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Transcript of CSCE555 Bioinformatics Lecture 18 Network Biology Meeting: MW 4:00PM-5:15PM SWGN2A21 Instructor: Dr....
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CSCE555 BioinformaticsCSCE555 BioinformaticsLecture 18 Network Biology
Meeting: MW 4:00PM-5:15PM SWGN2A21
Instructor: Dr. Jianjun Hu
Course page: http://www.scigen.org/csce555
University of South CarolinaDepartment of Computer Science and Engineering
2008 www.cse.sc.edu.
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OutlineOutline
Biological Networks & DatabasesBackground of graphs and
networksThree types of bio-network
analysis◦Network statistics◦Network based functional annotation◦Bio-network reconstruction/inference
Summary
04/21/23 2
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Why network analysis: Why network analysis: Building models from parts Building models from parts listslists
Systems Biology view
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BIOLOGICAL NETWORKSBIOLOGICAL NETWORKS
Networks are found in biological systems of varying scales:
1. Evolutionary tree of life
2. Ecological networks 3. Expression networks4. Regulatory networks
- genetic control networks of organisms
5. The protein interaction network in cells6. The metabolic network in cells… more biological networks
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Examples of Biological Examples of Biological NetworksNetworks
Metabolic NetworksSignaling NetworksTranscription Regulatory
NetworksProtein-Protein Interaction
Networks
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Signaling & Metabolic Pathway Signaling & Metabolic Pathway NetworkNetworkA Pathway can be defined as a modular
unit of interacting molecules to fulfill a cellular function.
Signaling Pathway Networks◦ In biology a signal or biopotential is an electric
quantity (voltage or current or field strength), caused by chemical reactions of charged ions.
◦ refer to any process by which a cell converts one kind of signal or stimulus into another.
◦ Another use of the term lies in describing the transfer of information between and within cells, as in signal transduction.
Metabolic Pathway Networks◦ a series of chemical reactions occurring within a cell,
catalyzed by enzymes, resulting in either the formation of a metabolic product to be used or stored by the cell, or the initiation of another metabolic pathway
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A Signaling Pathway ExampleA Signaling Pathway Example
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A Metabolic Pathway ExampleA Metabolic Pathway Example
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Regulatory NetworkRegulatory Network
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Expression NetworkExpression Network A network representation of genomic data. Inferred from genomic data, i.e. microarray.
Gene co-expression network. Each node is a gene. Edge: co-expression relationship
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Example of a PPI NetworkExample of a PPI Network Yeast PPI network Nodes – proteins Edges – interactions
The color of a node indicates the phenotypic effect of removing the corresponding protein (red = lethal, green = non-lethal, orange = slow growth, yellow = unknown).
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How do we know that proteins How do we know that proteins interact? (PPI Identification interact? (PPI Identification methods)methods) Data
◦Yeast 2 hybrid assay◦Mass spectrometry◦Correlated m-RNA expression◦Genetic interactions
Analysis
◦Phylogenetic analysis◦Gene neighbors◦Co-evolution◦Gene clusters
Also see: Comparative assessment of large-scale data sets of protein-protein interactions – von Mering
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Protein Interaction Protein Interaction DatabasesDatabases Species-specific
◦ FlyNets - Gene networks in the fruit fly ◦ MIPS - Yeast Genome Database ◦ RegulonDB - A DataBase On Transcriptional Regulation in
E. Coli ◦ SoyBase ◦ PIMdb - Drosophila Protein Interaction Map database
Function-specific◦ Biocatalysis/Biodegradation Database ◦ BRITE - Biomolecular Relations in Information
Transmission and Expression ◦ COPE - Cytokines Online Pathfinder Encyclopaedia ◦ Dynamic Signaling Maps ◦ EMP - The Enzymology Database ◦ FIMM - A Database of Functional Molecular Immunology ◦ CSNDB - Cell Signaling Networks Database
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Protein Interaction Protein Interaction DatabasesDatabases Interaction type-specific
◦ DIP - Database of Interacting Proteins ◦ DPInteract - DNA-protein interactions ◦ Inter-Chain Beta-Sheets (ICBS) - A database of protein-
protein interactions mediated by interchain beta-sheet formation
◦ Interact - A Protein-Protein Interaction database ◦ GeneNet (Gene networks)
General◦ BIND - Biomolecular Interaction Network Database ◦ BindingDB - The Binding Database ◦ MINT - a database of Molecular INTeractions ◦ PATIKA - Pathway Analysis Tool for Integration and
Knowledge Acquisition ◦ PFBP - Protein Function and Biochemical Pathways
Project ◦ PIM (Protein Interaction Map)
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Pathway DatabasesPathway Databases KEGG (Kyoto Encyclopedia of Genes and Genomes)
http://www.genome.ad.jp/kegg/ Institute for Chemical Research, Kyoto University
PathDB http://www.ncgr.org/pathdb/index.html National Center for Genomic Resources
SPAD: Signaling PAthway Database Graduate School of Genetic Resources Technology.
