MicroRNA and microRNA target database - Revision history

Headbomb: ce

2025-03-30T08:13:39Z

← Previous revision		Revision as of 08:13, 30 March 2025
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	\| title = Prediction methods for microRNA targets in bilaterian animals: Toward a better understanding by biologists		\| title = Prediction methods for microRNA targets in bilaterian animals: Toward a better understanding by biologists
	\| doi = 10.1016/j.csbj.2021.10.025		\| doi = 10.1016/j.csbj.2021.10.025
	\| journal = Comput Struct Biotechnol J.		\| journal = Comput Struct Biotechnol J
	\| volume = 19		\| volume = 19
	\| pages = 5811–5825		\| pages = 5811–5825

Simopnn: /* microRNA databases */ I have added RNAcentral to the list. The work is in progress I' ll make more edit

2025-03-23T11:21:27Z

microRNA databases: I have added RNAcentral to the list. The work is in progress I' ll make more edit

← Previous revision		Revision as of 11:21, 23 March 2025
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	! Name		! Name
	! Description \|\| type\|\| Link \|\| References		! Description \|\| type\|\| Link \|\| References
		⚫	\|-
		⚫	\|'''[[miRBase]]'''
		⚫	\|miRBase database is the most used database of published miRNA sequences and annotation. \|\| [[database]] \|\| [http://www.mirbase.org/ website] \|\| <ref name="pmid17991681">{{cite journal \|vauthors=Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ \|title=miRBase: tools for microRNA genomics. \|journal=Nucleic Acids Res. \|volume=36 \|pages=D154–D158 \|year=2008 \|issue=Database issue \|pmid=17991681 \|doi=10.1093/nar/gkm952 \|pmc=2238936}}</ref>
			\|-
			\|'''[[RNAcentral]]'''
			\| RNAcentral is a centralised database of non‐coding RNA sequences collated from expert non‐coding RNA databases, model organism databases and sequence accession databases. It provides a unique access point for more than 40 repositories and unique identifiers to ncRNA molecules, to facilitate data integration\|\| [[database]] \|\| [https://rnacentral.org/ website] \|\| <ref name="pmid33106848">{{cite journal \|vauthors= RNAcentral C \|title= RNAcentral 2021: Secondary Structure Integration, Improved Sequence Search and New Member Databases. \|journal=Nucleic Acids Res. \|volume=49 \|issue=Database issue \|pages= D212–D220\|year=2021 \|pmid= 33106848\| doi=10.1093/nar/gkaa921 \|pmc=7779037}}</ref>
	\|-		\|-
	\|'''[[deepBase]]'''		\|'''[[deepBase]]'''
	\|deepBase is a database for annotating and discovering small and long ncRNAs (microRNAs, siRNAs, piRNAs...) from high-throughput [[deep sequencing]] data. \|\| [[database]] \|\| [https://web.archive.org/web/20100926143225/http://deepbase.sysu.edu.cn/ website] \|\| <ref name="pmid19966272">{{cite journal \|vauthors=Yang JH, Shao P, Zhou H, Chen YQ, Qu LH \|title=deepBase: a database for deeply annotating and mining deep sequencing data. \|journal=Nucleic Acids Res. \|volume=38 \|issue=Database issue \|pages=D123-130 \|year=2010 \|pmid=19966272 \|doi=10.1093/nar/gkp943 \|pmc=2808990}}</ref>		\|deepBase is a database for annotating and discovering small and long ncRNAs (microRNAs, siRNAs, piRNAs...) from high-throughput [[deep sequencing]] data. \|\| [[database]] \|\| [https://web.archive.org/web/20100926143225/http://deepbase.sysu.edu.cn/ website] \|\| <ref name="pmid19966272">{{cite journal \|vauthors=Yang JH, Shao P, Zhou H, Chen YQ, Qu LH \|title=deepBase: a database for deeply annotating and mining deep sequencing data. \|journal=Nucleic Acids Res. \|volume=38 \|issue=Database issue \|pages=D123-130 \|year=2010 \|pmid=19966272 \|doi=10.1093/nar/gkp943 \|pmc=2808990}}</ref>
⚫	\|-
⚫	\|'''[[miRBase]]'''
⚫	\|miRBase database is a ~~searchable~~ database of published miRNA sequences and annotation. \|\| [[database]] \|\| [http://www.mirbase.org/ website] \|\| <ref name="pmid17991681">{{cite journal \|vauthors=Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ \|title=miRBase: tools for microRNA genomics. \|journal=Nucleic Acids Res. \|volume=36 \|pages=D154–D158 \|year=2008 \|issue=Database issue \|pmid=17991681 \|doi=10.1093/nar/gkm952 \|pmc=2238936}}</ref>
	\|-		\|-
	\|'''[[microRNA.org]]'''		\|'''[[microRNA.org]]'''

