A new method for measuring functional similarity of microRNAs

@inproceedings{Yu2011ANM,
  title={A new method for measuring functional similarity of microRNAs},
  author={Guangchuang Yu and Chuan-le Xiao and Xiaochen Bo and Chun-hua Lu and Yide Qin and Sheng Zhan and Qing‐Yu He},
  year={2011}
}
MicroRNAs (miRNAs) are a group of small RNAs with regulatory roles at post-transcriptional level. Although they have been clustered based on their sequence or structure similarities, there is still no effective method to determine their functional similarities due to the lack of miRNAs functional annotation. To address this critical need, we presented here a novel  method for systematic study of functional similarities among human miRNAs by using their target genes GO semantic similarities. The… 

Figures from this paper

A New Ontology-Based Method for Functional Composed Comparison of MicroRNAs

CFSim, a method that uses Gene Ontology (GO) and the disease ontology MeSH to compute miRNAs composed similarity by combining different information related to them, is proposed and evaluated and shown that it is efficient and efficient in sense that the functional similarity between miRNAAs in the same family was higher compared to other mi RNAs from distinct families.

Inferring plant microRNA functional similarity using a weighted protein-protein interaction network

A novel method based on calculating the weighted shortest path between two target genes was introduced, and for the first time, a protein-protein interaction network with semantic similarity weights generated using Gene Ontology terms was employed to calculate the functional similarity of plant miRNAs.

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.

A new system for human microRNA functional evaluation and network

A new method to quantitatively measure the functional relevance among microRNAs that is solely based on the Gene Ontology and integrated functional annotation data from public pathways and PFam gene databases is presented.

MiRGOFS: a GO‐based functional similarity measurement for miRNAs, with applications to the prediction of miRNA subcellular localization and miRNA‐disease association

A new method to measure the functional similarity for miRNAs, called miRGOFS, which has two notable features: it adopts a new GO semantic similarity metric which considers both common ancestors and descendants of GO terms, and weights each GO term by its statistical significance.

Functional similarities between microRNAs inferred from biomedical texts

This study applied a biomedical text-mining method to assess miRNA functional similarities and found that majority of the top ten candidates have been validated by experimental evidence and has higher reliability, larger coverage, and superior performance in prioritising disease-related miRNAs.

A path-based measurement for human miRNA functional similarities using miRNA-disease associations

This study develops a novel path-based calculation method of miRNA functional similarity based on miRNA-disease associations, called MFSP, which obtains higher average functional similarity of intra-family and intra-cluster selected groups and the constructed mi RNA functional network is a scale-free and small-world network.

Functional similarity analysis of human virus-encoded miRNAs

The functional similarities among human viral miRNAs were measured by using a method reported previously, and higher order functions regulated by viral miRNA functions were also identified by KEGG pathway analysis on their targets.

Inferring the soybean (Glycine max) microRNA functional network based on target gene network

A new method to measure the functional similarity of miRNAs considering both the site accessibility and the interactive context of target genes in functional gene networks is proposed and the miRFNs of soybean are constructed, which is the first study on soybean miRNA on the network level and the core methods can be easily extended to other species.

References

SHOWING 1-10 OF 59 REFERENCES

Inferring the human microRNA functional similarity and functional network based on microRNA-associated diseases

A method to infer the pairwise functional similarity and functional network for human miRNAs based on the structures of their disease relationships and can be easily extended to other species when sufficient miRNA-associated disease data are available for specific species.

Structural profiles of human miRNA families from pairwise clustering

This work clustering the human pre-miRNA sequences based on pairwise, sequence and secondary structure alignment using FOLDALIGN, followed by global multiple alignment of obtained clusters by WAR, successfully determined the common secondary structure for four FOLDalIGN clusters.

Human microRNA clusters: genomic organization and expression profile in leukemia cell lines.

miRBase: tools for microRNA genomics

The overlap of miRNA sequences with annotated transcripts, both protein- and non-coding, are described and graphical views of the locations of a wide range of genomic features in model organisms allow for the first time the prediction of the likely boundaries of many miRNA primary transcripts.

Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application

GOmir introduces miRNA predicted targets accompanied by a full gene description, functional analysis and detailed gene ontology clustering and a reverse search initiated by a potential target can also be conducted.

Origin and Evolution of Human microRNAs From Transposable Elements

The results indicate that TEs provide a natural mechanism for the origination miRNAs that can contribute to regulatory divergence between species as well as a rich source for the discovery of as yet unknown miRNA genes.

A new measure for functional similarity of gene products based on Gene Ontology

A new method for comparing sets of GO terms and for assessing the functional similarity of gene products and a proposed map of the functional space provides a new global view on the functional relationships between gene products or protein families.

Evaluation of GO-based functional similarity measures using S. cerevisiae protein interaction and expression profile data

This study evaluated five functional similarity methods using both protein-protein interaction (PPI) and expression data of S. cerevisiae and demonstrated the reliability of current approaches that elevate the similarities of GO terms to the similarity of proteins.

Characterization of microRNA expression profiles in normal human tissues

A global view of tissue distribution of miRNAs in relation to their chromosomal locations and genomic structures is presented to support their tissue-specific functional roles to regulate the physiologies of the normal tissues in which they are expressed.

Origin, evolution, and biological role of miRNA cluster in DLK-DIO3 genomic region in placental mammals.

Analysis of the mir-379/mir-656 miRNA cluster located within the imprinted DLK-DIO3 region on human chromosome 14 suggests that emergence of this cluster was one of the factors that facilitated evolution of the placental mammals.
...