Abstract
Phenotypic traits, such as seed development, are a consequence of complex biochemical interactions among genes, proteins and metabolites, but the underlying mechanisms that operate in a coordinated and sequential manner remain elusive. Here, we address this issue by developing a computational algorithm to monitor proteome changes during the course of trait development. The algorithm is built within the mixture-model framework in which each mixture component is modeled by a specific group of proteins that display a similar temporal pattern of expression in trait development. A nonparametric approach based on Legendre orthogonal polynomials was used to fit dynamic changes of protein expression, increasing the power and flexibility of protein clustering. By analyzing a dataset of proteomic dynamics during early embryogenesis of the Chinese fir, the algorithm has successfully identified several distinct types of proteins that coordinate with each other to determine seed development in this forest tree commercially and environmentally important to China. The algorithm will find its immediate applications for the characterization of mechanistic underpinnings for any other biological processes in which protein abundance plays a key role.
Keywords: Functional clustering, Unsupervised analysis, Dynamic proteomics, Seed development, Forest tree.
Current Genomics
Title:A Computational Algorithm for Functional Clustering of Proteome Dynamics During Development
Volume: 15 Issue: 3
Author(s): Yaqun Wang, Ningtao Wang, Han Hao, Yunqian Guo, Yan Zhen, Jisen Shi and Rongling Wu
Affiliation:
Keywords: Functional clustering, Unsupervised analysis, Dynamic proteomics, Seed development, Forest tree.
Abstract: Phenotypic traits, such as seed development, are a consequence of complex biochemical interactions among genes, proteins and metabolites, but the underlying mechanisms that operate in a coordinated and sequential manner remain elusive. Here, we address this issue by developing a computational algorithm to monitor proteome changes during the course of trait development. The algorithm is built within the mixture-model framework in which each mixture component is modeled by a specific group of proteins that display a similar temporal pattern of expression in trait development. A nonparametric approach based on Legendre orthogonal polynomials was used to fit dynamic changes of protein expression, increasing the power and flexibility of protein clustering. By analyzing a dataset of proteomic dynamics during early embryogenesis of the Chinese fir, the algorithm has successfully identified several distinct types of proteins that coordinate with each other to determine seed development in this forest tree commercially and environmentally important to China. The algorithm will find its immediate applications for the characterization of mechanistic underpinnings for any other biological processes in which protein abundance plays a key role.
Export Options
About this article
Cite this article as:
Wang Yaqun, Wang Ningtao, Hao Han, Guo Yunqian, Zhen Yan, Shi Jisen and Wu Rongling, A Computational Algorithm for Functional Clustering of Proteome Dynamics During Development, Current Genomics 2014; 15 (3) . https://dx.doi.org/10.2174/1389202915666140407212147
DOI https://dx.doi.org/10.2174/1389202915666140407212147 |
Print ISSN 1389-2029 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-5488 |
Call for Papers in Thematic Issues
Advanced AI Techniques in Big Genomic Data Analysis
The thematic issue on "Advanced AI Techniques in Big Genomic Data Analysis" aims to explore the cutting-edge methodologies and applications of artificial intelligence (AI) in the realm of genomic research, where vast amounts of data pose both challenges and opportunities. This issue will cover a broad spectrum of AI-driven strategies, ...read more
Advanced Computational Algorithms and Artificial Intelligence in Clinical Pharmacogenomics
In the era of personalized medicine, understanding the relationship between genetics and drug response is crucial. This issue delves into innovative methodologies, leveraging deep computational analysis and artificial intelligence, to enhance the field of Clinical Pharmacogenomics. The interdisciplinary approach harnesses the power of advanced high-throughput genotyping technologies, sophisticated computational analysis, ...read more
Applications of Single-cell Sequencing Technology in Reproductive Medicine
Single cell sequencing (SCS) technology utilizes individual cells' genetic material to sequence their genome, transcriptome, and epigenetics at the molecular level. It offers insights into cell heterogeneity and enables the study of limited biological materials. Since its recognition as a valuable technique in 2011, single cell sequencing has yielded numerous ...read more
Big Data in Cancer Research
Cancer is a significant threat to human life and health, remaining a highly aggressive killer. It is a leading cause of death worldwide and represents a crucial medical issue for humanity. However, in the past decade, the effectiveness of new synthetic anticancer agents has not matched the current clinical speculation. ...read more
Related Journals
- 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
-
Biofunctional Peptides from Milk Proteins: Mineral Binding and Cytomodulatory Effects
Current Pharmaceutical Design Fluorescent Cisplatin Analogues and Cytotoxic Activity
Current Medicinal Chemistry TRPM8, a Sensor for Mild Cooling in Mammalian Sensory Nerve Endings
Current Pharmaceutical Biotechnology Pharmacogenetic Aspects of Drug Metabolizing Enzymes in Busulfan Based Conditioning Prior to Allogenic Hematopoietic Stem Cell Transplantation in Children
Current Drug Metabolism Structure Function Relationships of KTS Disintegrins and Design of Antiangiogenic Drugs
Letters in Drug Design & Discovery Electrocatalytic Determination of Cysteamine Uses a Nanostructure Based Electrochemical Sensor in Pharmaceutical Samples
Current Analytical Chemistry Applications of Nanosystems to Anticancer Drug Therapy (Part II. Dendrimers, Micelles, Lipid-based Nanosystems)
Recent Patents on Anti-Cancer Drug Discovery The Design of Vectors for RNAi Delivery System
Current Pharmaceutical Design The Clinical Impact of Quantitative Cell-free DNA, KRAS, and BRAF Mutations on Response to Anti-EGFR Treatment in Patients with Metastatic Colorectal Cancer
Current Pharmaceutical Design The Diversity of Epithelial Secreted Mucins
Current Organic Chemistry Molecular Basis for the Neuroprotective Properties of FKBP-Binding Immunophilin Ligands
Current Medicinal Chemistry - Central Nervous System Agents Targeted Therapies in Metastatic Melanoma: Toward a Clinical Breakthrough?
Anti-Cancer Agents in Medicinal Chemistry Selenium-Rich Foods: a Promising Approach to Colorectal Cancer Prevention
Current Pharmaceutical Biotechnology Effect of Thawing Conditions on Polyphenol Content and Antioxidant Activity of Frozen Haskap Berries (<i>Lonicera caerulea L.</i>)
Current Nutrition & Food Science Diagnostic and Therapeutic Uses of Nanomaterials in the Brain
Current Medicinal Chemistry Optimization of Aqueous Extraction of the Australian Maroon Bush (<i>Scaevola Spinescens</i> R. Br.) to Maximize Bioactive Compound and Antioxidant Yield
Current Nutraceuticals Preparation of Botanical Samples for Biomedical Research
Endocrine, Metabolic & Immune Disorders - Drug Targets Advances in Bioconjugation
Current Organic Chemistry Identification and Induction of Cytochrome P450s Involved in the Metabolism of Flavone-8-Acetic Acid in Mice
Drug Metabolism Letters High Yield Immobilization and Stabilization of Oxidoreductases Using Magnetic Nanosupports and Their Potential Applications: An Update
Current Catalysis