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 [19962 Associated PubMed Articles listed on BioPortfolio]

TarPmiR: a new approach for microRNA target site prediction.

The identification of microRNA (miRNA) target sites is fundamentally important for studying gene regulation. There are dozens of computational methods available for miRNA target site prediction. Despi...

H19 derived microRNA-675 regulates cell proliferation and migration through CDK6 in glioma.

The long non-coding RNA (LncRNA) H19 is one of the most highly abundant and conserved transcripts involved in the mammalian development and tumorigenesis. H19 is expressed in both embryonic cells and ...

STarMir Tools for Prediction of microRNA Binding Sites.

MicroRNAs (miRNAs) are a class of endogenous short noncoding RNAs that regulate gene expression by targeting messenger RNAs (mRNAs), which results in translational repression and/or mRNA degradation. ...

CASP 11 Target Classification.

Protein target structures for the Critical Assessment of Structure Prediction round 11 (CASP11) and CASP ROLL were split into domains and classified into categories suitable for assessment of template...

MicroRNA Let-7b inhibits keratinocyte migration in cutaneous wound healing by targeting IGF2BP2.

Wound healing is a complex process involves proliferation and migration of keratinocyte for closure of epidermal injuries. A member of microRNA family let-7b, have been expressed in mammalian skin but...

Clinical Trials [4536 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.

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...

The Utility of Circulating Tumour Cells and Plasma microRNA in Esophageal Adenocarcinoma

Circulating microRNA (circ miRNA) and circulating tumor cell (CTC) levels are hypothesized to be associated with response to chemoradiation in patients undergoing treatment for locally adv...

MicroRNA Mediates Volatile Anesthetics Preconditioning Induced Artery Protection

It has been reported that volatile anesthetics preconditioning mediates protection of organ via microRNA. We want to study on the effects of isoflurane preconditioning on expression of mic...

Molecular Mechanisms Leading to Chemoresistance in Epithelial Ovarian Cancer

Epithelial ovarian cancer is the most lethal gynecological malignancy in developed countries and the fifth most common cause of cancer-related death in women. Poor prognosis is due to chal...

Medical and Biotech [MESH] Definitions

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)

Carrying out of specific physical routines or procedures by one who is trained or skilled in physical activity. Performance is influenced by a combination of physiological, psychological, and socio-cultural factors.

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