Biological networks
Bing Zhang
Department of Biomedical Informatics
Vanderbilt University
bing.zhang@vanderbilt.edu
Protein-protein interaction (PPI)

Definition

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Physical association of two or more
protein molecules
RNA polymerase II, 12 subunits
Examples

Receptor-ligand interactions
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Kinase-substrate interactions
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Transcription factor-co-activator
interactions
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Multiprotein complex, e.g. multimeric
enzymes
Cramer et al. Science 292:1863, 2001
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Significance of protein interaction


3
Most proteins mediate their function through interacting
with other proteins

To form molecular machines

To participate in various regulatory processes
Distortions of protein interactions can cause diseases
BCHM352, Spring 2011
Yeast two-hybrid
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Method
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Pros
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Bait strain: a protein of interest, bait (B), fused
to a DNA-binding domain (DBD)
Prey strains: ORFs fused to a transcriptional
activation domain (AD)
Mate the bait strain to prey strains and plate
diploid cells on selective media (e.g. without
Histidine)
If bait and prey interact in the diploid cell, they
reconstitute a transcription factor, which
activates a reporter gene whose expression
allows the diploid cell to grow on selective
media
Pick colonies, isolate DNA, and sequence to
identify the ORF interacting with the bait
High-throughput
Can detect transient interactions
Cons


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False positives
Non-physiological (done in the yeast nucleus)
Can’t detect multiprotein complexes
Uetz P. Curr Opin Chem Biol. 6:57, 2002
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Tandem affinity purification
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Method
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Pros
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TAP tag: Protein A, Calmodulin binding
domain, TEV protease cleavage site
Bait protein gene is fused with the DNA
sequences encoding TAP tag
Tagged bait is expressed in cells and forms
native complexes
Complexes purified by TAP method
Components of each complex are identified
through gel separation followed by MS/MS
High-throughput
Physiological setting
Can detect large stable protein complexes
Cons
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High false positives
Can’t detect transient interactions
Can’t detect interactions not present under
the given condition
Tagging may disturb complex formation
Binary interaction relationship is not clear
Chepelev et al. Biotechnol & Biotechnol 22:1, 2008
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Large scale protein interaction identification
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
Experimental
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Yeast two-hybrid
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Tandem affinity purification
Computational
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Gene fusion
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Ortholog interaction
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Phylogenetic profiling
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Microarray gene co-expression
Valencia et al. Curr. Opin. Struct. Biol, 12:368, 2002
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Protein interaction data in the public domain
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Database of Interacting Proteins (DIP)
http://dip.doe-mbi.ucla.edu/
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The Molecular INTeraction database (MINT)
http://mint.bio.uniroma2.it/mint/
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The Biomolecular Interaction Network Database (BIND)
http://www.binddb.org/
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The General Repository for Interaction Datasets (BioGRID)
http://www.thebiogrid.org/
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Human Protein Reference Database (HPRD)
http://www.hprd.org
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Online Predicted Human Interaction Database (OPHID)
http://ophid.utoronto.ca
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The Munich Information Center for Protein Sequences (MIPS)
http://mips.gsf.de
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HPRD
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Protein interaction networks
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Saccharomyces cerevisiae
Drosophila melanogaster
Jeong et al. Nature, 411:41, 2001
Giot et al. Science, 302:1727, 2003
Caenorhabditis elegans
Homo sapiens
Li et al. Science, 303:540, 2004
Rual et al. Nature, 437:1173, 2005
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Gene regulatory networks
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Experimental
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Chromatin immunoprecipitation (ChIP)
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ChIP-chip
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ChIP-seq
Computational
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Promoter sequence analysis
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Reverse engineering from microarray gene
expression data
Public databases
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Transfac (http://www.gene-regulation.com)
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MSigDB
(http://www.broadinstitute.org/gsea/msigdb)
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hPDI (http://bioinfo.wilmer.jhu.edu/PDI/ )
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Shen-orr et al. Nat Genet, 31:64, 2002
KEGG metabolic network
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Network visualization tools
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Cytoscape
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http://www.cytoscape.org
Gehlenborg et al. Nature Methods, 7:S56, 2010
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Graph representation of networks
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Graph: a graph is a set of objects called nodes or vertices
connected by links called edges. In mathematics and computer
science, a graph is the basic object of study in graph theory.
node
edge
RNA polymerase II
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Cramer et al. Science 292:1863, 2001
BCHM352, Spring 2011
Undirected graph vs directed graph
Protein interaction network
Nodes: protein
Edges: physical interaction
Undirected
Krogan et al. Nature 440:637, 2006
Lee et al. Science 298:799, 2002
Metabolic network
Transcriptional regulatory network
Nodes: metabolites
Nodes: transcription factors and genes
Edges: enzymes
Edges: transcriptional regulation
Directed
Directed
Substrate->Product
TF->target gene
Ravasz et al. Science 297:1551, 2002
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Fhl1
RPL2B
Degree, path, shortest path
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Degree: the number of edges adjacent to a node. A simple measure
of the node centrality.

