Graph Theory application in Bioinformatics

Sultan MehmoodMSCSF14M019

PUCIT

2

Biological Terminology

• Protein complex• Domain• Molecular Pathway• Homology– Orthology– Paralogy

3

Graph TerminologyNode Edge

Directed/UndirectedDegree

Shortest Path/Geodesic distanceNeighborhood

SubgraphComplete Graph

CliqueDegree Distribution

Hubs

4

Examples of Biological Networks

– Protein-Protein Interaction Networks– Metabolic Networks– Signaling Networks– Transcription Regulatory Networks We will discuss here only Protein-Protein

Interaction Networks

5

What is meant by a Protein-Protein Interaction (PPI) Network

6

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).

7

A Human PPI Network

8

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

9

Why is it useful to study structure of PPI networks?

• Common properties of biological networks

• Can help us relate network structure to biological function

• Protein’s relative position in a network

• Correlate conserved functional modules with protein complexes