Abstract
DNA microarrays are devices capable of detecting the identity and abundance of numerous DNA or RNA segments in samples. They are used for analyzing gene expressions, identifying genetic markers and detecting mutations on a genomic scale. The fundamental chemical mechanism of DNA microarrays is the hybridization between probes and targets due to the hydrogen bonds of nucleotide base pairing. Since the cross hybridization is inevitable, and probes or targets may form undesirable secondary or tertiary structures, the microarray data contain noise and depend on experimental conditions. It is crucial to apply proper statistical algorithms to obtain useful signals from noisy data. After we obtained the signals of a large amount of probes, we need to derive the biomedical information such as the existence of a transcript in a cell, the difference of expression levels of a gene in multiple samples, and the type of a genetic marker. Furthermore, after the expression levels of thousands of genes or the genotypes of thousands of single nucleotide polymorphisms are determined, it is usually important to find a small number of genes or markers that are related to a disease, individual reactions to drugs, or other phenotypes. All these applications need careful data analyses and reliable algorithms.
Keywords: alternative splicing, clustering, gene expression, genotyping, in situ synthesis, microarray, oligonucleotide and photolithography
Current Medicinal Chemistry
Title: High Density DNA Microarrays: Algorithms and Biomedical Applications
Volume: 11 Issue: 16
Author(s): Wei-Min Liu
Affiliation:
Keywords: alternative splicing, clustering, gene expression, genotyping, in situ synthesis, microarray, oligonucleotide and photolithography
Abstract: DNA microarrays are devices capable of detecting the identity and abundance of numerous DNA or RNA segments in samples. They are used for analyzing gene expressions, identifying genetic markers and detecting mutations on a genomic scale. The fundamental chemical mechanism of DNA microarrays is the hybridization between probes and targets due to the hydrogen bonds of nucleotide base pairing. Since the cross hybridization is inevitable, and probes or targets may form undesirable secondary or tertiary structures, the microarray data contain noise and depend on experimental conditions. It is crucial to apply proper statistical algorithms to obtain useful signals from noisy data. After we obtained the signals of a large amount of probes, we need to derive the biomedical information such as the existence of a transcript in a cell, the difference of expression levels of a gene in multiple samples, and the type of a genetic marker. Furthermore, after the expression levels of thousands of genes or the genotypes of thousands of single nucleotide polymorphisms are determined, it is usually important to find a small number of genes or markers that are related to a disease, individual reactions to drugs, or other phenotypes. All these applications need careful data analyses and reliable algorithms.
Export Options
About this article
Cite this article as:
Liu Wei-Min, High Density DNA Microarrays: Algorithms and Biomedical Applications, Current Medicinal Chemistry 2004; 11 (16) . https://dx.doi.org/10.2174/0929867043364739
DOI https://dx.doi.org/10.2174/0929867043364739 |
Print ISSN 0929-8673 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-533X |
Call for Papers in Thematic Issues
Advances in Medicinal Chemistry: From Cancer to Chronic Diseases.
The broad spectrum of the issue will provide a comprehensive overview of emerging trends, novel therapeutic interventions, and translational insights that impact modern medicine. The primary focus will be diseases of global concern, including cancer, chronic pain, metabolic disorders, and autoimmune conditions, providing a broad overview of the advancements in ...read more
Approaches to the treatment of chronic inflammation
Chronic inflammation is a hallmark of numerous diseases, significantly impacting global health. Although chronic inflammation is a hot topic, not much has been written about approaches to its treatment. This thematic issue aims to showcase the latest advancements in chronic inflammation treatment and foster discussion on future directions in this ...read more
Cellular and Molecular Mechanisms of Non-Infectious Inflammatory Diseases: Focus on Clinical Implications
The Special Issue covers the results of the studies on cellular and molecular mechanisms of non-infectious inflammatory diseases, in particular, autoimmune rheumatic diseases, atherosclerotic cardiovascular disease and other age-related disorders such as type II diabetes, cancer, neurodegenerative disorders, etc. Review and research articles as well as methodology papers that summarize ...read more
Chalcogen-modified nucleic acid analogues
Chalcogen-modified nucleosides, nucleotides and oligonucleotides have been of great interest to scientific research for many years. The replacement of oxygen in the nucleobase, sugar or phosphate backbone by chalcogen atoms (sulfur, selenium, tellurium) gives these biomolecules unique properties resulting from their altered physical and chemical properties. The continuing interest in ...read more
- 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
- Announcements
Related Articles
-
Addressing MIST (Metabolites in Safety Testing): Bioanalytical Approaches to Address Metabolite Exposures in Humans and Animals
Current Drug Metabolism Design, Synthesis and Molecular Docking Studies of Novel Thiadiazole Analogues with Potential Antimicrobial and Antiinflammatory Activities
Anti-Inflammatory & Anti-Allergy Agents in Medicinal Chemistry Advances in Immunological Treatment of Allergy
Current Medicinal Chemistry - Anti-Inflammatory & Anti-Allergy Agents Binding Model of Capsaicin is Able to Reach the Peripheral Anionic Site of Acetylcholinesterase
Current Bioactive Compounds Genetic Insights into Sporadic Parkinson's Disease Pathogenesis
Current Genomics Thromboembolic Complications in Severe COVID-19: Current Antithrombotic Strategies and Future Perspectives
Cardiovascular & Hematological Disorders-Drug Targets Granulomatous Lung Disease. Disease for Pulmomologists: Diagnosis and Treatment
Current Respiratory Medicine Reviews Dietary Phytoestrogens: Neuroprotective Role in Parkinson’s Disease
Current Neurovascular Research Potential Impacts of Prebiotics and Probiotics on Cancer Prevention
Anti-Cancer Agents in Medicinal Chemistry HIV-1 Prophylactic Vaccine Trials in Thailand
Current HIV Research Relative Expression of Mouse Udp-glucuronosyl Transferase 2b1 Gene in the Livers, Kidneys, and Hearts: The Influence of Nonsteroidal Anti-inflammatory Drug Treatment
Current Drug Metabolism Antigenic Peptide Vaccination: Provoking Immune Response and Clinical Benefit for Cancer
Current Immunology Reviews (Discontinued) Helminth Infections and Cardiovascular Diseases: Toxocara Species is Contributing to the Disease
Current Cardiology Reviews Diabetic CVD – Focus on Vitamin D
Cardiovascular & Hematological Agents in Medicinal Chemistry New Insight into P-Glycoprotein as a Drug Target
Anti-Cancer Agents in Medicinal Chemistry Protein Misfolding in Disease: Cause or Response?
Current Medicinal Chemistry - Immunology, Endocrine & Metabolic Agents Inflammatory Mechanisms of Injury and Recovery after Intracerebral Hemorrhage
Current Immunology Reviews (Discontinued) Pulmonary Manifestations of Rheumatoid Arthritis, Psoriatic Arthritis and Peripheral Spondyloarthritis: Prevalence, Diagnostic Approach and Treatment Options
Current Rheumatology Reviews Hypoxia and Inflammation in Prostate Cancer Progression. Cross-talk with Androgen and Estrogen Receptors and Cancer Stem Cells
Endocrine, Metabolic & Immune Disorders - Drug Targets Successful Desensitization of Three Patients with Hypersensitivity Reactions to Omalizumab
Current Drug Safety