Abstract
To understand most cellular processes, one must understand how genetic information is processed. A formidable challenge is the dissection of gene regulatory networks to delineate how eukaryotic cells coordinate and govern patterns of gene expression that ultimately lead to a phenotype. In this paper, we review several approaches for modeling eukaryotic gene regulatory networks and for reverse engineering such networks from experimental observations. Since we are interested in elucidating the transcriptional regulatory mechanisms of colon cancer progression, we use this important biological problem to illustrate various aspects of modeling gene regulation. We discuss four important models: gene networks, transcriptional regulatory systems, Boolean networks, and dynamical Bayesian networks. We review state-of-the-art functional genomics techniques, such as gene expression profiling, cisregulatory element identification, TF target gene identification, and gene silencing by RNA interference, which can be used to extract information about gene regulation. We can employ this information, in conjunction with appropriately designed reverse engineering algorithms, to construct a computational model of gene regulation that sufficiently predicts experimental observations. In the last part of this review, we focus on the problem of reverse engineering transcriptional regulatory networks by gene perturbations. We mathematically formulate this problem and discuss the role of experimental resolution in our ability to reconstruct accurate models of gene regulation. We conclude, by discussing a promising approach for inferring a transcriptional regulatory system from microarray data obtained by gene perturbations.
Keywords: adenomatous polyposis coli (apc) gene, rna interference, boolean networks, transcriptional regulatory system, dynamic bayesian networks, cis-regulatory elements
Current Pharmaceutical Design
Title: Computational and Experimental Approaches for Modeling Gene Regulatory Networks
Volume: 13 Issue: 14
Author(s): J. Goutsias and N. H. Lee
Affiliation:
Keywords: adenomatous polyposis coli (apc) gene, rna interference, boolean networks, transcriptional regulatory system, dynamic bayesian networks, cis-regulatory elements
Abstract: To understand most cellular processes, one must understand how genetic information is processed. A formidable challenge is the dissection of gene regulatory networks to delineate how eukaryotic cells coordinate and govern patterns of gene expression that ultimately lead to a phenotype. In this paper, we review several approaches for modeling eukaryotic gene regulatory networks and for reverse engineering such networks from experimental observations. Since we are interested in elucidating the transcriptional regulatory mechanisms of colon cancer progression, we use this important biological problem to illustrate various aspects of modeling gene regulation. We discuss four important models: gene networks, transcriptional regulatory systems, Boolean networks, and dynamical Bayesian networks. We review state-of-the-art functional genomics techniques, such as gene expression profiling, cisregulatory element identification, TF target gene identification, and gene silencing by RNA interference, which can be used to extract information about gene regulation. We can employ this information, in conjunction with appropriately designed reverse engineering algorithms, to construct a computational model of gene regulation that sufficiently predicts experimental observations. In the last part of this review, we focus on the problem of reverse engineering transcriptional regulatory networks by gene perturbations. We mathematically formulate this problem and discuss the role of experimental resolution in our ability to reconstruct accurate models of gene regulation. We conclude, by discussing a promising approach for inferring a transcriptional regulatory system from microarray data obtained by gene perturbations.
Export Options
About this article
Cite this article as:
Goutsias J. and Lee H. N., Computational and Experimental Approaches for Modeling Gene Regulatory Networks, Current Pharmaceutical Design 2007; 13 (14) . https://dx.doi.org/10.2174/138161207780765945
DOI https://dx.doi.org/10.2174/138161207780765945 |
Print ISSN 1381-6128 |
Publisher Name Bentham Science Publisher |
Online ISSN 1873-4286 |
Call for Papers in Thematic Issues
"Tuberculosis Prevention, Diagnosis and Drug Discovery"
The Nobel Prize-winning discoveries of Mycobacterium tuberculosis and streptomycin have enabled an appropriate diagnosis and an effective treatment of tuberculosis (TB). Since then, many newer diagnosis methods and drugs have been saving millions of lives. Despite advances in the past, TB is still a leading cause of infectious disease mortality ...read more
Current Pharmaceutical challenges in the treatment and diagnosis of neurological dysfunctions
Neurological dysfunctions (MND, ALS, MS, PD, AD, HD, ALS, Autism, OCD etc..) present significant challenges in both diagnosis and treatment, often necessitating innovative approaches and therapeutic interventions. This thematic issue aims to explore the current pharmaceutical landscape surrounding neurological disorders, shedding light on the challenges faced by researchers, clinicians, and ...read more
Emerging and re-emerging diseases
Faced with a possible endemic situation of COVID-19, the world has experienced two important phenomena, the emergence of new infectious diseases and/or the resurgence of previously eradicated infectious diseases. Furthermore, the geographic distribution of such diseases has also undergone changes. This context, in turn, may have a strong relationship with ...read more
Melanoma and Non-Melanoma Skin Cancer Treatment: Standard of Care and Recent Advances
In this thematic issue, we aim to provide a standard of care of the diagnosis and treatment of melanoma and non-melanoma skin cancer. The editor will invite authors from different countries who will write review articles of melanoma and non-melanoma skin cancers. The Diagnosis, Staging, Surgical Treatment, Non-Surgical Treatment all ...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
-
Targeting Epigenetic Modifiers in Cancer
Current Medicinal Chemistry Drug Metabolizing Enzymes and Transporters mRNA in Peripheral Blood Mononuclear Cells of Healthy Subjects: Biological Variations and Importance of Preanalytical Steps
Current Drug Metabolism Pharmacological Drug Delivery Strategies for Improved Therapeutic Effects: Recent Advances
Current Pharmaceutical Design Fungal Proteins with Antiproliferative and Anticancer Activities
Protein & Peptide Letters Notch Signalling Pathways and Their Importance in the Treatment of Cancers
Current Drug Targets Essential Polymers Helping Patients with Obesity
Current Applied Polymer Science Activin Receptor-Like Kinase 1: a Novel Anti-angiogenesis Target from TGF-β Family
Mini-Reviews in Medicinal Chemistry The Role of Folate-supplementation in Depression: A Narrative Review
Current Psychopharmacology Cancer Stem Cells: A New Paradigm for Understanding Tumor Growth and Progression and Drug Resistance
Current Medicinal Chemistry Regulation of Mesenchymal Phenotype by MicroRNAs in Cancer
Current Cancer Drug Targets Identification of Key mRNAs, miRNAs, and mRNA-miRNA Network Involved in Papillary Thyroid Carcinoma
Current Bioinformatics Angiopoietin-2 Axis Inhibitors: Current Status and Future Considerations for Cancer Therapy
Current Angiogenesis (Discontinued) Modulation of Angiogenesis for Cancer Prevention: Strategies Based On Antioxidants and Copper Deficiency
Current Pharmaceutical Design α-Methylene-γ-lactones as a Novel Class of Anti-leukemic Agents
Anti-Cancer Agents in Medicinal Chemistry Small Molecule Toxins Targeting Tumor Receptors
Current Pharmaceutical Design Vitamin Bs, One Carbon Metabolism and Prostate Cancer
Mini-Reviews in Medicinal Chemistry Emerging Insight into MAPK Inhibitors and Immunotherapy in Colorectal Cancer
Current Medicinal Chemistry Near-infrared Light Activatable Multimodal Gold Nanostructures Platform: An Emerging Paradigm for Cancer Therapy
Current Cancer Drug Targets The CXCL12/CXCR4 Axis as a Therapeutic Target in Cancer and HIV-1 Infection
Current Medicinal Chemistry Metabolomics as a Tool for Drug Discovery and Personalised Medicine. A Review
Current Topics in Medicinal Chemistry