Mouse Fly Worm |
Interaction prediction for your own sequence |
Assessment of interactions between RNA sequences based on PITA algorithm Using known miRNAs or user-provided miRNA sequences |
http://genie.weizmann.ac.il/pubs/mir07/mir07_prediction.html |
[72] |
|
psRNATarget |
Plant |
miRNA target prediction |
Reverse complementary matching between miRNA and target transcript using a proven scoring schema Target site accessibility evaluation by calculating unpaired energy
|
http://plantgrn.noble.org/psRNATarget/ |
[73] |
|
RNA22 v2 |
Human Mouse Fly Worm |
Interaction prediction for your own sequence |
Identifying microRNA binding sites and their corresponding heteroduplexes Interaction prediction between a desired miRNA and target sequence
|
http://cm.jefferson.edu/rna22/Interactive/ |
[61] |
|
TAPIR |
Plant |
miRNA target prediction |
Search for plant miRNA targets using a fast and a precise algorithm User defined score and free energy ratio |
http://bioinformatics.psb.ugent.be/webtools/tapir/ |
[74] |
|
miRNA Target Prediction Resources |
|||||
|
Composite Target Prediction Resources |
|||||
|
Resource |
Organism |
Main feature |
Unique features |
URL |
Reference |
|
miRWalk 2.0 |
Human Mouse Rat |
User-friendly composite target prediction resource |
Combining miRNA target prediction results from DIANA-microT, miRanda, MirTarget2, RNAhybrid, PicTar4, PicTar5, PITA, RNA22, TargetScan and miRWalk Search of binding sites within 5´ UTR, CDS and 3´UTR Search in all or longer transcripts Predicted targets are diagrammed to pathways and diseases
|
[75] |
|
|
BcmicrO |
Human |
Composite target prediction resource |
Combines the prediction of TargetScan, miRanda, PicTar, mirTarget, PITA, and Diana microT
|
http://compgenomics.utsa.edu/gene/gene_1.php |
[76] |
|
ComiR |
Human Mouse Worm Fly |
Composite target prediction resource |
Combining miRNA target prediction results from miRanda, PITA, TargetScan and mirSVR Using miRNA expression to improve and combine multiple miRNA targets
|
http://www.benoslab.pitt.edu/comir/ |
\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>ComiR: Combinatorial microRNA target prediction tool</title><secondary-title>Nucleic Acids Res</secondary-title><alt-title>Nucleic acids research</alt-title></titles><periodical><full-title>Nucleic Acids Res</full-title><abbr-1>Nucleic acids research</abbr-1></periodical><alt-periodical><full-title>Nucleic Acids Res</full-title><abbr-1>Nucleic acids research</abbr-1></alt-periodical><pages>W159-64</pages><volume>41</volume><number>Web Server issue</number><keywords><keyword>3' Untranslated Regions</keyword><keyword>Algorithms</keyword><keyword>Animals</keyword><keyword>Caenorhabditis elegans/genetics</keyword><keyword>Drosophila melanogaster/genetics</keyword><keyword>Gene Expression Regulation</keyword><keyword>Humans</keyword><keyword>Internet</keyword><keyword>Mice</keyword><keyword>MicroRNAs/*metabolism</keyword><keyword>Polymorphism, Single Nucleotide</keyword><keyword>RNA, Messenger/chemistry/*metabolism</keyword><keyword>*Software</keyword></keywords><dates><year>2013</year><pub-dates><date>Jul</date></pub-dates></dates><isbn>1362-4962 (Electronic)
0305-1048 (Linking)</isbn><accession-num>23703208</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/23703208</url></related-urls></urls><custom2>3692082</custom2><electronic-resource-num>10.1093/nar/gkt379</electronic-resource-num></record></Cite></EndNote>[77] |
|
HocTar |
Human |
Composite target prediction resource |
Integrating miRNA target predictions of miRanda, TargetScan and PicTar
|
