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Cui Q: TransmiR: a transcription factor-microRNA regulation database
- Nucleic Acids Res (Database Issue
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Research Article Genome-Wide Analysis of Human MicroRNA Stability
, 2013
"... Copyright © 2013 Yang Li et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Increasing studies have shown thatmicroRNA (miRNA) st ..."
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Copyright © 2013 Yang Li et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Increasing studies have shown thatmicroRNA (miRNA) stability plays important roles in physiology. However, the global picture of miRNA stability remains largely unknown. Here, we had analyzed genome-wide miRNA stability across 10 diverse cell types using miRNA arrays.We found thatmiRNA stability shows high dynamics and diversity both within individual cells and across cell types. Strikingly, we observed a negative correlation betweenmiRNA stability andmiRNAexpression level, which is different from current findings on other biological molecules such as proteins and mRNAs that show positive and not negative correlations between stability and expression level. This finding indicates that miRNA has a distinct action mode, which we called “rapid production, rapid turnover; slow production, slow turnover. ” This mode further suggests that high expression miRNAs normally degrade fast and may endow the cell with special properties that facilitate cellular status-transition. Moreover, we revealed that the stability of
Research Article A miRNA-Driven Inference Model to Construct Potential Drug-Disease Associations for Drug Repositioning
"... License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Increasing evidence discovered that the inappropriate expression of microRNAs (miRNAs) will lead to many kinds of complex diseases and drugs can regulate the expressio ..."
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License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Increasing evidence discovered that the inappropriate expression of microRNAs (miRNAs) will lead to many kinds of complex diseases and drugs can regulate the expression level of miRNAs. Therefore human diseases may be treated by targeting some specific miRNAs with drugs, which provides a new perspective for drug repositioning. However, few studies have attempted to computationally predict associations between drugs and diseases via miRNAs for drug repositioning. In this paper, we developed an inference model to achieve this aim by combining experimentally supported drug-miRNA associations and miRNA-disease associations with the assumption that drugs will form associations with diseases when they share some significantmiRNA partners. Experimental results showed excellent performance of our model. Case studies demonstrated that some of the strongly predicted drug-disease associations can be confirmed by the publicly accessible database CTD (www.ctdbase.org), which indicated the usefulness of our inference model. Moreover, candidate miRNAs as molecular hypotheses underpinning the associations were listed to guide future experiments. The predicted results were released for further studies. We expect that this study will provide help in our understanding of drug-disease association prediction and in the roles of miRNAs in drug repositioning. 1.
Editorial Cardiac Biomarkers
, 2015
"... which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Cardiac biomarkers have evolved as essential tools in cardiol-ogy over the last 50 years, that is, for primary and secondary prevention, the diagnosis and management of acute m ..."
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which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Cardiac biomarkers have evolved as essential tools in cardiol-ogy over the last 50 years, that is, for primary and secondary prevention, the diagnosis and management of acute myocar-dial infarction (AMI), and the diagnosis and risk stratification of heart failure (HF). We are beginning an era when it may be possible for biomarkers to direct treatment to optimize patient management. This is already the case with cardiac troponin (cTn) but should be the goal with all biomarkers. This special issue is a compilation of timely reviews and original articles on this topic. More than 60 years ago in 1954 Karmen et al. [1] first reported that release of aspartate aminotransferase (AST), formerly glutamate oxaloacetate transaminase (GOT), from necrotic cardiac myocytes could be detected in the serum
Article A Large-Scale Analysis of the Relationship of Synonymous SNPs Changing MicroRNA Regulation with Functionality and Disease
"... Abstract: Historically, owing to not changing amino acid composition of protein sequences, synonymous mutations are commonly assumed to be neutral during evolution and therefore have no effect on the phenotype and disease. Here, based on observations from large-scale analysis of genomic data, we pre ..."
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Abstract: Historically, owing to not changing amino acid composition of protein sequences, synonymous mutations are commonly assumed to be neutral during evolution and therefore have no effect on the phenotype and disease. Here, based on observations from large-scale analysis of genomic data, we predicted the putative synonymous SNPs that could result in functional consequences and disease risk through changing the microRNA-mediated gene regulation. We found that nearly half of the synonymous SNPs could affect protein expression by changing microRNA regulation in human genome and these SNPs significantly prefer to be associated with human diseases and traits. The synonymous SNPs changing microRNA-mediated gene regulation tend to be more under recent positive selection, prefer to affect gene expression, and implicate in human disease. We conclude that the miRNA-mediated regulation changes could be a potential mechanism for the contributions of synonymous SNPs to protein functions and disease risks.
The Human microRNA Disease Database (HMDD;
, 2013
"... HMDD v2.0: a database for experimentally ..."
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Research Article Prediction of MicroRNA-Disease Associations Based on Social Network Analysis Methods
"... which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MicroRNAs constitute an important class of noncoding, single-stranded, ∼22 nucleotide long RNA molecules encoded by endogenous genes. They play an important role in regulating ..."
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which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MicroRNAs constitute an important class of noncoding, single-stranded, ∼22 nucleotide long RNA molecules encoded by endogenous genes. They play an important role in regulating gene transcription and the regulation of normal development. MicroRNAs can be associated with disease; however, only a fewmicroRNA-disease associations have been confirmed by traditional experimental approaches.We introduce twomethods to predictmicroRNA-disease association.Thefirstmethod, KATZ, focuses on integrating the social network analysis method with machine learning and is based on networks derived from known microRNA-disease associations, disease-disease associations, and microRNA-microRNA associations. The other method, CATAPULT, is a supervised machine learning method. We applied the two methods to 242 known microRNA-disease associations and evaluated their performance using leave-one-out cross-validation and 3-fold cross-validation. Experiments proved that our methods outperformed the state-of-the-art methods. 1.
Review Roles of microRNAs in the Hepatitis B Virus Infection and Related Diseases
, 2013
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The new epidemic Middle East Respiratory Syndrome
"... Copyright © 2014 Md Mahmudul Hasan et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The new epidemic Middle East Respiratory Sy ..."
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Copyright © 2014 Md Mahmudul Hasan et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The new epidemic Middle East Respiratory Syndrome (MERS) is caused by a type of human coronavirus called MERS-CoV which has global fatality rate of about 30%. We are investigating potential antiviral therapeutics against MERS-CoV by using host microRNAs (miRNAs) which may downregulate viral gene expression to quell viral replication. We computationally predicted potential 13 cellular miRNAs from 11 potential hairpin sequences of MERS-CoV genome. Our study provided an interesting
