Laboratoire bioinformatique | UQAM
Groupe de recherche en biochimie du developpement et de l'adaptation des plantes | UQAM
Wheat MicroRNA Portal
Université du Québec à Montréal

microRNA {{apmir_id}}

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Contents
Expression in the different libraries
Associated hairpins evidences {{datajson.appre.length}}
Associated target genes {{datajson.target.length}}
GO of associated target genes {{datajson.go.length}}
Biological process {{goBiological_process}} Molecular function {{goMolecular_function}} Cellular component {{goCellular_component}}
Associated Ests (miRNA genes) {{datajson.ests.length}}
Expression in experimental conditions
{{datajson.mirna.apMir_ID}} {{datajson.mirna.Seq}} {{datajson.mirna.Seq_length}}nt
Note: This microRNA is not yet validated.

miRBase related in wheat
{{c.Hit_ID}}  {{c.Family}} family
({{datajson.conserved.length-f.length}} more in other species...)
More informations
Expression in the different libraries (total expression: {{datajson.mirna.Total_Exp}})
Note:
See the libraries page for description of each
libraries.
Raw abundance corresponds to the occurences
of the microRNAs in the sequenced libraries

Associated hairpins evidences

Associated target genes

Link to data Type Descriptions Informations
{{r[1]}}
{{r[2]}}

GO of associated target genes

Type GoSlim and Go Descriptions Informations
{{r[2]}}

Associated ESTs (miRNA genes)

Link to data Type Descriptions
{{r[1]}}
{{r[2]}}

Expression in experimental conditions

Conditions RPM A10 RPM B10 Fold change P-value (adjusted) Z-Score Regulation12
{{conditions[mirna.ZLA_B]}} {{mirna.RPM_A|round100}} {{mirna.RPM_B|round100}} {{mirna.Fold_Change|number:3}}- {{mirna.P_value_adj}} {{mirna.Z_SCORE|round1000}}
1 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
2 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).
3 Batuwita, R. and Palade, V. (2009) microPred: effective classification of pre-miRNAs for human miRNA gene prediction. Bioinformatics, 25, 989-995. PMID: 19233894
4 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 mirDup
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.
5 The Plantae (P) dataset includes only miRNAs specific to plants (Viridiplantae).
6 The Monocot (M) dataset includes only miRNAs specific to monocotyledons.
7 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
8 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
9 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
10 Normalized expression of microRNAS in the libraries
11 New* The Wheat (W) dataset (Triticum aestivum)
12 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.
 Mohamed Amine Remita, Etienne Lord   Made with JQuery, Angular.js, Bootstrap, D3, NVD3 and jqplot