Tutorial 12 Biological networks

Biological networks STRING: Protein-Protein interactions BioGRID: Physical and genetic interactions Cytoscape: Network visualization

STRING Protein-Protein interaction network http://string-db.org/

Protein-Protein association

Filtering network edges by evidence type

Increasing the network

Edges in a protein-protein network can represent different features

How can a network be represented in a text format

GO enrichment in STRING

BioGrid Physical and genetic interactions https://thebiogrid.org/

What are genetic interactions? More about the physical and genetic evidence in BioGRID: https://wiki.thebiogrid.org/doku.php/experimental_systems

Cytoscape Network visualization http://www.cytoscape.org/

http://www.cytoscape.org/

Nodes Weights of edges

Source node Target node Edge Weights You can change column meaning

Network visualization Nodes and edges info

Change network visualization

Edges weights now represent the experimental evidence score

Attributes can be added for nodes as well

The layout can depend on the node attributes

A short reminder Degree: the number of edges that a node has. The node with the highest degree in the graph

A short reminder Closeness: measure how close is a node to all other nodes in the network. The nodes with the highest closeness

A short reminder Betweenness: quantify the number of shortest paths that pass through a node. The node with the highest betweenness

Analyzing the network in Cytoscape

Visualizing node features on the netwrok

Features per node/edge are also available as a table

Features per node/edge are also available as a table

Hope you enjoyed the course!! Thank you! Hope you enjoyed the course!!