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 visual attributes. A user can define how each node attribute and edge attribute will be visualized using framework called VizMapper.

Mapper type

Passthrough Mapper

Symb:APLP2

Brief Description

Network attributes are passed directly through to visual attributes. The most common use case is to specify node and/or edge labels. For example, this mapper can label all nodes with their gene symbols.

Discrete network attributes are mapped to discrete visual

Discrete

Exp L: 10.9 Mapper -Natotdreibluabtels:.SFymobr(ePxaassmthproleu,gha)discretemappercanmapgene

- Edge color: functions to node colors so thaAtPBnodes can be colored differently

Physical  Purple B1 depending on its gene function.

Continuous (CDoisncrteitneu)ousnetworkattributesaremappedto(pseudo)

APL

Mapper

continuous visual attributes. For example, a continuous mapper

ID2

- Node color: Depends on expression level (Continuous)

P1

Symb:APLP1 Exp L: 5.1

can map gene expression levels to brightness of color of corresponding node.

Genetic  Red

0 10 VizMapper

3/5

(1) Prepare edge attribute table (1) Prepare node attribute table

Tick appropriate box when importing text file

Tick appropriate box when importing text file

3. Importing network and edge attributes

Edge attributes (which usually represent network) can be prepared as table format. They can be imported to Cytoscape from File --> Import --> Network from Table pull-down menu.

4. Importing node attributes

Node attributes can also be prepared as table format. They can be imported to Cytoscape from File --> Import --> Attribute from Table pull-down menu.

(2) Load the edge attribute table

(2) Load the node attribute table

4/5

5. Visualization by VizMapper

One can use VisMapper to define visual styles of

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