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2025-03-22T22:08:03Z

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← Previous revision		Revision as of 22:08, 22 March 2025
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	\| pages = 343–349		\| pages = 343–349
	\| year = 2004		\| year = 2004
			\| issue = 7006
	\| pmid = 15372041		\| pmid = 15372041
			\| bibcode = 2004Natur.431..343M
	}}</ref>		}}</ref>
	Since target recognition occurs through base pairing, several predictors have been developed which aim to predict potential mRNA targets based on sequence complementarity and other features <ref>{{Cite journal		Since target recognition occurs through base pairing, several predictors have been developed which aim to predict potential mRNA targets based on sequence complementarity and other features <ref>{{Cite journal
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	\| pages = e05005		\| pages = e05005
	\| year = 2015		\| year = 2015
			\| doi-access = free
	\| pmid = 26267216		\| pmid = 26267216
			\| pmc = 4532895
	}}</ref>		}}</ref>
	<ref>{{Cite journal		<ref>{{Cite journal
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	\| journal = Comput Struct Biotechnol J.		\| journal = Comput Struct Biotechnol J.
	\| volume = 19		\| volume = 19
	\| pages = ~~5811-5825~~		\| pages = 5811–5825
	\| year = 2021		\| year = 2021
	\| pmid = 34765096		\| pmid = 34765096
			\| pmc = 8567327
	}}</ref>		}}</ref>
	These resources must be distinguished from databases that collect observed experimental interactions.		These resources must be distinguished from databases that collect observed experimental interactions.
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	\| pages = 1005–1017		\| pages = 1005–1017
	\| year = 2018		\| year = 2018
			\| issue = 8
	\| pmid = 29871895		\| pmid = 29871895
			\| pmc = 6049505
	}}</ref>		}}</ref>
	<ref>{{Cite journal		<ref>{{Cite journal
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	\| year = 2023		\| year = 2023
	\| pmid = 37819683		\| pmid = 37819683
			\| pmc = 10566539
	}}</ref>		}}</ref>
	.		.
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	\|-		\|-
	\|'''[[MBSTAR]]'''		\|'''[[MBSTAR]]'''
	\|Multiple Instance approach for finding out true or functional microRNA binding sites. \|\| webserver, predictions \|\| [http://www.isical.ac.in/~bioinfo_miu/MBStar30.htm predictions] \|\| <ref name="pmid25614300">{{cite journal \|vauthors=Bandyopadhyay S, Ghosh D, Mitra R, Zhao Z \|title=MBSTAR: multiple instance learning for predicting specific functional binding sites in microRNA targets. \|journal=Sci. Rep.\|volume=5\|year=2015 \|pmid=25614300 \|doi=10.1038/srep08004 \|pages=8004 \|pmc=4648438\|bibcode=2015NatSR...~~5E8004B~~}}</ref>		\|Multiple Instance approach for finding out true or functional microRNA binding sites. \|\| webserver, predictions \|\| [http://www.isical.ac.in/~bioinfo_miu/MBStar30.htm predictions] \|\| <ref name="pmid25614300">{{cite journal \|vauthors=Bandyopadhyay S, Ghosh D, Mitra R, Zhao Z \|title=MBSTAR: multiple instance learning for predicting specific functional binding sites in microRNA targets. \|journal=Sci. Rep.\|volume=5\|year=2015 \|pmid=25614300 \|doi=10.1038/srep08004 \|pages=8004 \|pmc=4648438\|bibcode=2015NatSR...5.8004B}}</ref>
	\|-		\|-
	\|colspan="5" \| <small>.</small>		\|colspan="5" \| <small>.</small>

Simopnn at 18:58, 22 March 2025

2025-03-22T18:58:00Z

← Previous revision		Revision as of 18:58, 22 March 2025
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	\| pmid = 26267216		\| pmid = 26267216
	}}</ref>		}}</ref>
	.<ref>{{Cite journal		<ref>{{Cite journal
	\| last1 = Quillet		\| last1 = Quillet
	\| first1 = A.		\| first1 = A.
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	\| pmid = 29871895		\| pmid = 29871895
	}}</ref>		}}</ref>
	.<ref>{{Cite journal		<ref>{{Cite journal
	\| last1 = Panni		\| last1 = Panni
	\| first1 = S.		\| first1 = S.