Path: a sequence of nodes such that from each of its nodes there is
an edge to the next node in the sequence.

Shortest path: a path between two nodes such that the sum of the
distance of its constituent edges is minimized.
YDL176W
Degree: 3
Fhl1
Out degree: 4
In degree: 0
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Obama vs Lady Gaga: who is more influential?
Twitter following
(out degree)
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Twitter followers
(in degree)
701,301
Obama
7,035,548
144,263
Gaga
8,873,525
0
Eminem
3,509,469
Network properties (I): hubs
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Random network
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Scale-free network
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130 nodes, 215 edges
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130 nodes, 215 edges
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Homogeneous: most nodes
have approximately the
same number of links
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Five red nodes with the
highest number of links
reach 27% of the nodes
Heterogeneous: the majority
of the nodes have one or
two links but a few nodes
have a large number of links

Five red nodes with the
highest degrees reach 60%
of the nodes (hubs)
Albert et al., Nature, 406:378, 2000
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Scale-free biological networks
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Metabolic network
C. elegans
Protein interaction network
H. sapiens
Jeong et al, Nature, 407:651, 2000
Stelzl et al. Cell, 122:957, 2005
BCHM352, Spring 2011
Gene co-expression network
S. cerevisiae
Noort et al, EMBO Reports,5:280, 2004
Network properties (II): small world network
Wichita
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Stanly Milgram’s small world
experiment
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Social network

Average path length between
two person
Boston
Omaha

"If you do not know the target person on a personal 
basis, do not try to contact him directly. Instead,
mail this folder to a personal acquaintance who is
more likely than you to know the target person."
Small world network: a graph
in which most nodes can be
reached from every other by a
small number of steps.
Biological interpretation:
Efficiency in transfer of biological
information
Six degrees of separation
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Network properties (III): motifs

Network motifs: Patterns
that occur in the real
network significantly more
often than in randomized
networks.

Three-node patterns
Milo et al., Science, 298:824, 2002
Feed-forward loop
Feedback loop
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Network properties (IV): modularity
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
Modularity refers to a group of
physically or functionally linked
molecules (nodes) that work
together to achieve a relatively
distinct function.

Examples
Protein interaction modules
Palla et al, Nature, 435:841, 2005

Transcriptional module: a set of coregulated genes sharing a common
function

Protein complex: assembly of
proteins that build up some cellular
machinery, commonly spans a
dense sub-network of proteins in a
protein interaction network

Signaling pathway: a chain of
interacting proteins propagating a
signal in the cell
BCHM352, Spring 2011
Gene co-expression modules
Shi et al, BMC Syst Biol, 4:74, 2010
Network distance vs functional similarity

Proteins that lie closer to one another in a protein interaction
network are more likely to have similar function and involve in
similar biological process.
Sharan et al. Mol Syst Biol, 3:88, 2007
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Network-based disease gene prioritization
Kohler et al. Am J Hum Genet. 82:949, 2008
For a specific disease, candidate genes can be ranked based on their proximity
to known disease genes.
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Summary
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Biological networks


Graph representation of networks

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Graph, node, edge, undirected graph, directed graph, degree, path, shortest path
Network properties
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Hubs and scale-free degree distribution
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Small-world
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Motifs
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Modularity
Network-based applications
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Protein-protein interaction network; Gene regulatory network; Metabolic network
Disease gene prioritization
BCHM352, Spring 2011