Kyushu University. Cytokine Signaling Pathway DB.
Dept. of Biochemistry. Kumamoto Univ. EcoCyc and MetaCyc
Stanford Research Institute BIND (Biomolecular Interaction Network Database)
UBC, Univ. of Toronto
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KEGGKEGG Pathway Database: Computerize current knowledge
of molecular and cellular biology in terms of the pathway of interacting molecules or genes.
Genes Database: Maintain gene catalogs of all sequenced organisms and link each gene product to a pathway component
Ligand Database: Organize a database of all chemical compounds in living cells and link each compound to a pathway component
Pathway Tools: Develop new bioinformatics technologies for functional genomics, such as pathway comparison, pathway reconstruction, and pathway design
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Network Properties
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Properties of networksProperties of networks Small world effectTransitivity/ ClusteringScale Free EffectMaximum degreeNetwork Resilience and robustnessMixing patterns and assortativityCommunity structureEvolutionary originBetweenness centrality of vertices
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Biological Networks Biological Networks PropertiesProperties Power law degree distribution: Rich get
richerSmall World: A small average path length
◦Mean shortest node-to-node pathRobustness: Resilient and have strong
resistance to failure on random attacks and vulnerable to targeted attacks
Hierarchical Modularity: A large clustering coefficient◦How many of a node’s neighbors are
connected to each other
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Graph TerminologyGraph TerminologyNode Edge
Directed/UndirectedDegree
Shortest Path/Geodesic distanceNeighborhood
SubgraphComplete Graph
CliqueDegree Distribution
Hubs
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GraphsGraphs Graph G=(V,E) is a set of vertices V and edges E
A subgraph G’ of G is induced by some V’ V and E’ E
Graph properties:◦ Connectivity (node degree, paths)◦ Cyclic vs. acyclic◦ Directed vs. undirected
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Network MeasuresNetwork Measures
Degree ki
Degree distribution P(k)
Mean path length
Network Diameter
Clustering Coefficient
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Paths:metabolic, signaling pathways
Cliques:protein complexes
Hubs:regulatory modules
Subgraphs:maximally weighted
Network AnalysisNetwork Analysis
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Sparse Sparse vsvs Dense Graphs Dense GraphsG(V, E) where |V|=n, |E|=m the
number of vertices and edges
Graph is sparse if m~n
Graph is dense if m~n2
Complete graph when m=n2
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Connected ComponentsConnected Components
G(V,E)|V| = 69|E| = 71
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Connected ComponentsConnected Components
G(V,E)|V| = 69|E| = 716
connected components
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PathsPathsA path is a sequence {x1, x2,…, xn} such that (x1,x2), (x2,x3), …, (xn-1,xn) are edges of the graph.
A closed path xn=x1 on a graph is called a graph cycle or circuit.
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Shortest-Path between Shortest-Path between nodesnodes
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Shortest-Path between Shortest-Path between nodesnodes
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Longest Shortest-PathLongest Shortest-Path
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Network Measures: Network Measures: DegreeDegree
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P(k) is probability of each degree k, i.e fraction of nodes having that degree.
For random networks, P(k) is normally distributed.
For real networks the distribution is often a power-law:
P(k) ~ k
Such networks are said to be scale-free
Degree DistributionDegree Distribution
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1
2
2
kk
nkn
C III
k: neighbors of I
nI: edges between
node I’s neighbors
The density of the network surrounding node I, characterized as the number of triangles through I. Related to network modularity
The center node has 8 (grey) neighbors
There are 4 edges between the neighbors
C = 2*4 /(8*(8-1)) = 8/56 = 1/7
Clustering CoefficientClustering Coefficient
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Interesting Properties of Network Types
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Small-world Network Small-world Network Every node can be reached from every
other by a small number of hops or steps
High clustering coefficient and low mean-shortest path length◦ Random graphs don’t necessarily have high
clustering coefficients
Social networks, the Internet, and biological networks all exhibit small-world network characteristics
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Small world effectSmall world effectmost pairs of vertices in the network seem to
be connected by a short path
l is mean geodesic distance dij is the geodesic distance between vertex i and vertex j
l ~ log(N)
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Scale-Free Networks are Scale-Free Networks are RobustRobustComplex systems (cell, internet, social
networks), are resilient to component failure
Network topology plays an important role in this robustness◦ Even if ~80% of nodes fail, the remaining ~20% still
maintain network connectivity
Attack vulnerability if hubs are selectively targeted
In yeast, only ~20% of proteins are lethal when deleted, and are 5 times more likely to have degree k>15 than k<5.
