Multi-Level Data Integration and Data Mining in Systems Biology

Multi-Level Data Integration and Data Mining in Systems Biology

Roberta Alfieri (CNR - Institute for Biomedical Technologies, Italy and CILEA, Italy) and Luciano Milanesi (CNR - Institute for Biomedical Technologies, Italy)
Copyright: © 2009 |Pages: 21
DOI: 10.4018/978-1-60566-076-9.ch028
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Abstract

This chapter aims to describe data integration and data mining techniques in the context of systems biology studies. It argues that the different methods available in the field of data integration can be very useful in making research in the field of systems biology easier. Moreover data mining is an important task to take into account in this context, therefore in this chapter, some aspects of data mining applied to systems biology specific case studies shall be discussed. The availability of a large number of specific resources, especially for the experimental researchers, is something difficult for users who tried to explore gene, protein, and pathway data for the first time. This chapter finally aims to highlight the complexity in the systems biology data and to provide an overview of the data integration and mining approaches in the context of systems biology using a specific example for the Cell Cycle database and the Cell Cycle models simulation.
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Introduction

In the context of the application of biomedical science to systems biology, the availability of many different database and data resources, and a huge amount of heterogeneous data are continuously accumulating, became a crucial point in the last few years. In the field of the medical sciences, and, more in particular in the systems biology context, it is largely recognized that successful data integration has become essential in order to improve the possibility to better explore the knowledge space in many different biological studies. Experimental researchers and computer scientists can discover through data integration new and interesting relationships that enable them to make better and faster decisions for example about disease targets and drug molecules. Moreover, the collection of related information has been shown to be an essential component in biomedical and systems biology research, particularly in the genomics, proteomics and pathways information area.

The necessity for data integration is widely approved in the bioinformatics and systems biology community since bioinformatics data are currently spread across the internet and throughout organizations in a wide variety of formats. Moreover the achievement of interesting results in most bioinformatics and systems biology-related activities, from functional characterization of genomic and proteomic data to the development of mathematical models of biological processes, requires an integrated view of all relevant data useful to accomplish those tasks. The challenges of data integration may be addressed using a wide variety of approaches. While each approach has advantages and limits, it can be difficult to evaluate which approach suits a particular need best without fully understanding the data integration landscape. The data integration methods aim to facilitate detailed and accurate investigation on specific gene, protein or pathway since high information content should be useful both for data mining and mathematical modelling of the biological process of interest. In this chapter the different data integration approaches and some practical example of data integration are illustrated in the specific field of the cell cycle process. The importance of the cell cycle in the shifting from a healthy to a pathological state in some specific experimental conditions which are illustrated in the context of the need to create an integrated system capable to collect the most important information related to cell cycle genes and proteins, which are drawn from the analysis of the cell cycle information available in literature and the existing pathway databases.

There is another important technique used for the knowledge discovery is the data mining approach. Data mining system has become widely used in the context of biomedical science and systems biology as it makes the prediction of the behaviours and the future trends for a biological system possible, allowing taking knowledge-driven decisions. In its general definition data mining can also be considered as the process of analyzing data from different perspectives and summarizing it into useful information, which can be used to increase the current knowledge about a specific biological process. Technically, data mining is the process of finding correlations or patterns among many fields in large relational databases. An example of data mining application in systems biology in the context of the mathematical modelling of a biological process is illustrated in this chapter.

Moreover the use of bioinformatic tools, data mining and data integration can help researchers to better studying the modelling complexity, by screening of the potential model components in order to find the emergent properties of a biological system, which is one of the main aims of systems biology studies. Finally the main advantage of using the data mining and the data integration approaches in the context of systems biology investigations, are presented.

Key Terms in this Chapter

Cell Cycle: The series of events that take place in a eukaryotic cell leading to its replication. These events can be divided in two broad periods: interphase, during which the cell grows, accumulating nutrients needed for mitosis and duplicating its DNA, and the mitotic or M phase, during which the cell splits itself into two distinct cells, often called daughter cells . The cell cycle is a crucial process for the organisms life, by which a single-celled fertilized egg develops into a mature organism, as well as the process by which hair, skin, blood cells, and some internal organs are renewed.

