Graph Theory Application to the Study of Functional Brain ...
Graph theory Application
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Transcript of Graph theory Application
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Biological Terminology
• Protein complex• Domain• Molecular Pathway• Homology– Orthology– Paralogy
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Graph TerminologyNode Edge
Directed/UndirectedDegree
Shortest Path/Geodesic distanceNeighborhood
SubgraphComplete Graph
CliqueDegree Distribution
Hubs
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Examples of Biological Networks
– Protein-Protein Interaction Networks– Metabolic Networks– Signaling Networks– Transcription Regulatory Networks We will discuss here only Protein-Protein
Interaction Networks
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Example 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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Why is it useful to study PPI networks?
• Proteins are workhorses of cell• Carry out catalytic reactions, transport, Form
viral caspids• Transmit information from DNA to RNA, traverse
membranes, • Form regulated channel, make possible
synthesis of new proteins• Responsible for degradation of unnecessary
proteins, vehicles of immune response
• A prime way to predict protein function is through identification of binding partners
• If the function of at least one of the components with which the protein interacts is known, that should let us assign its function(s) and the pathway(s)
• Hence, through the intricate network of these interactions we can map cellular pathways, their interconnectivities and their dynamic regulation