Simopnn: I have improved the description of the resources listed, the work is in progress, I will add more information

2025-03-22T18:56:17Z

I have improved the description of the resources listed, the work is in progress, I will add more information

@@ Line 12: / Line 12: @@
 | pmc =3794896
 }}</ref>
 ==microRNA target gene databases==

Diannaa: Attribution: A previous edit contained content copied from the Wikipedia page at MirGeneDB; see its history for attribution. (See WP:RIA for more information.)

2024-09-19T21:57:36Z

Attribution: A previous edit contained content copied from the Wikipedia page at MirGeneDB; see its history for attribution. (See WP:RIA for more information.)

← Previous revision		Revision as of 21:57, 19 September 2024
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	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.<ref>{{Cite journal		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.<ref>{{Cite journal
	\| last1 = Bartel \| first1 = D. P.		\| last1 = Bartel
			\| first1 = D. P.
	\| title = MicroRNAs: Target Recognition and Regulatory Functions		\| title = MicroRNAs: Target Recognition and Regulatory Functions
	\| doi = 10.1016/j.cell.2009.01.002		\| doi = 10.1016/j.cell.2009.01.002

Michbich: added MirGeneDB

2024-09-18T08:40:19Z

added MirGeneDB

← Previous revision		Revision as of 08:40, 18 September 2024
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	\|-		\|-
	\|'''[[miRwalk]]'''		\|'''[[miRwalk]]'''
	\|Aggregates and compare results from other miRNA-to-mRNA databases \|\| database, webserver \|\| [http://www.umm.uni-heidelberg.de/apps/zmf/mirwalk/] \|\| <ref name="pmid21605702">{{cite journal \|vauthors=Dweep H, Sticht C, Pandey P, Gretz N \|title=miRWalk-database: prediction of possible miRNA binding sites by "walking" the genes of three genomes \|journal= Journal of Biomedical Informatics\|volume=44\|issue=5 \|pages=839–47\|year=2011 \|pmid=21605702 \|doi= 10.1016/j.jbi.2011.05.002\|doi-access=free}}</ref>		\|Aggregates and compare results from other miRNA-to-mRNA databases \|\| database, webserver \|\| [http://www.umm.uni-heidelberg.de/apps/zmf/mirwalk/]\|\| <ref name="pmid21605702">{{cite journal \|vauthors=Dweep H, Sticht C, Pandey P, Gretz N \|title=miRWalk-database: prediction of possible miRNA binding sites by "walking" the genes of three genomes \|journal= Journal of Biomedical Informatics\|volume=44\|issue=5 \|pages=839–47\|year=2011 \|pmid=21605702 \|doi= 10.1016/j.jbi.2011.05.002\|doi-access=free}}</ref>
	\|-		\|-
	\|'''[[MBSTAR]]'''		\|'''[[MBSTAR]]'''
