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

Citations

Remita, M.A., Lord, E., Agharbaoui, Z., Leclercq, M., Badawi, M.A.; Sarhan, F. and Diallo, A.B. A novel comprehensive wheat miRNA database, including related bioinformatics software Current Plant Biology (2016) http://dx.doi.org/10.1016/j.cpb.2016.10.003

Agharbaoui Z., Leclercq M., Remita M.A., Badawi M.A., Lord E., Houde M., Danyluk J., Diallo A.B., and Sarhan F. An integrative approach to identify hexaploid wheat miRNAome associated with development and tolerance to abiotic stress  BMC genomics 16.1 (2015): 339.  PMID: 25903161

References for methods used in this database

Tapir
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
HHMMiR
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
microPred (mipred)
Batuwita, R. and Palade, V. (2009) microPred: effective classification of pre-miRNAs for human miRNA gene prediction. Bioinformatics, 25, 989-995. PMID: 19233894
mirDup (v1.2)
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
MIRcheck
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
MIRcheck (Meyers et al. parameters)
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
RNAFold (Vienna package v1.8.4)
Hofacker, IL. (2003) Vienna Rna secondary structure server. Nucleic Acids Research, 31(13), 3429-3431. PMID: 12824340

Included data and methods

Jin W, Li N, Zhang B, Wu F, Li W, Guo A and Deng Z. (2008) Identification and verification of microRNA in wheat (Triticum aestivum). J Plant Res. 121(3):351-5.

Wei B, Cai T, Zhang R, Li A, Huo N, Li S, Gu YQ, Vogel J, Jia J, Qi Y and Mao L. (2009) Novel microRNAs uncovered by deep sequencing of small RNA transcriptomes in bread wheat (Triticum aestivum L.) and Brachypodium distachyon (L.) Beauv. Funct. Integr. Genomics. 9(4):499-511.

Han Y, Luan F, Zhu H, Shao Y, Chen A, Lu C, Luo Y and Zhu B. (2009) Computational identification of microRNAs and their targets in wheat (Triticum aestivum L.). Sci China C Life Sci.52(11):1091-100.

Xin M, Wang Y, Yao Y, Xie C, Peng H, Ni Z and Sun Q. (2010) Diverse set of microRNAs are responsive to powdery mildew infection and heat stress in wheat (Triticum aestivum L.). BMC Plant Biol. 10:123.

Yin ZJ and Shen FF. (2010) Identification and characterization of conserved microRNAs and their target genes in wheat (Triticum aestivum). Genet Mol Res. 22;9(2):1186-96.

Lucas SJ and Budak H. (2012) Sorting the wheat from the chaff: identifying miRNAs in genomic survey sequences of Triticum aestivum chromosome 1AL. PLoS One.7(7):e40859.

Li YF, Zheng Y, Jagadeeswaran G and Sunkar R. (2013) Characterization of small RNAs and their target genes in wheat seedlings using sequencing-based approaches. Plant Sci.203-204:17-24.

Pandey B, Gupta OP, Pandey DM, Sharma I and Sharma P. (2013) Identification of new stress-induced microRNA and their targets in wheat using computational approach. Plant Signal Behav. 8(5):e23932.

Meng F, Liu H, Wang K, Liu L, Wang S, Zhao Y, Yin J and Li Y. (2013) Development-associated microRNAs in grains of wheat (Triticum aestivum L.). BMC Plant Biol. 13:140.

Han J, Kong ML, Xie H, Sun QP, Nan ZJ, Zhang QZ and Pan JB. (2013) Identification of miRNAs and their targets in wheat (Triticum aestivum L.) by EST analysis. Genet Mol Res. 12(3):3793-805.

Wang B, Sun YF, Song N, Wang XJ, Feng H, Huang LL and Kang ZS. (2013) Identification of UV-B-induced microRNAs in wheat. Genet Mol Res. 12(4):4213-21.

Han R, Jian C, Lv J, Yan Y, Chi Q, Li Z, Wang Q, Zhang J, Liu X and Zhao H. (2014) Identification and characterization of microRNAs in the flag leaf and developing seed of wheat (Triticum aestivum L.). BMC Genomics. 15:289.

Pandey R, Joshi G, Bhardwaj AR, Agarwal M and Katiyar-Agarwal S. (2014) A comprehensive genome-wide study on tissue-specific and abiotic stress-specific miRNAs in Triticum aestivum. PLoS One. 9(4):e95800.

Sun F, Guo G, Du J, Guo W, Peng H, Ni Z, Sun Q and Yao Y. (2014) Whole-genome discovery of miRNAs and their targets in wheat (Triticum aestivum L.). BMC Plant Biol. 14:142.

Kozomara A and Griffiths-Jones S. (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 39(Database issue):D152-7.

Agharbaoui Z, Leclercq M, Remita MA, Badawi M. A, Lord E, Houde M, Danyluk J, Diallo AB, and Sarhan F, (2015) An integrative approach to identify hexaploid wheat miRNAome associated with development and tolerance to abiotic stress  BMC genomics 16.1 (2015): 339. 
 Mohamed Amine Remita, Etienne Lord   Made with JQuery, Angular.js, Bootstrap, D3, NVD3 and jqplot