Abstract
Background: Dysregulated pathway identification is an important task which can gain insight into the underlying biological processes of disease. Current pathway-identification methods focus on a set of co-expression genes and single pathways and ignore the correlation between genes and pathways.
Objective: This study takes into account the internal correlations not only between genes but also pathways to explore the underlying dysregulated pathways of Alzheimer's disease (AD), the most common form of dementia.
Methods: In order to find the significantly differential genes for AD, mutual information (MI) is used to measure interdependencies between genes other than expression valves. Then, by integrating the topology information from KEGG, the significant pathways involved in the feature genes are identified. Next, the distance correlation (DC) is applied to measure the pairwise pathway crosstalks since DC has the advantage of detecting nonlinear correlations when compared to Pearson correlation. Finally, the pathway pairs with significantly different correlations between normal and AD samples are known as dysregulated pathways.
Results: We identified 33 dysregulated pathway pairs related to AD in which the crosstalks score calculated by DC greatly changed from normal to AD samples. The molecular biology analysis demonstrated that many dysregulated pathways related to AD pathogenesis have been discovered successfully by the internal correlation detection.
Conclusion: Our studies on the identification of the dysregulated pathways in the development and deterioration of AD will help to find new effective target genes which are closely related to the pathogenesis of AD and provide important theoretical guidance for drug design.
Keywords: Dysregulated pathway identification, internal correlation, Alzheimer's disease, mutual information, pathway crosstalk, distance correlation.
Combinatorial Chemistry & High Throughput Screening
Title:Dysregulated Pathway Identification of Alzheimer's Disease Based on Internal Correlation Analysis of Genes and Pathways
Volume: 20 Issue: 10
Author(s): Wei Kong*, Xiaoyang Mou, Benteng Di, Jin Deng, Ruxing Zhong and Shuaiqun Wang
Affiliation:
- College of Information Engineering, Shanghai Maritime University, Shanghai 201306,China
Keywords: Dysregulated pathway identification, internal correlation, Alzheimer's disease, mutual information, pathway crosstalk, distance correlation.
Abstract: Background: Dysregulated pathway identification is an important task which can gain insight into the underlying biological processes of disease. Current pathway-identification methods focus on a set of co-expression genes and single pathways and ignore the correlation between genes and pathways.
Objective: This study takes into account the internal correlations not only between genes but also pathways to explore the underlying dysregulated pathways of Alzheimer's disease (AD), the most common form of dementia.
Methods: In order to find the significantly differential genes for AD, mutual information (MI) is used to measure interdependencies between genes other than expression valves. Then, by integrating the topology information from KEGG, the significant pathways involved in the feature genes are identified. Next, the distance correlation (DC) is applied to measure the pairwise pathway crosstalks since DC has the advantage of detecting nonlinear correlations when compared to Pearson correlation. Finally, the pathway pairs with significantly different correlations between normal and AD samples are known as dysregulated pathways.
Results: We identified 33 dysregulated pathway pairs related to AD in which the crosstalks score calculated by DC greatly changed from normal to AD samples. The molecular biology analysis demonstrated that many dysregulated pathways related to AD pathogenesis have been discovered successfully by the internal correlation detection.
Conclusion: Our studies on the identification of the dysregulated pathways in the development and deterioration of AD will help to find new effective target genes which are closely related to the pathogenesis of AD and provide important theoretical guidance for drug design.