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	\|'''[[miRGen 2.0\|miRGen 4.0]]'''		\|'''[[miRGen 2.0\|miRGen 4.0]]'''
	\|DIANA-miRGen v4: indexing promoters and regulators for more than 1500 microRNAs \|\| [[database]] \|\| [http://www.microrna.gr/mirgenv4 website] \|\| <ref name="pmid33245765">{{cite journal \|vauthors=Perdikopanis N, Georgakilas GK, Grigoriadis D, Pierros V, Kavakiotis I, Alexiou P, Hatzigeorgiou A \|title=DIANA-miRGen v4: indexing promoters and regulators for more than 1500 microRNAs \|journal=Nucleic Acids Res \|volume=49 \|issue=D1 \|pages=D151-159 \|year=2021 \|pmid=33245765 \|doi=10.1093/nar/gkaa1060 \|doi-access=free \|pmc=7778932}}</ref>		\|DIANA-miRGen v4: indexing promoters and regulators for more than 1500 microRNAs \|\| [[database]] \|\| [http://www.microrna.gr/mirgenv4 website] \|\| <ref name="pmid33245765">{{cite journal \|vauthors=Perdikopanis N, Georgakilas GK, Grigoriadis D, Pierros V, Kavakiotis I, Alexiou P, Hatzigeorgiou A \|title=DIANA-miRGen v4: indexing promoters and regulators for more than 1500 microRNAs \|journal=Nucleic Acids Res \|volume=49 \|issue=D1 \|pages=D151-159 \|year=2021 \|pmid=33245765 \|doi=10.1093/nar/gkaa1060 \|doi-access=free \|pmc=7778932}}</ref>
			\|-
			\|'''[[MirGeneDB]]'''
			\|MirGeneDB is a database of manually curated microRNA genes that have been validated and annotated. MirGeneDB 2.1 includes more than 16,000 microRNA gene entries representing more than 1,500 miRNA families from 75 metazoan species. All microRNAs can be browsed, searched and downloaded.
			\|[[database]]
			\|[https://mirgenedb.org/ website]
			\|<ref name="mirgenedbNAR">{{cite journal \|last1=Fromm \|first1=Bastian \|last2=Høye \|first2=Eirik \|last3=Domanska \|first3=Diana \|last4=Zhong \|first4=Xiangfu \|last5=Aparicio-Puerta \|first5=Ernesto \|last6=Ovchinnikov \|first6=Vladimir \|last7=Umu \|first7=Sinan U \|last8=Chabot \|first8=Peter J \|last9=Kang \|first9=Wenjing \|last10=Aslanzadeh \|first10=Morteza \|last11=Tarbier \|first11=Marcel \|last12=Mármol-Sánchez \|first12=Emilio \|last13=Urgese \|first13=Gianvito \|last14=Johansen \|first14=Morten \|last15=Hovig \|first15=Eivind \|last16=Hackenberg \|first16=Michael \|last17=Friedländer \|first17=Marc R \|last18=Peterson \|first18=Kevin J \|title=MirGeneDB 2.1: toward a complete sampling of all major animal phyla \|journal=Nucleic Acids Research \|volume=50 \|issue=D1 \|pages=D204–D210 \|date=November 2021 \|pmid=34850121 \|pmc=8728275 \|doi=10.1093/nar/gkab1101 \|url=https://doi.org/10.1093/nar/gkab1101}}</ref>
	\|-		\|-
	\|'''[[miRNAMap]]'''		\|'''[[miRNAMap]]'''