Data Mining: The process through which large amounts of data are sorted with the aim to extract from them relevant information. This term is increasingly used in the sciences to extract information from the enormous data sets generated by modern experimental and observational methods, especially in the biological context. It can be defined as the nontrivial extraction of previously unknown and potentially useful information from data and databases.

Data Warehouse: The main repository of an organization’s historical data, its corporate memory. It contains the raw material for management’s decision support system. The critical factor leading to the use of a data warehouse is that a data analyst can perform complex queries and analysis, such as data mining, on the information without slowing down the operational systems. The data in the data warehouse is organized so that all the data elements relating to the same real-world event or object are linked together.

Mathematical Model: An abstract model that uses mathematical language to describe the behaviour of a system. Mathematical models are used particularly in the natural sciences and engineering disciplines (such as physics, biology, and electrical engineering) but also in the social sciences (such as economics, sociology and political science). It can be defined as the representation of the essential aspects of an existing system (or a system to be constructed) which presents knowledge of that system in usable form.

Data Integration: The process of combining data existing in different sources and providing the user with a unified view of these data. This process is useful in many situations, in particular in the scientific environment when raise out the necessity of combining research results from different bioinformatics repositories. Data integration appears with increasing frequency as the volume and the need to share existing data explodes.

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Table of Contents
Foreword
Ralf Herwig
Preface
Andriani Daskalaki
Acknowledgment
Andriani Daskalaki
Chapter 1
Peter Ghazal
An increasing number of biological experiments and more recently clinical based studies are being conducted using large-scale genomic, proteomic and... Sample PDF
Pathway Biology Approach to Medicine
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Chapter 2
Peter Wellstead, Sree Sreenath, Kwang-Hyun Cho
In this chapter the authors describe systems and control theory concepts for systems biology and the corresponding implications for medicine. The... Sample PDF
Systems and Control Theory for Medical Systems Biology
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Chapter 3
S. Nikolov
In this chapter we investigate how the inclusion of time delay alters the dynamic properties of (a) delayed protein cross talk model, (b) time delay... Sample PDF
Mathematical Description of Time Delays in Pathways Cross Talk
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Chapter 4
Elisabeth Maschke-Dutz
In this chapter basic mathematical methods for the deterministic kinetic modeling of biochemical systems are described. Mathematical analysis... Sample PDF
Deterministic Modeling in Medicine
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Chapter 5
Andrew Kuznetsov
Biologists have used a reductionist approach to investigate the essence of life. In the last years, scientific disciplines have merged with the aim... Sample PDF
Synthetic Biology as a Proof of Systems Biology
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Chapter 6
Tuan D. Pham
Computational models have been playing a significant role for the computer-based analysis of biological and biomedical data. Given the recent... Sample PDF
Computational Models for the Analysis of Modern Biological Data
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Chapter 7
Vanathi Gopalakrishnan
This chapter provides a perspective on 3 important collaborative areas in systems biology research. These areas represent biological problems of... Sample PDF
Computer Aided Knowledge Discovery in Biomedicine
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Chapter 8
Thomas Meinel
The function of proteins is a main subject of research in systems biology. Inference of function is now, more than ever, required by the upcoming of... Sample PDF
Function and Homology of Proteins Similar in Sequence: Phylogenetic Profiling
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Chapter 9
Nikolaos G. Sgourakis, Pantelis G. Bagos, Stavros J. Hamodrakas
GPCRs comprise a wide and diverse class of eukaryotic transmembrane proteins with well-established pharmacological significance. As a consequence of... Sample PDF
Computational Methods for the Prediction of GPCRs Coupling Selectivity
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Chapter 10
Pantelis G. Bagos, Stavros J. Hamodrakas
ß-barrel outer membrane proteins constitute the second and less well-studied class of transmembrane proteins. They are present exclusively in the... Sample PDF
Bacterial ß-Barrel Outer Membrane Proteins: A Common Structural Theme Implicated in a Wide Variety of Functional Roles
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Chapter 11
L.K. Flack
Clustering methods are used to place items in natural patterns or convenient groups. They can be used to place genes into clusters to have similar... Sample PDF
