Advertisement

Topics

Improving performance of mammalian microRNA target prediction.

Summary of "Improving performance of mammalian microRNA target prediction."


ABSTRACT:

BACKGROUND:
MicroRNAs (miRNAs) are single-stranded non-coding RNAs known to regulate a wide range of cellular processes by silencing the gene expression at the protein and/or mRNA levels. Computational prediction of miRNA targets is essential for elucidating the detailed functions of miRNA. However, the prediction specificity and sensitivity of the existing algorithms are still poor to generate meaningful, workable hypotheses for subsequent experimental testing. Constructing a richer and more reliable training data set and developing an algorithm that properly exploits this data set would be the key to improve the performance current prediction algorithms.
RESULTS:
A comprehensive training data set is constructed for mammalian miRNAs with its positive targets obtained from the most up-to-date miRNA target depository called miRecords and its negative targets derived from 20 microarray data. A new algorithm SVMicrO is developed, which assumes a 2-stage structure including a site support vector machine (SVM) followed by a UTR-SVM. SVMicrO makes prediction based on 21 optimal site features and 18 optimal UTR features, selected by training from a comprehensive collection of 113 site and 30 UTR features. Comprehensive evaluation of SVMicrO performance has been carried out on the training data, proteomics data, and immunoprecipitation (IP) pull-down data. Comparisons with some popular algorithms demonstrate consistent improvements in prediction specificity, sensitivity and precision in all tested cases. All the related materials including source code and genome-wide prediction of human targets are available at http://compgenomics.utsa.edu/svmicro.html.
CONCLUSIONS:
A 2-stage SVM based new miRNA target prediction algorithm called SVMicrO is developed. SVMicrO is shown to be able to achieve robust performance. It holds the promise to achieve continuing improvement whenever better training data that contain additional verified or high confidence positive targets and properly selected negative targets are available.

Affiliation

Journal Details

This article was published in the following journal.

Name: BMC bioinformatics
ISSN: 1471-2105
Pages: 476

Links

DeepDyve research library

PubMed Articles [21424 Associated PubMed Articles listed on BioPortfolio]

MicroRNA-155 targets MAP3K10 and regulates osteosarcoma cell growth.

Osteosarcoma is the most common type of bone cancer prevalent in young adults. Recent studies suggested that aberrant microRNA expression plays an essential role in osteosarcoma pathogenesis. In this ...

Drug-Target Interaction Prediction using Ensemble Learning and Dimensionality Reduction.

Experimental prediction of drug-target interactions is expensive, time-consuming and tedious. Fortunately, computational methods help narrow down the search space for interaction candidates to be furt...

Deep learning-based drug-target interaction prediction.

Identifying interactions between known drugs and targets is a major challenge in drug repositioning. In silico prediction of drug target interaction (DTI) can speed up the experimental work which is e...

EPMDA: an expression profile-based computational model for microRNA-dsease association prediction.

MicroRNA has become a new star molecule for understanding multiple biological processes and the mechanism of various complex human diseases. Even though a number of computational models have been prop...

The microRNA-449 family inhibits TGF-β-mediated liver cancer cell migration by targeting SOX4.

Modulation of microRNA expression is considered for treatment of hepatocellular carcinoma (HCC). Therefore, we characterized the epigenetically regulated microRNA-449 family (miR-449a, miR-449b, miR-4...

Clinical Trials [5630 Associated Clinical Trials listed on BioPortfolio]

Physiopathological and Therapeutic Value of microRNA in the Progression of Carotid Artery Plaques: Carotid Protocol and microRNA

Molecular analysis of the atheroma plaque. Screening for a novel biomarker of carotid status.

Expression Profiling of microRNA Following Administration of Dexmedetomidine

The purpose of the study is to find out the differential expression profiling of microRNA before and after adiministration of dexmedetomidine in patients undergoing procedures, and then in...

microRNA of Human Epidermal Growth Factor Receptor 2 (HER2)Positive Patient Treated With Herceptin

This projective observational study is planned to enroll more than 300 advanced breast cancer patients, who were proved as Her-2 positive using fluorescence in situ hybridization (FISH) an...

Carbohydrate Availability and microRNA Expression

This investigation will examine the impact of skeletal muscle glycogen stores on skeletal muscle and circulating microRNA expression and exogenous carbohydrate oxidation. Primary Objectiv...

Transcriptome Study of Acute Myocardial Infarction

This study aims to compare whole-blood microarray gene-expression profiling between patients with acute myocardial infarction and normal participants without cardiovascular diseases. First...

Medical and Biotech [MESH] Definitions

Chemically-engineered oligonucleotides used to selectively inhibit expression of target genes through sequence-specific binding of corresponding microRNA (miRNA) sites.

Predicting the time of OVULATION can be achieved by measuring the preovulatory elevation of ESTRADIOL; LUTEINIZING HORMONE or other hormones in BLOOD or URINE. Accuracy of ovulation prediction depends on the completeness of the hormone profiles, and the ability to determine the preovulatory LH peak.

Small double-stranded, non-protein coding RNAs, 21-25 nucleotides in length generated from single-stranded microRNA gene transcripts by the same RIBONUCLEASE III, Dicer, that produces small interfering RNAs (RNA, SMALL INTERFERING). They become part of the RNA-INDUCED SILENCING COMPLEX and repress the translation (TRANSLATION, GENETIC) of target RNA by binding to homologous 3'UTR region as an imperfect match. The small temporal RNAs (stRNAs), let-7 and lin-4, from C. elegans, are the first 2 miRNAs discovered, and are from a class of miRNAs involved in developmental timing.

Performance of an act one or more times, with a view to its fixation or improvement; any performance of an act or behavior that leads to learning.

Planning that has the goals of improving health, improving accessibility to health services, and promoting efficiency in the provision of services and resources on a comprehensive basis for a whole community. (From Facts on File Dictionary of Health Care Management, 1988, p299)

Quick Search
Advertisement
 


DeepDyve research library

Relevant Topics

Bioinformatics
Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...

Nutrition
Within medicine, nutrition (the study of food and the effect of its components on the body) has many different roles. Appropriate nutrition can help prevent certain diseases, or treat others. In critically ill patients, artificial feeding by tubes need t...


Searches Linking to this Article