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2023-12-03T03:29:30Z

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← Previous revision		Revision as of 03:29, 3 December 2023
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	\|-		\|-
	\|'''[http://www.targetscan.org TargetScan]'''		\|'''[http://www.targetscan.org 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 \|\| [http://www.targetscan.org/ website] \|\| <ref name="Lewis et al., Cell 2005">{{cite journal\|last=Lewis\|first=BP\|author2=Burge CB \|author3=Bartel DP \|title=Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets\|journal=Cell\|date=Jan 14, 2005\|volume=120\|issue=1\|pages=15–20\|pmid=15652477\|doi=10.1016/j.cell.2004.12.035\|doi-access=free}}</ref><ref name="Grimson et al., Mol Cell 2007">{{cite journal\|last=Grimson\|first=A\|author2=Farh, KK \|author3=Johnston, WK \|author4=Garrett-Engele, P \|author5=Lim, LP \|author6= Bartel, DP \|title=MicroRNA targeting specificity in mammals: determinants beyond seed pairing.\|journal=Molecular Cell\|date=Jul 6, 2007\|volume=27\|issue=1\|pages=91–105\|pmid=17612493\|doi=10.1016/j.molcel.2007.06.017 \|pmc=3800283}}</ref><ref name="Friedman et al., Genome Res 2009">{{cite journal\|last=Friedman\|first=RC\|author2=Farh, KK \|author3=Burge, CB \|author4= Bartel, DP \|title=Most mammalian mRNAs are conserved targets of microRNAs.\|journal=Genome Research\|date=January 2009\|volume=19\|issue=1\|pages=92–105\|doi=10.1101/gr.082701.108\|pmid=18955434\|pmc=2612969}}</ref><ref name="Garcia et al., Nat Struct Mol Biol 2011">{{cite journal\|last=Garcia\|first=DM\|author2=Baek, D \|author3=Shin, C \|author4=Bell, GW \|author5=Grimson, A \|author6= Bartel, DP \|title=Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs.\|journal=Nature Structural & Molecular Biology\|date=Sep 11, 2011\|volume=18\|issue=10\|pages=1139–46\|pmid=21909094\|doi=10.1038/nsmb.2115\|pmc=3190056\|url=http://dspace.mit.edu/bitstream/1721.1/82943/1/Bartel_Weak%20seed-pairing.pdf}}</ref><ref name=":0">{{Cite journal\|title=Predicting effective microRNA target sites in mammalian mRNAs ~~\|url=http://elifesciences.org/content/4/e05005~~ \|journal=eLife \|date=2015-08-12 \|issn=2050-084X \|pmc=4532895 \|pmid=26267216 \|pages=e05005 \|volume=4 \|doi=10.7554/eLife.05005 \|first1=Vikram \|last1=Agarwal \|first2=George W. \|last2=Bell \|first3=Jin-Wu \|last3=Nam \|first4=David P. \|last4=Bartel \|~~url~~-~~status~~=~~dead \|archive-url=https://web.archive.org/web/20150827183007/http://elifesciences.org/content/4/e05005 \|archive-date=2015-08-27~~ }}</ref><ref>{{cite journal \|last1=Agarwal \|first1=V \|last2=Subtelny \|first2=AO \|last3=Thiru \|first3=P \|last4=Ulitsky \|first4=I \|last5=Bartel \|first5=DP \|title=Predicting microRNA targeting efficacy in Drosophila. \|journal=Genome Biology \|date=4 October 2018 \|volume=19 \|issue=1 \|pages=152 \|doi=10.1186/s13059-018-1504-3 \|pmid=30286781\|pmc=6172730 }}</ref>		\|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 \|\| [http://www.targetscan.org/ website] \|\| <ref name="Lewis et al., Cell 2005">{{cite journal\|last=Lewis\|first=BP\|author2=Burge CB \|author3=Bartel DP \|title=Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets\|journal=Cell\|date=Jan 14, 2005\|volume=120\|issue=1\|pages=15–20\|pmid=15652477\|doi=10.1016/j.cell.2004.12.035\|doi-access=free}}</ref><ref name="Grimson et al., Mol Cell 2007">{{cite journal\|last=Grimson\|first=A\|author2=Farh, KK \|author3=Johnston, WK \|author4=Garrett-Engele, P \|author5=Lim, LP \|author6= Bartel, DP \|title=MicroRNA targeting specificity in mammals: determinants beyond seed pairing.