Export Options
About this article
Cite this article as:
Kong Wei *, Mou Xiaoyang , Di Benteng, Deng Jin , Zhong Ruxing and Wang Shuaiqun, Dysregulated Pathway Identification of Alzheimer's Disease Based on Internal Correlation Analysis of Genes and Pathways, Combinatorial Chemistry & High Throughput Screening 2017; 20 (10) . https://dx.doi.org/10.2174/1386207320666171121112235
DOI https://dx.doi.org/10.2174/1386207320666171121112235 |
Print ISSN 1386-2073 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-5402 |
Call for Papers in Thematic Issues
Artificial Intelligence Methods for Biomedical, Biochemical and Bioinformatics Problems
Recently, a large number of technologies based on artificial intelligence have been developed and applied to solve a diverse range of problems in the areas of biomedical, biochemical and bioinformatics problems. By utilizing powerful computing resources and massive amounts of data, methods based on artificial intelligence can significantly improve the ...read more
Eco-friendly Agents for Biological Control of Pathogenic Diseases
The discovery of an alternative biological approach to disease management includes work on medicinal products derived from natural sources as a starting point for the development of eco-friendly agents for these diseases and the injuries they cause, as well as reducing human contact with hazardous chemicals and their residues. We ...read more
Emerging trends in diseases mechanisms, noble drug targets and therapeutic strategies: focus on immunological and inflammatory disorders
Recently infectious and inflammatory diseases have been a key concern worldwide due to tremendous morbidity and mortality world Wide. Recent, nCOVID-9 pandemic is a good example for the emerging infectious disease outbreak. The world is facing many emerging and re-emerging diseases out breaks at present however, there is huge lack ...read more
Exploring Spectral Graph Theory in Combinatorial Chemistry
Scope of the Thematic Issue: Combinatorial chemistry involves the synthesis and analysis of a large number of diverse compounds simultaneously. Traditional methods rely on brute force experimentation, which can be time-consuming and resource-intensive. Spectral Graph Theory, a branch of mathematics dealing with the properties of graphs in relation to the ...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
Related Articles
-
Origin and Evolution of China Pharmacopoeia and Its Implication for Traditional Medicines
Mini-Reviews in Medicinal Chemistry Lysine Acetyltransferases CBP and p300 as Therapeutic Targets in Cognitive and Neurodegenerative Disorders
Current Pharmaceutical Design The Influence of Sex Hormones on Pulmonary Vascular Reactivity: Possible Vasodilator Therapies for the Treatment of Pulmonary Hypertension
Current Vascular Pharmacology Maternal Fish Oil Supplementation: The Prodrom of Synaptic Protection in Alzheimers Disease
Current Nutrition & Food Science Pharmacological Inhibition of Platelet Reactivity. Clinical and Pharmacodynamic Effects
Current Vascular Pharmacology Dopamine Targeting Drugs for the Treatment of Schizophrenia: Past, Present and Future
Current Topics in Medicinal Chemistry An Overview of New Possible Treatments of Alzheimer's Disease, Based on Natural Products and Semi-Synthetic Compounds
Current Medicinal Chemistry Herbal Medicines for Diabetes Management and its Secondary Complications
Current Diabetes Reviews Drug Delivery Systems for Imaging and Therapy of Parkinson's Disease
Current Neuropharmacology The Updated Role of Oxidative Stress in Subarachnoid Hemorrhage
Current Drug Delivery A Scientometrics Analysis and Visualization of Depressive Disorder
Current Neuropharmacology Tolfenamic Acid Interrupts the De Novo Synthesis of the β-Amyloid Precursor Protein and Lowers Amyloid Beta Via a Transcriptional Pathway
Current Alzheimer Research Management of Inflammation by Natural Polyphenols: A Comprehensive Mechanistic Update
Current Medicinal Chemistry The Role of Berberine in the Multi-Target Treatment of Senile Dementia
Current Topics in Medicinal Chemistry Protein-Protein Interactions and Aggregation Inhibitors in Alzheimer’s Disease
Current Topics in Medicinal Chemistry Fluoride Interactions: From Molecules to Disease
Current Signal Transduction Therapy Neurotoxicity and Side-Effects of Highly Active Antiretroviral Therapy [HAART] on the Central and Peripheral Nerve System
Anti-Inflammatory & Anti-Allergy Agents in Medicinal Chemistry Evidence for Predominance of CCR5-Using HIV-1 Strains During Highly Active Antiretroviral Therapy
Current HIV Research The Effects of Olprinone, a Phosphodiesterase 3 Inhibitor, on Systemic and Cerebral Circulation
Current Vascular Pharmacology Mortality and Treatment Costs have a Great Impact on the Cost- Effectiveness of Disease Modifying Treatment in Alzheimer’s Disease - A Simulation Study
Current Alzheimer Research