\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>HOCTAR database: a unique resource for microRNA target prediction</title><secondary-title>Gene</secondary-title><alt-title>Gene</alt-title></titles><periodical><full-title>Gene</full-title><abbr-1>Gene</abbr-1></periodical><alt-periodical><full-title>Gene</full-title><abbr-1>Gene</abbr-1></alt-periodical><pages>51-8</pages><volume>480</volume><number>1-2</number><keywords><keyword>Computational Biology/methods</keyword><keyword>*Databases, Factual</keyword><keyword>*Gene Expression Regulation</keyword><keyword>Humans</keyword><keyword>*MicroRNAs</keyword><keyword>Reproducibility of Results</keyword></keywords><dates><year>2011</year><pub-dates><date>Jul 1</date></pub-dates></dates><isbn>1879-0038 (Electronic)
0378-1119 (Linking)</isbn><accession-num>21435384</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/21435384</url></related-urls></urls><custom2>3113163</custom2><electronic-resource-num>10.1016/j.gene.2011.03.005</electronic-resource-num></record></Cite></EndNote>[78] |
|
|
mirDIP |
Human |
Composite target prediction source |
Merging microRNA predictions twelve microRNA prediction datasets from DIANA-microT, microcosm, miRanda, PicTar, PITA, RNA22 and TargetScan algorithms Finding signaling pathway-associated microRNAs
|
[79] |
|
|
miRecords |
Mammals Fish Worm Fly |
Composite target prediction source for nine species |
Combining of predicted miRNA targets produced by 11 algorithms DIANA-microT, MicroInspector, miRanda, MirTarget2, miTarget, NBmiRTar, PicTar, PITA, RNA22, RNAhybrid and TargetScan Target predictions can be pooled with the validated interactions
|
http://c1.accurascience.com/miRecords/ |
[80] |
|
miRGate |
Human Mouse Rat |
Composite target prediction resource |
Using miRanda, Pita, RNAHybrid, Microtar, TargetScan, TarBase, mirTarBase and miRecords Analyze miRNA and gene isoforms lists under a common and consistent space of annotations
|
http://mirgate.bioinfo.cnio.es/miRGate/ |
[81] |
|
miRGator v3.0 |
Human |
Composite target prediction resource |
Joining the results of PicTar, TargetScan, miRanda, microcosm, PITA and miRDB algorithms Containing microRNA diversity, expression profiles and target relationships |
[82] |
|
|
miRNA body map |
Human Mouse Rat |
Composite target prediction resource |
Integration of predicted miRNA targets produced by eight miRNA target algorithms PITA, DIANA-microT, Microcosm, RNA22, TargetScan, miRDB, TarBase and miRecords miRNA function and their effect on pathways
|
http://mellfire.ugent.be/public/body_map/ |
[83] |
|
miRNAMap 2.0 |
Human |
Composite target prediction resource |
Combining miRNA targeting results of Miranda, RNAHybrid and TargetScan algorithms
|
[84] |
|
|
miRSystem |
Human Mouse |
Composite target prediction resource |
Combining miRNA targeting of DIANA, miRanda, miRBridge, PicTar, PITA, rna22 and TargetScan algorithms
|
http://mirsystem.cgm.ntu.edu.tw/index.php |
[85] |
|
mirTarPri |
Human |
Composite target prediction based on functional genomic data |
Prioritizing candidate mirRNA targets in the context of functional genomic data Using Gene Ontology and protein protein interaction networks Provides mirRNA target list of TargetScan, PicTar, PITA,DIANA-microT, miRanda, RNAhybrid tarBase, mirRecord and mir2Disease
|
http://www.bio-bigdata.com/mirTarPri/ |
[86] |
|
miRò v 2.0 |
Human |
Composite target prediction resource |
Integration miRNA target predictions of miRanda, PicTar, TargetScan and miRecords algorithms |
http://microrna.osumc.edu/miro/home/about?page_name=About |
[87] |
|
mirRor Suite |
|||||