\|journal=Molecular Cell\|date=Jul 6, 2007\|volume=27\|issue=1\|pages=91–105\|pmid=17612493\|doi=10.1016/j.molcel.2007.06.017 \|pmc=3800283}}</ref><ref name="Friedman et al., Genome Res 2009">{{cite journal\|last=Friedman\|first=RC\|author2=Farh, KK \|author3=Burge, CB \|author4= Bartel, DP \|title=Most mammalian mRNAs are conserved targets of microRNAs.\|journal=Genome Research\|date=January 2009\|volume=19\|issue=1\|pages=92–105\|doi=10.1101/gr.082701.108\|pmid=18955434\|pmc=2612969}}</ref><ref name="Garcia et al., Nat Struct Mol Biol 2011">{{cite journal\|last=Garcia\|first=DM\|author2=Baek, D \|author3=Shin, C \|author4=Bell, GW \|author5=Grimson, A \|author6= Bartel, DP \|title=Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs.\|journal=Nature Structural & Molecular Biology\|date=Sep 11, 2011\|volume=18\|issue=10\|pages=1139–46\|pmid=21909094\|doi=10.1038/nsmb.2115\|pmc=3190056\|url=http://dspace.mit.edu/bitstream/1721.1/82943/1/Bartel_Weak%20seed-pairing.pdf}}</ref><ref name=":0">{{Cite journal\|title=Predicting effective microRNA target sites in mammalian mRNAs \|journal=eLife \|date=2015-08-12 \|issn=2050-084X \|pmc=4532895 \|pmid=26267216 \|pages=e05005 \|volume=4 \|doi=10.7554/eLife.05005 \|first1=Vikram \|last1=Agarwal \|first2=George W. \|last2=Bell \|first3=Jin-Wu \|last3=Nam \|first4=David P. \|last4=Bartel \|doi-access=free }}</ref><ref>{{cite journal \|last1=Agarwal \|first1=V \|last2=Subtelny \|first2=AO \|last3=Thiru \|first3=P \|last4=Ulitsky \|first4=I \|last5=Bartel \|first5=DP \|title=Predicting microRNA targeting efficacy in Drosophila. \|journal=Genome Biology \|date=4 October 2018 \|volume=19 \|issue=1 \|pages=152 \|doi=10.1186/s13059-018-1504-3 \|pmid=30286781\|pmc=6172730 \|doi-access=free }}</ref>
	\|-		\|-
	\|'''[[TarBase]]'''		\|'''[[TarBase]]'''
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	\|'''[[Diana-microT]]'''		\|'''[[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\|\|[https://web.archive.org/web/20101208180159/http://diana.cslab.ece.ntua.gr/microT/ webserver] \|\| <ref name="pmid19765283">{{cite journal \|vauthors=Maragkakis M, Alexiou P, Papadopoulos GL, Reczko M, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Simossis VA, Sethupathy P, Vergoulis T, Koziris N, Sellis T, Tsanakas P, Hatzigeorgiou AG \|title=Accurate microRNA target prediction correlates with protein repression levels. \|journal=BMC Bioinformatics \|volume=10 \|pages=295 \|year=2009 \|pmid=19765283 \|doi=10.1186/1471-2105-10-295\|pmc=2752464}}</ref>		\|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\|\|[https://web.archive.org/web/20101208180159/http://diana.cslab.ece.ntua.gr/microT/ webserver] \|\| <ref name="pmid19765283">{{cite journal \|vauthors=Maragkakis M, Alexiou P, Papadopoulos GL, Reczko M, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Simossis VA, Sethupathy P, Vergoulis T, Koziris N, Sellis T, Tsanakas P, Hatzigeorgiou AG \|title=Accurate microRNA target prediction correlates with protein repression levels. \|journal=BMC Bioinformatics \|volume=10 \|pages=295 \|year=2009 \|pmid=19765283 \|doi=10.1186/1471-2105-10-295\|pmc=2752464 \|doi-access=free }}</ref>
	\|-		\|-
	\|'''[[miRecords]]'''		\|'''[[miRecords]]'''

