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Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach.

Publication ,  Conference
Ding, J; Li, D; Ohler, U; Guan, J; Zhou, S
Published in: BMC Genomics
June 11, 2012

BACKGROUND: MiRNA are about 22nt long small noncoding RNAs that post transcriptionally regulate gene expression in animals, plants and protozoa. Confident identification of MiRNA-Target Interactions (MTI) is vital to understand their function. Currently, several integrated computational programs and databases are available for animal miRNAs, the mechanisms of which are significantly different from plant miRNAs. METHODS: Here we present an integrated MTI prediction and analysis toolkit (imiRTP) for Arabidopsis thaliana. It features two important functions: (i) combination of several effective plant miRNA target prediction methods provides a sufficiently large MTI candidate set, and (ii) different filters allow for an efficient selection of potential targets. The modularity of imiRTP enables the prediction of high quality targets on genome-wide scale. Moreover, predicted MTIs can be presented in various ways, which allows for browsing through the putative target sites as well as conducting simple and advanced analyses. RESULTS: Results show that imiRTP could always find high quality candidates compared with single method by choosing appropriate filter and parameter. And we also reveal that a portion of plant miRNA could bind target genes out of coding region. Based on our results, imiRTP could facilitate the further study of Arabidopsis miRNAs in real use. All materials of imiRTP are freely available under a GNU license at (http://admis.fudan.edu.cn/projects/imiRTP.htm).

Duke Scholars

Published In

BMC Genomics

DOI

EISSN

1471-2164

Publication Date

June 11, 2012

Volume

13 Suppl 3

Issue

Suppl 3

Start / End Page

S3

Location

England

Related Subject Headings

  • Software
  • Reproducibility of Results
  • RNA, Plant
  • RNA, Messenger
  • MicroRNAs
  • Genome, Plant
  • Computational Biology
  • Bioinformatics
  • Arabidopsis
  • Algorithms
 

Citation

APA
Chicago
ICMJE
MLA
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Ding, J., Li, D., Ohler, U., Guan, J., & Zhou, S. (2012). Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach. In BMC Genomics (Vol. 13 Suppl 3, p. S3). England. https://doi.org/10.1186/1471-2164-13-S3-S3
Ding, Jiandong, Danqing Li, Uwe Ohler, Jihong Guan, and Shuigeng Zhou. “Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach.” In BMC Genomics, 13 Suppl 3:S3, 2012. https://doi.org/10.1186/1471-2164-13-S3-S3.
Ding J, Li D, Ohler U, Guan J, Zhou S. Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach. In: BMC Genomics. 2012. p. S3.
Ding, Jiandong, et al. “Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach.BMC Genomics, vol. 13 Suppl 3, no. Suppl 3, 2012, p. S3. Pubmed, doi:10.1186/1471-2164-13-S3-S3.
Journal cover image

Published In

BMC Genomics

DOI

EISSN

1471-2164

Publication Date

June 11, 2012

Volume

13 Suppl 3

Issue

Suppl 3

Start / End Page

S3

Location

England

Related Subject Headings

  • Software
  • Reproducibility of Results
  • RNA, Plant
  • RNA, Messenger
  • MicroRNAs
  • Genome, Plant
  • Computational Biology
  • Bioinformatics
  • Arabidopsis
  • Algorithms