Bonnet E, He Y, Billiau K, Van de Peer Y. (2010) TAPIR, a web server for the prediction of plant microRNA targets, including target mimics.
Bioinformatics. 26(12):1566-8. doi: 10.1093/bioinformatics/btq233. PMID: 20430753
Kadri, S., Hinman, V., Benos, P. V. (2009). HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models.
BMC Bioinformatics 10(Suppl. 1):S35.10.1186/1471-2105-10-S1-S35. PMID: 19208136
Training set for HHMMiR was Triticum aestivum
microRNAs from miRBase (revision 19).
Batuwita, R. and Palade, V. (2009) microPred: effective classification of pre-miRNAs for human miRNA gene prediction.
Bioinformatics, 25, 989-995. PMID: 19233894
Leclercq, M., Diallo, A.B and Blanchette, M. (2013) Computational prediction of the localization of microRNAs within their pre-miRNA.
Nucleic Acids Res. 41(15):7200-7211. PMID: 23748953
Note: the mirDup* version used in this study differs from the original one on the 35 retained features that are relevant for plants
The different training set for the mirDup are based on the microRNAs of miRBase (revision 19 or 20)
Kozomara A, Griffiths-Jones S. (2014) miRBase: annotating high confidence microRNAs using deep sequencing data.
NAR 2014 42:D68-D73 PMID: 21037258
The mirBase (B) dataset includes miRNAs identified by cloning or sequencing from all species.
The Plantae (P) dataset includes only miRNAs specific to plants (Viridiplantae
The Monocot (M) dataset includes only miRNAs specific to monocotyledons.
Jones-Rhoades, M.W. and Bartel, D.P. (2004). Computational identification of plant MicroRNAs and their targets, including a stress-induced miRNA.
Mol. Cell, 14, 787-799. PMID: 15200956
Meyers, B.C., Axtell, M.J., Bartel, B., Bartel, D.P., Baulcombe, D., Bowman, J.L., Cao, X., Carrington, J.C., Chen, X., Green, P.J., Griffiths-Jones, S., Jacobsen, S.E., Mallory, A.C., Martienssen, R.A., Poethig, R.S., Qi, Y., Vaucheret, H., Voinnet, O., Watanabe, Y., Weigel, D., Zhu, J.K. (2008) Criteria for annotation of plant microRNAs.
Plant Cell 20:3186–3190. PMID: 19074682
Secondary structures of the extracted sequences were folded with RNAfold from ViennaRNA v1.8.4 package
Hofacker, IL. (2003) Vienna Rna secondary structure server.
Nucleic Acids Research, 31(13), 3429-3431. PMID: 12824340
Vizualisation and rendering of secondary structures is provided by VARNA
Darty, K., Denise, A. and Ponty, Y. (2009) VARNA: Interactive drawing and editing of the RNA secondary structure
Bioinformatics, 25(15), 1974-1975. PMID: 19398448
Normalized expression of microRNAS in the libraries
New* The Wheat (W) dataset (Triticum aestivum
An upregulated microRNA (noted by
) has a fold change greater than 2 and an adjusted p-value less than 0.05;
A downregulated microRNA (noted by
) has a fold change between 0 and 0.5 (1/2) and an adjusted p-value less than 0.05.