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2023-07-05T12:16:11Z

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← Previous revision		Revision as of 12:16, 5 July 2023
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	\|'''[[PicTar]]'''		\|'''[[PicTar]]'''
	\|PicTar is Combinatorial microRNA target predictions. \|\| database, webserver, predictions \|\| [https://web.archive.org/web/20080724163022/http://pictar.bio.nyu.edu/ website] \|\| <ref name="pmid15806104">{{cite journal \|vauthors=Krek A, Grün D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, Rajewsky N \|title=Combinatorial microRNA target predictions. \|journal=Nat Genet \|volume=37 \|issue=5 \|pages=495–500 \|year=2005 \|pmid=15806104 \|doi=10.1038/ng1536}}</ref>		\|PicTar is Combinatorial microRNA target predictions. \|\| database, webserver, predictions \|\| [https://web.archive.org/web/20080724163022/http://pictar.bio.nyu.edu/ website] \|\| <ref name="pmid15806104">{{cite journal \|vauthors=Krek A, Grün D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, Rajewsky N \|title=Combinatorial microRNA target predictions. \|journal=Nat Genet \|volume=37 \|issue=5 \|pages=495–500 \|year=2005 \|pmid=15806104 \|doi=10.1038/ng1536\|s2cid=22672750 }}</ref>
	\|-		\|-
	\|'''[[PITA (software)\|PITA]]'''		\|'''[[PITA (software)\|PITA]]'''
	\|PITA, incorporates the role of target-site accessibility, as determined by base-pairing interactions within the mRNA, in microRNA target recognition.\|\|webserver, predictions \|\| [http://genie.weizmann.ac.il/pubs/mir07/mir07_data.html predictions] \|\| <ref name="pmid17893677">{{cite journal \|vauthors=Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E \|title=The role of site accessibility in microRNA target recognition. \|journal=Nat Genet \|volume=39 \|issue=10 \|pages=1278–84 \|year=2007 \|pmid=17893677 \|doi=10.1038/ng2135}}</ref>		\|PITA, incorporates the role of target-site accessibility, as determined by base-pairing interactions within the mRNA, in microRNA target recognition.\|\|webserver, predictions \|\| [http://genie.weizmann.ac.il/pubs/mir07/mir07_data.html predictions] \|\| <ref name="pmid17893677">{{cite journal \|vauthors=Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E \|title=The role of site accessibility in microRNA target recognition. \|journal=Nat Genet \|volume=39 \|issue=10 \|pages=1278–84 \|year=2007 \|pmid=17893677 \|doi=10.1038/ng2135\|s2cid=1721807 }}</ref>
	\|-		\|-
	\|'''[[RepTar (database)\|RepTar]]'''		\|'''[[RepTar (database)\|RepTar]]'''
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	\|'''[[RNA22]]'''		\|'''[[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 \|\| [http://cm.jefferson.edu/rna22v1.0/ predictions] [http://cm.jefferson.edu/rna22v2/ custom] \|\| <ref name="pmid16990141">{{cite journal \|vauthors=Miranda KC, Huynh T, Tay Y, Ang YS, Tam WL, Thomson AM, Lim B, Rigoutsos I \|title=A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. \|journal=Cell \|volume=126 \|issue=6 \|pages=1203–17 \|year=2006 \|pmid=16990141 \|doi=10.1016/j.cell.2006.07.031\|url=http://cbio.ensmp.fr/~jvert/svn/bibli/local/Miranda2006pattern-based.pdf }}</ref>		\|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 \|\| [http://cm.jefferson.edu/rna22v1.0/ predictions] [http://cm.jefferson.edu/rna22v2/ custom] \|\| <ref name="pmid16990141">{{cite journal \|vauthors=Miranda KC, Huynh T, Tay Y, Ang YS, Tam WL, Thomson AM, Lim B, Rigoutsos I \|title=A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. \|journal=Cell \|volume=126 \|issue=6 \|pages=1203–17 \|year=2006 \|pmid=16990141 \|doi=10.1016/j.cell.2006.07.031\|s2cid=12749133 \|url=http://cbio.ensmp.fr/~jvert/svn/bibli/local/Miranda2006pattern-based.pdf }}</ref>
	\|-		\|-
	\|'''[[miRTarBase]]'''		\|'''[[miRTarBase]]'''
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	\|-		\|-
	\|'''[[miRwalk]]'''		\|'''[[miRwalk]]'''
	\|Aggregates and compare results from other miRNA-to-mRNA databases \|\| database, webserver \|\| [http://www.umm.uni-heidelberg.de/apps/zmf/mirwalk/] \|\| <ref name="pmid21605702">{{cite journal \|vauthors=Dweep H, Sticht C, Pandey P, Gretz N \|title=miRWalk-database: prediction of possible miRNA binding sites by "walking" the genes of three genomes. \|journal=~~JBI~~\|volume=44\|issue=5 \|pages=839–47\|year=2011 \|pmid=21605702 \|doi= 10.1016/j.jbi.2011.05.002\|doi-access=free}}</ref>		\|Aggregates and compare results from other miRNA-to-mRNA databases \|\| database, webserver \|\| [http://www.umm.uni-heidelberg.de/apps/zmf/mirwalk/] \|\| <ref name="pmid21605702">{{cite journal \|vauthors=Dweep H, Sticht C, Pandey P, Gretz N \|title=miRWalk-database: prediction of possible miRNA binding sites by "walking" the genes of three genomes \|journal= Journal of Biomedical Informatics\|volume=44\|issue=5 \|pages=839–47\|year=2011 \|pmid=21605702 \|doi= 10.1016/j.jbi.2011.05.002\|doi-access=free}}</ref>
	\|-		\|-
	\|'''[[MBSTAR]]'''		\|'''[[MBSTAR]]'''
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	==Further reading==		==Further reading==