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Hierarchical NetworksHierarchical Networks
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Detecting Hierarchical Detecting Hierarchical OrganizationOrganization
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Other Interesting FeaturesOther Interesting FeaturesCellular networks are assortative, hubs tend
not to interact directly with other hubs.
Hubs tend to be “older” proteins (so far claimed for protein-protein interaction networks only)
Hubs also seem to have more evolutionary pressure—their protein sequences are more conserved than average between species (shown in yeast vs. worm)
Experimentally determined protein complexes tend to contain solely essential or non-essential proteins—further evidence for modularity.
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Network ModelsNetwork Models
Random NetworkScale free NetworkHierarchical Network
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Random Network IRandom Network I
The Erdös–Rényi (ER) model of a random network starts with N nodes and connects each pair of nodes with probability p, which creates a graph with approximately pN(N–1)/2 randomly placed links
The node degrees follow a Poisson distribution
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Random Network IIRandom Network II
Mean shortest path l ~ log N, which indicates that it is characterized by the small-world property. Random graphs have served as idealized models of certain gene networks, ecosystems and the spread of infectious diseases and computer viruses.
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Scale Free Networks IScale Free Networks I
Power-law degree distribution: P(k) ~ k –γ, where γ is the degree exponent. Usually 2-3 The network’s properties are determined by hubsThe network is often generated by a growth process called Barabási–Albert model
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Scale Free Networks IIScale Free Networks IIScale-free networks with degree exponents 2<γ<3, a range that is observed in most biological and non-biological networks like the Internet backbone, the World Wide Web, metabolic reaction network and telephone call graphs.
The mean shortest path length is proportional to log(n)/log(log(n))
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PREFERENTIAL ATTACHMENT on Growth: the probability that a new vertex will be connected to vertex i depends on the connectivity of that vertex:
How Scale-free networks are How Scale-free networks are formed? formed?
( ) ii
jj
kk
k
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Hierarchical Networks IHierarchical Networks I To account for the coexistence of
modularity, local clustering and scale-free topology in many real systems it has to be assumed that clusters combine in an iterative manner, generating a hierarchical network
The hierarchical network model seamlessly integrates a scale-free
topology with an inherent modular structure by generating a network that has a power-law degree distribution with degree exponent γ = 1 + ln4/ln3 = 2.26
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Hierarchical Networks IIHierarchical Networks IIIt has a large system-size independent
average clustering coefficient <C> ~ 0.6. The most important signature of hierarchical modularity is the scaling of the clustering coefficient, which follows C(k) ~ k –1 a straight line of slope –1 on a log–log plot
A hierarchical architecture implies that sparsely connected nodes are part of highly clustered areas, with communication between the different highly clustered neighborhoods being maintained by a few hubsSome examples of hierarchical scale free networks.
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Problems of Network Problems of Network BiologyBiology Network Inference
Micro Array, Protein Chips, other high throughput assay methods
Function prediction
The function of 40-50% of the new proteins is unknown
Understanding biological function is important for: Study of fundamental biological processes Drug design Genetic engineering
Functional module detection Cluster analysis
Topological Analysis Descriptive and Structural Locality Analysis Essential Component Analysis
Dynamics Analysis Signal Flow Analysis Metabolic Flux Analysis Steady State, Response, Fluctuation Analysis
Evolution Analysis Biological Networks are very rich networks with very limited,
noisy, and incomplete information. Discovering underlying principles is very challenging.
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SummarySummaryThe problem: Identify
Differentially expressed genes from Microarray data
How to identify: t-test and Rank product
How to evaluate significance of identified genes
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Reference & Reference & AcknowledgementsAcknowledgements Albert Barabasi et al
◦ Network Biology: understanding the cell’s functional organization
Jing-Dong et al◦ Evidence for dynamically organized
modularity in the yeast protein–protein interaction network
Woochang Hwang