Clustering Methods for Gene-Expression Data
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Chapter 12
George Sakellaropoulos, Antonis Daskalakis, George Nikiforidis, Christos Argyropoulos
The presentation and interpretation of microarray-based genome-wide gene expression profiles as complex biological entities are considered to be... Sample PDF
Uncovering Fine Structure in Gene Expression Profile by Maximum Entropy Modeling of cDNA Microarray Images and Kernel Density Methods
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Chapter 13
Wasco Wruck
This chapter describes the application of the BeadArrayTM technology for gene expression profiling. It introduces the BeadArrayTM technology, shows... Sample PDF
Gene Expression Profiling with the BeadArrayTM Platform
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Chapter 14
Djork-Arné Clevert, Axel Rasche
Readers shall find a quick introduction with recommendations into the preprocessing of Affymetrix GeneChip® microarrays. In the rapidly growing... Sample PDF
The Affymetrix GeneChip® Microarray Platform
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Chapter 15
Jacek Majewski
Eukaryotic genes have the ability to produce several distinct products from a single genomic locus. Recent developments in microarray technology... Sample PDF
Alternative Isoform Detection Using Exon Arrays
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Chapter 16
Prerak Desai
The use of systems biology to study complex biological questions is gaining ground due to the ever-increasing amount of genetic tools and genome... Sample PDF
Gene Expression in Microbial Systems for Growth and Metabolism
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Chapter 17
Heike Stier
Alternative splicing is an important part of the regular process of gene expression. It controls time and tissue dependent expression of specific... Sample PDF
Alternative Splicing and Disease
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Chapter 18
Axel Kowald
Aging is a complex biological phenomenon that practically affects all multicellular eukaryotes. It is manifested by an ever increasing mortality... Sample PDF
Mathematical Modeling of the Aging Process
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Chapter 19
Evgenia Makrantonaki
This chapter introduces an in vitro model as a means of studying human hormonal aging. For this purpose, human sebaceous gland cells were maintained... Sample PDF
The Sebaceous Gland: A Model of Hormonal Aging
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Chapter 20
R. Seigneuric, N.A.W. van Riel, M.H.W. Starmans, A. van Erk
Complex diseases such as cancer have multiple origins and are therefore difficult to understand and cure. Highly parallel technologies such as DNA... Sample PDF
Systems Biology Applied to Cancer Research
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Chapter 21
Matej Orešic, Antonio Vidal-Puig
In this chapter the authors report on their experience with the analysis and modeling of data obtained from studies of animal models related to... Sample PDF
Systems Biology Strategies in Studies of Energy Homeostasis In Vivo
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Chapter 22
Axel Rasche
We acquired new computational and experimental prospects to seek insight and cure for millions of afflicted persons with an ancient malady. Type 2... Sample PDF
Approaching Type 2 Diabetes Mellitus by Systems Biology
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Chapter 23
Alia Benkahla, Lamia Guizani-Tabbane, Ines Abdeljaoued-Tej, Slimane Ben Miled, Koussay Dellagi
This chapter reports a variety of molecular biology informatics and mathematical methods that model the cell response to pathogens. The authors... Sample PDF
Systems Biology and Infectious Diseases
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Chapter 24
Daniela Albrecht, Reinhard Guthke
This chapter describes a holistic approach to understand the molecular biology and infection process of human-pathogenic fungi. It comprises the... Sample PDF
Systems Biology of Human-Pathogenic Fungi
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Chapter 25
Jessica Ahmed
Secretases are aspartic proteases, which specifically trim important, medically relevant targets such as the amyloid-precursor protein (APP) or the... Sample PDF
Development of Specific Gamma Secretase Inhibitors
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Chapter 26
Paul Wrede
Peptides fulfill many tasks in controlling and regulating cellular functions and are key molecules in systems biology. There is a great demand in... Sample PDF
In Machina Systems for the Rational De Novo Peptide Design
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Chapter 27
Ferda Mavituna, Raul Munoz-Hernandez, Ana Katerine de Carvalho Lima Lobato
This chapter summarizes the fundamentals of metabolic flux balancing as a computational tool of metabolic engineering and systems biology. It also... Sample PDF
Applications of Metabolic Flux Balancing in Medicine
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Chapter 28
Roberta Alfieri, Luciano Milanesi
This chapter aims to describe data integration and data mining techniques in the context of systems biology studies. It argues that the different... Sample PDF
Multi-Level Data Integration and Data Mining in Systems Biology