	* {{cite journal \| last = Lee \| first = RC \|author2=Ambros V \| year = 2001 \| title = An extensive class of small RNAs in Caenorhabditis elegans \| journal = Science \| volume = 294 \| pages = 862–864 \| pmid = 11679672 \| doi = 10.1126/science.1065329 \| issue = 5543\| bibcode = 2001Sci...294..862L }}		* {{cite journal \| last = Lee \| first = RC \|author2=Ambros V \| year = 2001 \| title = An extensive class of small RNAs in Caenorhabditis elegans \| journal = Science \| volume = 294 \| pages = 862–864 \| pmid = 11679672 \| doi = 10.1126/science.1065329 \| issue = 5543\| bibcode = 2001Sci...294..862L \| s2cid = 33480585 }}
	* {{cite journal \| last = Ambros \| first = V \| year = 2001 \| title = microRNAs: tiny regulators with great potential \| journal = Cell \| volume = 107 \| pages = 823–826 \| pmid = 11779458 \| doi = 10.1016/S0092-8674(01)00616-X \| issue = 7\| doi-access = free }}		* {{cite journal \| last = Ambros \| first = V \| year = 2001 \| title = microRNAs: tiny regulators with great potential \| journal = Cell \| volume = 107 \| pages = 823–826 \| pmid = 11779458 \| doi = 10.1016/S0092-8674(01)00616-X \| issue = 7\| doi-access = free }}

GreenC bot: Rescued 3 archive links. Wayback Medic 2.5

2022-06-15T13:54:23Z

Rescued 3 archive links. Wayback Medic 2.5

← Previous revision		Revision as of 13:54, 15 June 2022
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	\|'''[[deepBase]]'''		\|'''[[deepBase]]'''
	\|deepBase is a database for annotating and discovering small and long ncRNAs (microRNAs, siRNAs, piRNAs...) from high-throughput [[deep sequencing]] data. \|\| [[database]] \|\| [https://~~www~~.~~webcitation~~.org/~~5tyh2Lsae?url=~~http://deepbase.sysu.edu.cn/ website] \|\| <ref name="pmid19966272">{{cite journal \|vauthors=Yang JH, Shao P, Zhou H, Chen YQ, Qu LH \|title=deepBase: a database for deeply annotating and mining deep sequencing data. \|journal=Nucleic Acids Res. \|volume=38 \|issue=Database issue \|pages=D123-130 \|year=2010 \|pmid=19966272 \|doi=10.1093/nar/gkp943 \|pmc=2808990}}</ref>		\|deepBase is a database for annotating and discovering small and long ncRNAs (microRNAs, siRNAs, piRNAs...) from high-throughput [[deep sequencing]] data. \|\| [[database]] \|\| [https://web.archive.org/web/20100926143225/http://deepbase.sysu.edu.cn/ website] \|\| <ref name="pmid19966272">{{cite journal \|vauthors=Yang JH, Shao P, Zhou H, Chen YQ, Qu LH \|title=deepBase: a database for deeply annotating and mining deep sequencing data. \|journal=Nucleic Acids Res. \|volume=38 \|issue=Database issue \|pages=D123-130 \|year=2010 \|pmid=19966272 \|doi=10.1093/nar/gkp943 \|pmc=2808990}}</ref>
	\|-		\|-
	\|'''[[miRBase]]'''		\|'''[[miRBase]]'''
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	* [http://cupidtool.sourceforge.net/ Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks]		* [http://cupidtool.sourceforge.net/ Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks]
	* [http://www.mirbase.org/ miRBase database]		* [http://www.mirbase.org/ miRBase database]
	* [https://~~www~~.~~webcitation~~.org/~~5tyh2Lsae?url=~~http://deepbase.sysu.edu.cn/ deepBase database]		* [https://web.archive.org/web/20100926143225/http://deepbase.sysu.edu.cn/ deepBase database]
	* [http://www.targetscan.org/ TargetScan]		* [http://www.targetscan.org/ TargetScan]
	* [http://pictar.mdc-berlin.de picTar]		* [http://pictar.mdc-berlin.de picTar]
	* [https://~~www~~.~~webcitation~~.org/~~5rRSC3tvh?url=~~http://mirecords.biolead.org/ miRecords database]		* [https://web.archive.org/web/20100719165016/http://mirecords.biolead.org/ miRecords database]
	* [https://web.archive.org/web/20101125042543/http://diana.cslab.ece.ntua.gr/tarbase/ TarBase database]		* [https://web.archive.org/web/20101125042543/http://diana.cslab.ece.ntua.gr/tarbase/ TarBase database]
	* [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&N4=MREH01\|SIGMA&N5=SEARCH_CONCAT_PNO\|BRAND_KEY&F=SPEC Target ID Library]		* [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&N4=MREH01\|SIGMA&N5=SEARCH_CONCAT_PNO\|BRAND_KEY&F=SPEC Target ID Library]