Network biology
Encyclopedia
Biological network is any network that applies to biological system
s. A network is any system with sub-units that are linked into a whole, such as species units linked into a whole food web
. Biological networks provide a mathematical analysis
of connections found in ecological
, evolutionary
, and physiological studies, such as neural networks
.
s with nodes
and edges. Amino acids can be represented as a network of atom
s such as carbon
, nitrogen
and oxygen
.
As early as the 1980s, researchers started viewing DNA
or genome
s as the dynamic storage of a language system with precise computable finite states
represented as a finite state machine
(Searls, 1993). Recent complex system
s research has also suggested some far-reaching commonality in the organization of information in problems from biology, computer science
, and physics
, such as the Bose–Einstein condensate
(a special state of matter, Bianconi and A.L. Barabási, 2001).
Bioinformatics truly shifted its focus from individual gene
s, proteins, structures and search algorithm
s to large-scale networks often denoted as -omes such as biome
, interactome
, genome
and proteome
. Now biologists are finding the links between the Internet
and metabolic pathway
s, structural interactions of proteins via a network topology
or scale-free network
.
s (PPIs) are the most intensely analyzed networks in biology. There are over 130 PPI detection methods. Y2H is a commonly used experimental technique for binary interactions. For more complex interactions mass spectrometric techniques and extended graph theory are used.
.
Biological system
In biology, a biological system is a group of organs that work together to perform a certain task. Common systems, such as those present in mammals and other animals, seen in human anatomy, are those such as the circulatory system, the respiratory system, the nervous system, etc.A group of systems...
s. A network is any system with sub-units that are linked into a whole, such as species units linked into a whole food web
Food web
A food web depicts feeding connections in an ecological community. Ecologists can broadly lump all life forms into one of two categories called trophic levels: 1) the autotrophs, and 2) the heterotrophs...
. Biological networks provide a mathematical analysis
Graph theory
In mathematics and computer science, graph theory is the study of graphs, mathematical structures used to model pairwise relations between objects from a certain collection. A "graph" in this context refers to a collection of vertices or 'nodes' and a collection of edges that connect pairs of...
of connections found in ecological
Ecological network
An ecological network is a representation of the biotic interactions in an ecosystem, in which species are connected by pairwise interactions . These interactions can be trophic or symbiotic...
, evolutionary
Phylogenetic network
A phylogenetic network is any graph used to visualize evolutionary relationships between nucleotide sequences, genes, chromosomes, genomes, or species . They are employed when reticulate events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are...
, and physiological studies, such as neural networks
Neural Networks
Neural Networks is the official journal of the three oldest societies dedicated to research in neural networks: International Neural Network Society, European Neural Network Society and Japanese Neural Network Society, published by Elsevier...
.
Network biology from bioinformatics
Researchers can best represent and analyze the essence of biology’s layers as computable networks. For example, a protein can be modelled as a network of amino acidAmino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
s with nodes
Vertex (graph theory)
In graph theory, a vertex or node is the fundamental unit out of which graphs are formed: an undirected graph consists of a set of vertices and a set of edges , while a directed graph consists of a set of vertices and a set of arcs...
and edges. Amino acids can be represented as a network of atom
Atom
The atom is a basic unit of matter that consists of a dense central nucleus surrounded by a cloud of negatively charged electrons. The atomic nucleus contains a mix of positively charged protons and electrically neutral neutrons...
s such as carbon
Carbon
Carbon is the chemical element with symbol C and atomic number 6. As a member of group 14 on the periodic table, it is nonmetallic and tetravalent—making four electrons available to form covalent chemical bonds...
, nitrogen
Nitrogen
Nitrogen is a chemical element that has the symbol N, atomic number of 7 and atomic mass 14.00674 u. Elemental nitrogen is a colorless, odorless, tasteless, and mostly inert diatomic gas at standard conditions, constituting 78.08% by volume of Earth's atmosphere...
and oxygen
Oxygen
Oxygen is the element with atomic number 8 and represented by the symbol O. Its name derives from the Greek roots ὀξύς and -γενής , because at the time of naming, it was mistakenly thought that all acids required oxygen in their composition...
.
As early as the 1980s, researchers started viewing DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
or genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
s as the dynamic storage of a language system with precise computable finite states
State (computer science)
In computer science and automata theory, a state is a unique configuration of information in a program or machine. It is a concept that occasionally extends into some forms of systems programming such as lexers and parsers....
represented as a finite state machine
Finite state machine
A finite-state machine or finite-state automaton , or simply a state machine, is a mathematical model used to design computer programs and digital logic circuits. It is conceived as an abstract machine that can be in one of a finite number of states...