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Chapter 29
Hendrik Hache
In this chapter, different methods and applications for reverse engineering of gene regulatory networks that have been developed in recent years are... Sample PDF
Methods for Reverse Engineering of Gene Regulatory Networks
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Chapter 30
Alok Mishra
This chapter introduces the techniques that have been used to identify the genetic regulatory modules by integrating data from various sources. Data... Sample PDF
Data Integration for Regulatory Gene Module Discovery
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Chapter 31
Elizabeth Santiago-Cortés
Biological systems are composed of multiple interacting elements; in particular, genetic regulatory networks are formed by genes and their... Sample PDF
Discrete Networks as a Suitable Approach for the Analysis of Genetic Regulation
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Chapter 32
A. Maffezzoli
In this chapter, authors review main methods, approaches, and models for the analysis of neuronal network data. In particular, the analysis concerns... Sample PDF
Investigating the Collective Behavior of Neural Networks: A Review of Signal Processing Approaches
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Chapter 33
Paolo Vicini
This chapter describes the System for Population Kinetics (SPK), a novel Web service for performing population kinetic analysis. Population kinetic... Sample PDF
The System for Population Kinetics: Open Source Software for Population Analysis
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Chapter 34
Julia Adolphs
This chapter introduces the theory of optical spectra and excitation energy transfer of light harvesting complexes in photosynthesis. The light... Sample PDF
Photosynthesis: How Proteins Control Excitation Energy Transfer
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Chapter 35
Michael R. Hamblin
Photodynamic therapy (PDT) is a rapidly advancing treatment for multiple diseases. PDT involves the administration of a nontoxic drug or dye known... Sample PDF
Photodynamic Therapy: A Systems Biology Approach
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Chapter 36
Andriani Daskalaki
Photodynamic Therapy (PDT) involves administration of a photosensitizer (PS) either systemically or locally, followed by illumination of the lesion... Sample PDF
Modeling of Porphyrin Metabolism with PyBioS
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Chapter 37
Alexey R. Brazhe, Nadezda A. Brazhe, Alexey N. Pavlov, Georgy V. Maksimov
This chapter describes the application of interference microscopy and double-wavelet analysis to noninvasive study of cell structure and function.... Sample PDF
Interference Microscopy for Cellular Studies
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Chapter 38
Cathrin Dressler, Olaf Minet, Urszula Zabarylo, Jürgen Beuthan
This chapter deals with the mitochondrias’ stress response to heat, which is the central agent of thermotherapy. Thermotherapies function by... Sample PDF
Fluorescence Imaging of Mitochondrial Long-Term Depolarization in Cancer Cells Exposed to Heat-Stress
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Chapter 39
Athina Theodosiou, Charalampos Moschopoulos, Marc Baumann, Sophia Kossida
In previous years, scientists have begun understanding the significance of proteins and protein interactions. The direct connection of those with... Sample PDF
Protein Interactions and Diseases
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Chapter 40
Bernard de Bono
From a genetic perspective, disease can be interpreted in terms of a variation in molecular sequence or expression (dose) that impairs normal... Sample PDF
The Breadth and Depth of BioMedical Molecular Networks: The Reactome Perspective
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Chapter 41
Jorge Numata
Thermodynamics is one of the best established notions in science. Some recent work in biomolecular modeling has sacrificed its rigor in favor of... Sample PDF
Entropy and Thermodynamics in Biomolecular Simulation
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Chapter 42
Isabel Reinecke, Peter Deuflhard
In this chapter some model development concepts can be used for the mathematical modeling in physiology as well as a graph theoretical approach for... Sample PDF
Model Development and Decomposition in Physiology
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Chapter 43
Mohamed Derouich
Throughout the world, seasonal outbreaks of influenza affect millions of people, killing about 500,000 individuals every year. Human influenza... Sample PDF
A Pandemic Avian Influenza Mathematical Model
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Chapter 44
Mohamed Derouich
Dengue fever is a re-emergent disease affecting more than 100 countries. Its incidence rate has increased fourfold since 1970 with nearly half the... Sample PDF
Dengue Fever: A Mathematical Model with Immunization Program
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Chapter 45
Ross Foley
The field of histopathology has encountered a key transition point with the progressive move towards use of digital slides and automated image... Sample PDF
Automated Image Analysis Approaches in Histopathology
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About the Contributors