Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites.
mirSVR is a new machine learning method for ranking microRNA target sites by a down-regulation score. The algorithm trains a regression model on sequence and contextual features extracted from miRanda-predicted target sites. In a large-scale evaluation, miRanda-mirSVR is competitive with other target prediction methods in identifying target genes and predicting the extent of their downregulation at the mRNA or protein levels. Importantly, the method identifies a significant number of experimentally determined non-canonical and non-conserved sites.
Betel
Doron
D
Computational Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, 10065, NY, USA. betel@cbio.mskcc.org
Koppal
Anjali
A
Agius
Phaedra
P
Sander
Chris
C
Leslie
Christina
C
D000465:Algorithms; D001185:Artificial Intelligence; D001665:Binding Sites; D015536:Down-Regulation / Q000235:genetics; D035683:MicroRNAs / Q000235:genetics* / Q000494:pharmacology; D008958:Models, Molecular; D011506:Proteins / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D012044:Regression Analysis
D035683:MicroRNAs; D011506:Proteins; D012333:RNA, Messenger
RNA. 2008 Jul;14(7):1297-317
18463285
Genome Res. 2005 Aug;15(8):1034-50
16024819
Nat Struct Mol Biol. 2006 Sep;13(9):849-51
16921378
PLoS One. 2008 May 07;3(5):e2126
18461144
Nat Biotechnol. 2008 May;26(5):578-83
18438400
Nature. 2008 Sep 4;455(7209):58-63
18668040
Nat Rev Genet. 2008 Feb;9(2):102-14
18197166
Mol Cell Biol. 2005 Nov;25(21):9198-208
16227573
Curr Biol. 2006 Mar 7;16(5):460-71
16458514
Genes Dev. 2004 Jan 15;18(2):132-7
14729570
Nat Genet. 2005 May;37(5):495-500
15806104
BMC Bioinformatics. 2009 Sep 18;10:295
19765283
Nat Methods. 2008 Sep;5(9):813-9
19160516
Cell. 2007 Dec 28;131(7):1273-86
18155131
Genome Res. 2009 Nov;19(11):2009-20
19767416
Genome Res. 2009 Jan;19(1):92-105
18955434
PLoS Biol. 2004 Nov;2(11):e363
15502875
Mol Cell. 2007 Jul 6;27(1):91-105
17612493
Nature. 2009 Jul 23;460(7254):479-86
19536157
Mol Cell Biol. 2007 Mar;27(6):2240-52
17242205
Nucleic Acids Res. 2008 Mar;36(4):1153-62
18158304
Nat Biotechnol. 2009 Jun;27(6):549-55
19465925
Genome Res. 2010 Aug;20(8):1010-9
20508147
Mol Cell. 2009 Sep 11;35(5):610-25
19748357
Science. 2004 Apr 23;304(5670):594-6
15105502
RNA. 2008 Dec;14(12):2580-96
18978028
Nat Genet. 2007 Oct;39(10):1278-84
17893677
Nat Genet. 2002 Apr;30(4):363-4
11896390
Cell. 2010 Apr 2;141(1):129-41
20371350
Cell. 2007 Jun 29;129(7):1401-14
17604727
Cell. 2009 Jan 23;136(2):215-33
19167326
Mol Cell Biol. 2008 Sep;28(17):5369-80
18591254
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W451-4
16845047
Nature. 2008 Apr 17;452(7189):896-9
18368051
Nature. 2008 Sep 4;455(7209):64-71
18668037
Genome Biol. 2003;5(1):R1
14709173
RNA. 2007 Nov;13(11):1894-910
17872505