Abstract
Designing ontology to represent gene function is of vital importance for meeting the major challenge of integrating sequence data with the increasing amount of data from functional analyses of genes. Given that genes are expressed in temporally and spatially characteristic patterns, their products quite often reside in specific cellular compartments and may be part of one or more multi-component complexes. Genes may have more than one product and the products are functionally distinct. An overall strategy elucidating how an ontology-based gene function may be implemented using genomic databases is herein dissected. Knowing that gene products possess one or more biochemical, physiological or structural functions, the present strategy is suggested to lead towards physiological models. A review of the features of the currently available software tools for the implementation of the considered strategy is presented.
Keywords: Database, functional genomics, gene expression, gene ontology, physiology, systems biology, Model Structure Markup Language, physiology, cellular component ontology, International Nucleotide Sequence Database Collaboration
Current Bioinformatics
Title:From Ontology-Based Gene Function to Physiological Model
Volume: 7 Issue: 4
Author(s): Ajay Shiv Sharma, Hari Om Gupta and Petar M. Mitrasinovic
Affiliation:
Keywords: Database, functional genomics, gene expression, gene ontology, physiology, systems biology, Model Structure Markup Language, physiology, cellular component ontology, International Nucleotide Sequence Database Collaboration
Abstract: Designing ontology to represent gene function is of vital importance for meeting the major challenge of integrating sequence data with the increasing amount of data from functional analyses of genes. Given that genes are expressed in temporally and spatially characteristic patterns, their products quite often reside in specific cellular compartments and may be part of one or more multi-component complexes. Genes may have more than one product and the products are functionally distinct. An overall strategy elucidating how an ontology-based gene function may be implemented using genomic databases is herein dissected. Knowing that gene products possess one or more biochemical, physiological or structural functions, the present strategy is suggested to lead towards physiological models. A review of the features of the currently available software tools for the implementation of the considered strategy is presented.
Export Options
About this article
Cite this article as:
Shiv Sharma Ajay, Om Gupta Hari and M. Mitrasinovic Petar, From Ontology-Based Gene Function to Physiological Model, Current Bioinformatics 2012; 7 (4) . https://dx.doi.org/10.2174/157489312803901054
DOI https://dx.doi.org/10.2174/157489312803901054 |
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
-
Structural and Computational Biology of the Molecular Chaperone Hsp90: From Understanding Molecular Mechanisms to Computer-Based Inhibitor Design
Current Topics in Medicinal Chemistry Bugs and Drugs: Oncolytic Virotherapy in Combination with Chemotherapy
Current Pharmaceutical Biotechnology T Cell Tuning for Tumour Therapy: Enhancing Effector Function and Memory Potential of Therapeutic T cells
Current Gene Therapy Comprehensive Profiling of the Low Molecular Weight Proteins and Peptides in Weak Cation Exchange Beads Human Serum Retentate
Protein & Peptide Letters GSK3 Inhibitors and Disease
Mini-Reviews in Medicinal Chemistry FDG PET/CT in the Staging of Lung Cancer
Current Radiopharmaceuticals Acute Lymphoblastic Leukemia and Regulatory T cells: Biomarkers and Immunopathogenesis
Current Immunology Reviews (Discontinued) Antibodies as Crypts of Antiinfective and Antitumor Peptides
Current Medicinal Chemistry Lung Nodule Detection Using Polygon Approximation and Hybrid Features from CT Images
Current Medical Imaging Targeting P-glycoprotein for Effective Oral Anti-Cancer Chemotherapeutics
Current Cancer Drug Targets Histone Deacetylase Inhibitors: A Review on Class-I Specific Inhibition
Mini-Reviews in Medicinal Chemistry Targeting miRNAs for Drug Discovery: A New Paradigm
Current Molecular Medicine Combined Treatment with JFKD and Gefitinib Overcomes Drug Resistance in Non-Small Cell Lung Cancer
Current Pharmaceutical Biotechnology Structural Basis for Therapeutic Intervention of uPA/uPAR System
Current Drug Targets Suppression of Cancer Invasiveness by Dietary Compounds
Mini-Reviews in Medicinal Chemistry The Recent Development of Farnesyltransferase Inhibitors as Anticancer and Antimalarial Agents
Mini-Reviews in Medicinal Chemistry Pharmacovigilance Assessment of Cardiac Implications of Nicotine Replacement Therapy Among Smokers
Current Drug Safety Specific Targeting of Engineered Nanoparticles to Activated Macrophages
Current Nanoscience MicroRNAs in C. elegans Aging: Molecular Insurance for Robustness?
Current Genomics Enasidenib: First Mutant IDH2 Inhibitor for the Treatment of Refractory and Relapsed Acute Myeloid Leukemia
Anti-Cancer Agents in Medicinal Chemistry