Abstract
Gene regulation is a key factor in gaining a full understanding of molecular biology. microRNA (miRNA), a novel class of non-coding RNA, has recently been found to be one crucial class of post-transactional regulators, and play important roles in cancer. One essential step to understand the regulatory effect of miRNAs is the reliable prediction of their target mRNAs. Typically, the predictions are solely based on the sequence information, which unavoidably have high false detection rates. Recently, some novel approaches are developed to predict miRNA targets by integrating the typical algorithm with the paired expression profiles of miRNA and mRNA. Here we review and discuss these integrative approaches and propose a new algorithm called HCTarget. Applying HCtarget to the expression data in multiple myeloma, we predict target genes for ten specific miRNAs. The experimental verification and a loss of function study validate our predictions. Therefore, the integrative approach is a reliable and effective way to predict miRNA targets, and could improve our comprehensive understanding of gene regulation.
Keywords: Expression profile, integrative analysis, miRNA, target prediction, Gene regulation, molecular biology, cancer, BAYESIAN NETWORK APPROACH, STATISTICAL INFERENCE, ONTOLOGY ENRICHMENT ANALYSIS
Current Bioinformatics
Title:Integrative Approaches for microRNA Target Prediction: Combining Sequence Information and the Paired mRNA and miRNA Expression Profiles
Volume: 8 Issue: 1
Author(s): Naifang Su, Minping Qian and Minghua Deng
Affiliation:
Keywords: Expression profile, integrative analysis, miRNA, target prediction, Gene regulation, molecular biology, cancer, BAYESIAN NETWORK APPROACH, STATISTICAL INFERENCE, ONTOLOGY ENRICHMENT ANALYSIS
Abstract: Gene regulation is a key factor in gaining a full understanding of molecular biology. microRNA (miRNA), a novel class of non-coding RNA, has recently been found to be one crucial class of post-transactional regulators, and play important roles in cancer. One essential step to understand the regulatory effect of miRNAs is the reliable prediction of their target mRNAs. Typically, the predictions are solely based on the sequence information, which unavoidably have high false detection rates. Recently, some novel approaches are developed to predict miRNA targets by integrating the typical algorithm with the paired expression profiles of miRNA and mRNA. Here we review and discuss these integrative approaches and propose a new algorithm called HCTarget. Applying HCtarget to the expression data in multiple myeloma, we predict target genes for ten specific miRNAs. The experimental verification and a loss of function study validate our predictions. Therefore, the integrative approach is a reliable and effective way to predict miRNA targets, and could improve our comprehensive understanding of gene regulation.
Export Options
About this article
Cite this article as:
Su Naifang, Qian Minping and Deng Minghua, Integrative Approaches for microRNA Target Prediction: Combining Sequence Information and the Paired mRNA and miRNA Expression Profiles, Current Bioinformatics 2013; 8 (1) . https://dx.doi.org/10.2174/1574893611308010008
DOI https://dx.doi.org/10.2174/1574893611308010008 |
Print ISSN 1574-8936 |
Publisher Name Bentham Science Publisher |
Online ISSN 2212-392X |
- Author Guidelines
- Graphical Abstracts
- Fabricating and Stating False Information
- Research Misconduct
- Post Publication Discussions and Corrections
- Publishing Ethics and Rectitude
- Increase Visibility of Your Article
- Archiving Policies
- Peer Review Workflow
- Order Your Article Before Print
- Promote Your Article
- Manuscript Transfer Facility
- Editorial Policies
- Allegations from Whistleblowers
Related Articles
-
Piecing the Fragments Together: Dynamical Insights into the Enhancement
of BRD4-BD1 (BET Protein) Druggability in Cancer Chemotherapy
Using Novel 8-methyl-pyrrolo[1,2-a]pyrazin-1(2H)-one Derivatives
Current Pharmaceutical Biotechnology The Interest of Folic Acid in Targeted Photodynamic Therapy
Current Medicinal Chemistry New Promises to Cure Cancer and Other Genetic Diseases/Disorders: Epi-drugs Through Epigenetics
Current Topics in Medicinal Chemistry Encountering and Advancing Through Antiangiogenesis Therapy for Gliomas
Current Pharmaceutical Design Peniciketal A, A Novel Spiroketal Compound, Exerts Anticancer Effects by Inhibiting Cell Proliferation, Migration and Invasion of A549 Lung Cancer Cells
Anti-Cancer Agents in Medicinal Chemistry The Accomplices of NF-κB Lead to Radioresistance
Current Protein & Peptide Science Recent Patents of microRNAs as Biomarkers for Breast, Leukemia, Prostate and Cervical Cancers
Recent Patents on Biomarkers Sesterterpenoids with Anticancer Activity
Current Medicinal Chemistry Critical Review of Malondialdehyde Analysis in Biological Samples
Current Pharmaceutical Analysis Is Type D Personality Here to Stay? Emerging Evidence Across Cardiovascular Disease Patient Groups
Current Cardiology Reviews Microarray Analysis of Human Epithelial Cell Responses to Bacterial Interaction
Infectious Disorders - Drug Targets Thiourea and Guanidine Derivatives as Antimalarial and Antimicrobial Agents<sup>§</sup>
Current Topics in Medicinal Chemistry Radiation Therapy Plus Angiogenesis Inhibition with Bevacizumab: Rationale and Initial Experience
Reviews on Recent Clinical Trials Recent Patents Concerning Modulators of Protein Kinase C
Recent Patents on DNA & Gene Sequences A Review of Fertility Preservation with Radical Vaginal Trachelectomy and Laparoscopic Pelvic Lymphadenectomy in the Treatment of Early Cervical Cancer
Current Women`s Health Reviews Inorganic Nanomedicines and their Labeling for Biological Imaging
Current Topics in Medicinal Chemistry Use of Anticancer Platinum Compounds in Combination Therapies and Challenges in Drug Delivery
Current Medicinal Chemistry The Antiproliferative Effect of Soy (<i>Glycine max</i>) Isoflavones Contained in a Nutraceutical on Cancer Cell Lines
Current Nutraceuticals Advancement of Traditional Chinese Medicine in Regulation of Intestinal Flora: Mechanism-based Role in Disease Management
Recent Patents on Anti-Cancer Drug Discovery Patent Selections:
Recent Patents and Topics on Imaging (Discontinued)