Structural profiles of human miRNA families from pairwise clustering

@article{Kaczkowski2009StructuralPO,
  title={Structural profiles of human miRNA families from pairwise clustering},
  author={Bogumił Kaczkowski and Elfar Torarinsson and Kristin Reiche and Jakob Hull Havgaard and Peter F. Stadler and Jan Gorodkin},
  journal={Bioinformatics},
  year={2009},
  volume={25 3},
  pages={
          291-4
        }
}
UNLABELLED MicroRNAs (miRNAs) are a group of small, approximately 21 nt long, riboregulators inhibiting gene expression at a post-transcriptional level. Their most distinctive structural feature is the foldback hairpin of their precursor pre-miRNAs. Even though each pre-miRNA deposited in miRBase has its secondary structure already predicted, little is known about the patterns of structural conservation among pre-miRNAs. We address this issue by clustering the human pre-miRNA sequences based on… 

Figures and Tables from this paper

A new method for measuring functional similarity of microRNAs

This work presented here a novel method for systematic study of functional similarities among human miRNAs by using their target genes GO semantic similarities to aid to reveal the functional diversity of miRNA families.

Mining Featured Patterns of MiRNA Interaction Based on Sequence and Structure Similarity

The approach is able to identify known miRNA interaction and uncover novel patterns of miRNA regulatory network and joint entropy is applied to identify correlated miRNAs, which are more desirable from the perspective of the gene regulatory network.

Systematic analysis of genomic organization and heterogeneities of miRNA cluster in vertebrates

Large scale data is used and comprehensive analysis is presented to examine various features of genomic organization of miRNA clusters across seven vertebrates by a combination of comparative genomics and bioinformatics approaches, suggesting that this cooperated function or cooperative effects between miRNAs in clusters perhaps be affected by inter-miRNA distances.

Inferring Potential microRNA-microRNA Associations Based on Targeting Propensity and Connectivity in the Context of Protein Interaction Network

A novel graph theoretic property based computational framework and method, called miRFunSim, for quantifying the associations between miRNA pairs based on miRNAs targeting propensity and proteins connectivity in the integrated protein-protein interaction network is proposed and succeeded in uncovering the candidate liver cancer related mi RNAs.

Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches

A method to represent candidate structures in a feature space, which summarizes key sequence/structure characteristics of each candidate, and it is demonstrated that proximity in this feature space is related to sequence/Structure similarity, and this approach allows for a better interpretation of the results.

Exploration of miRNA families for hypotheses generation

The results unveil a subclass of miRNAs that may be regulated by genomic imprinting, and also suggest that some miRNA families may be species-specific, as well as chromosome- and/or strand-specific.

Discovering non-coding RNA elements in drosophila 3′ untranslated regions

An improved RNA structural clustering pipeline that takes into account the length-dependent distribution of the structural similarity measure is proposed and successfully identified 184 ncRNA clusters, of which 91.3% appear to be true RNA structural elements, based on RNAz's prediction.

GraphClust: alignment-free structural clustering of local RNA secondary structures

A novel linear-time, alignment-free method for comparing and clustering RNAs according to sequence and structure, which is comparable to state-of-the-art sequence–structure methods although achieving speedups of several orders of magnitude.

miRFam: an effective automatic miRNA classification method based on n-grams and a multiclass SVM

It is argued that miRFam is suitable for application as an automated method of family classification, and it is an important supplementary tool to the existing alignment-based small non-coding RNA (sncRNA) classification methods, since it only requires primary sequence information.
...

References

SHOWING 1-10 OF 39 REFERENCES

RNA stem-loops: to be or not to be cleaved by RNAse III.

Comparing known pre-miRNAs to other predicted noncoding transcripts obtained from comparative genomics scans, using the structure comparison program RNAforester, suggests that many nonc coding RNAs may be under selection to dodge the RNAi pathway.

Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes

RNApromo is developed, an efficient computational tool for identifying structural elements within mRNAs that are involved in specifying posttranscriptional regulations and identifying structural differences between pre-microRNAs of animals and plants, which provide insights into the mechanism of microRNA biogenesis.

Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix

The FOLDALIGN software package provides the molecular biologist with an efficient and user-friendly tool for searching for new ncRNAs by introducing a new divide and conquer method to limit the memory requirement during global alignment and backtrack of local alignment.

Mouse‐centric comparative transcriptomics of protein coding and non‐coding RNAs

The largest transcriptome reported so far comprises 60,770 mouse full‐length cDNA clones, and is an effective reference data set for comparative transcriptomics. The number of mouse cDNAs identified

The expansion of the metazoan microRNA repertoire

A comprehensive comparative study of all known miRNA families in animals suggests that microRNA innovation is an ongoing process and major expansions of the metazoan miRNA repertoire coincide with the advent of bilaterians, vertebrates, and (placental) mammals.

miRBase: microRNA sequences, targets and gene nomenclature

The miRBase database aims to provide integrated interfaces to comprehensive microRNA sequence data, annotation and predicted gene targets, and acts as an independent arbiter of microRNA gene nomenclature.

Rfam: an RNA family database

The first release of Rfam (1.0) contains 25 families, which annotate over 50 000 non-coding RNA genes in the taxonomic divisions of the EMBL nucleotide database.

The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members

Based on the known relationship of Argonaute/Piwi proteins with distinct classes of small RNAs, it can be predicted how many new classes ofsmall RNAs or silencing processes remain to be discovered.