(Searls, 1993). Recent complex system
Complex system
A complex system is a system composed of interconnected parts that as a whole exhibit one or more properties not obvious from the properties of the individual parts....
s research has also suggested some far-reaching commonality in the organization of information in problems from biology, computer science
Computer science
Computer science or computing science is the study of the theoretical foundations of information and computation and of practical techniques for their implementation and application in computer systems...
, and physics
Physics
Physics is a natural science that involves the study of matter and its motion through spacetime, along with related concepts such as energy and force. More broadly, it is the general analysis of nature, conducted in order to understand how the universe behaves.Physics is one of the oldest academic...
, such as the Bose–Einstein condensate
Bose–Einstein condensate
A Bose–Einstein condensate is a state of matter of a dilute gas of weakly interacting bosons confined in an external potential and cooled to temperatures very near absolute zero . Under such conditions, a large fraction of the bosons occupy the lowest quantum state of the external potential, at...
(a special state of matter, Bianconi and A.L. Barabási, 2001).
Bioinformatics truly shifted its focus from individual gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
s, proteins, structures and search algorithm
Search algorithm
In computer science, a search algorithm is an algorithm for finding an item with specified properties among a collection of items. The items may be stored individually as records in a database; or may be elements of a search space defined by a mathematical formula or procedure, such as the roots...
s to large-scale networks often denoted as -omes such as biome
Biome
Biomes are climatically and geographically defined as similar climatic conditions on the Earth, such as communities of plants, animals, and soil organisms, and are often referred to as ecosystems. Some parts of the earth have more or less the same kind of abiotic and biotic factors spread over a...
, interactome
Interactome
Interactome is defined as the whole set of molecular interactions in cells. It is usually displayed as a directed graph. Molecular interactions can occur between molecules belonging to different biochemical families and also within a given family...
, genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
and proteome
Proteome
The proteome is the entire set of proteins expressed by a genome, cell, tissue or organism. More specifically, it is the set of expressed proteins in a given type of cells or an organism at a given time under defined conditions. The term is a portmanteau of proteins and genome.The term has been...
. Now biologists are finding the links between the Internet
Internet
The Internet is a global system of interconnected computer networks that use the standard Internet protocol suite to serve billions of users worldwide...
and metabolic pathway
Metabolic pathway
In biochemistry, metabolic pathways are series of chemical reactions occurring within a cell. In each pathway, a principal chemical is modified by a series of chemical reactions. Enzymes catalyze these reactions, and often require dietary minerals, vitamins, and other cofactors in order to function...
s, structural interactions of proteins via a network topology
Network topology
Network topology is the layout pattern of interconnections of the various elements of a computer or biological network....
or scale-free network
Scale-free network
A scale-free network is a network whose degree distribution follows a power law, at least asymptotically. That is, the fraction P of nodes in the network having k connections to other nodes goes for large values of k as...
.
Protein-protein interactions
Protein-protein interactionProtein-protein interaction
Protein–protein interactions occur when two or more proteins bind together, often to carry out their biological function. Many of the most important molecular processes in the cell such as DNA replication are carried out by large molecular machines that are built from a large number of protein...
s (PPIs) are the most intensely analyzed networks in biology. There are over 130 PPI detection methods. Y2H is a commonly used experimental technique for binary interactions. For more complex interactions mass spectrometric techniques and extended graph theory are used.
DNA-protein interactions
DNA-protein interactions, as in transcription binding, is a research topic to study the binding of proteins to DNA. Recent technology includes Chip-chip, Chip-seq and Clip-seqCLIP-Seq
CLIP-Seq, also called HITS-CLIP, is a method in molecular biology, used for finding which RNA species interact with a particular RNA-binding protein...
.
See also
- List of omics topics in biology
- Applied Statistics
- BiostatisticsBiostatisticsBiostatistics is the application of statistics to a wide range of topics in biology...
- Computational BiologyComputational biologyComputational biology involves the development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems...
- Systems biologySystems biologySystems biology is a term used to describe a number of trends in bioscience research, and a movement which draws on those trends. Proponents describe systems biology as a biology-based inter-disciplinary study field that focuses on complex interactions in biological systems, claiming that it uses...
External links
- Networkbiology.org, NetworkBiology wiki site.
- LindingLab.org, Technical University of Denmark (DTU) studies Network Biology and Cellular Information Processing, and is also organizing the Denmark branch of the annual "Integrative Network Biology and Cancer" symposium series.