Tutorial Cytoscape

0. Introduction Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. A lot of plugins are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web (http://www.cytoscape.org).

This tutorial is intended for prospective users who want to quickly learn how to use Cytoscape, preferentially under supervision of Cytoscape users. Before beginning this tutorial, please prepare your PC and install Cytoscape. Also having Microsoft Excel is recommended.

1. Network and attributes

ID3

Edge ID

Source

Target

Interaction type

ID1 (pp) ID2

ID1

ID2

Physical

ID2 (gl) ID3

ID2

ID3

Genetic

ID1

Network ID2 Basic idea behind Cytoscape is simple. Cytoscape deals with nodes and edges,

which are two main components of a network (or a graph). Each node can have its own attributes such as gene symbol, expression level, etc. Also each edge can

Genetic

Symb:APLP1 Exp L: 5.1

Symb:APLP2

Symb

haveEixtsproewssnionattributes such as type of interaction, its strength, etc. Cytoscape

Edge Attributes

ID

ID1

APBB1

1.3

ID2

APLP1

5.1

ID3

APLP2

10.9

level

Exp L: 10.9

integrates these information ontoSymabn: AePtBwB1ork. Exp L: 1.3

ID1

Physical

ID3

Network with integrated information

Node Attributes

ID2

2 / 5

Symb:APBB1 Exp L: 1.3

ID1

Physical

ID3

Genetic

APL P2

2. Visualization

VizMapper performs visualization of given network. It maps node and edge attributes to

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