RWRMTN: a tool for predicting disease-associated microRNAs based on a microRNA-target gene network

BMC Bioinformatics
Duc-Hau Le, Trang T H Tran

Abstract

The misregulation of microRNA (miRNA) has been shown to cause diseases. Recently, we have proposed a computational method based on a random walk framework on a miRNA-target gene network to predict disease-associated miRNAs. The prediction performance of our method is better than that of some existing state-of-the-art network- and machine learning-based methods since it exploits the mutual regulation between miRNAs and their target genes in the miRNA-target gene interaction networks. To facilitate the use of this method, we have developed a Cytoscape app, named RWRMTN, to predict disease-associated miRNAs. RWRMTN can work on any miRNA-target gene network. Highly ranked miRNAs are supported with evidence from the literature. They then can also be visualized based on the rankings and in relationships with the query disease and their target genes. In addition, automation functions are also integrated, which allow RWRMTN to be used in workflows from external environments. We demonstrate the ability of RWRMTN in predicting breast and lung cancer-associated miRNAs via workflows in Cytoscape and other environments. Considering a few computational methods have been developed as software tools for convenient uses, RWRMTN is among the fir...Continue Reading

References

Dec 31, 2003·Cell·Benjamin P LewisChristopher B Burge
Oct 18, 2008·Nucleic Acids Research·Qinghua JiangYunlong Liu
Jun 11, 2010·BMC Systems Biology·Qinghua JiangYadong Wang
Mar 3, 2011·PloS One·Espen EnerlyAnne-Lise Børresen-Dale
May 25, 2011·Journal of Biomedical Informatics·Harsh DweepNorbert Gretz
Nov 15, 2011·Genes to Cells : Devoted to Molecular & Cellular Mechanisms·Neil H Tan GanaTakashi Okamoto
Aug 10, 2012·Molecular BioSystems·Xing ChenGui-Ying Yan
Nov 30, 2012·Nucleic Acids Research·Tanya BarrettAlexandra Soboleva
May 30, 2013·PloS One·Himanshu AroraWoong-Yang Park
Jul 1, 2014·Scientific Reports·Xing Chen, Gui-Ying Yan
Jul 6, 2014·Clinical Chemistry·Benjamin MederAndreas Keller
Jul 16, 2014·Database : the Journal of Biological Databases and Curation·Vincent J HenryArnaud Desfeux
Jun 11, 2015·Medical Science Monitor : International Medical Journal of Experimental and Clinical Research·Fei YuZhongwei Lv
Jul 15, 2015·Genomics, Proteomics & Bioinformatics·Yang LiuYongsheng Bai
Aug 2, 2015·Computational Biology and Chemistry·Duc-Hau Le
Sep 24, 2015·International Journal of Oncology·Guang SunZheli Xu
Apr 15, 2016·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Yuansheng LiuQuan Zou
May 25, 2016·Journal of Biomedical Semantics·Samir GuptaK Vijay-Shanker
Jul 20, 2017·Npj Aging and Mechanisms of Disease·Yoshitaka IshiharaNorimasa Miura
Oct 14, 2017·Bioinformatics·Nathan W WongXiaowei Wang
May 16, 2018·Journal of Biomedical Informatics·Guanghui LiPingjian Ding
Dec 1, 2018·Journal of Cellular and Molecular Medicine·Sheng-Peng YuJia-Wei Luo
Aug 29, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Ping XuanYingying Song
Oct 12, 2019·Nucleic Acids Research·Eric W SayersJames Ostell

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE19783

Methods Mentioned

BETA
transfection

Software Mentioned

OMICtools
Tar
CMP
miRPD
CyREST
CyREST Command API
DMPred
TargetScan
HTTP
Cytoscape menu

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.