CYTOSCAPE 使用说明

Tutorial:Basic Expression Analysis in

Cytoscape-Human

Slideshow Basic Expression Analysis in Cytoscape (30 min)

Handout Basic_Expression_Analysis_in_Cytoscape-Human.pdf (11 pages)

Tutorial Curators Kristina Hanspers, Alex Pico, Mike Smoot

Contents

[hide]

 1 Loading Network

 2 Loading expression data

 3

Visualizing Expression Data

o

3.1 Set the node color

o 3.2 Set the default node color

o 3.3 Set the node shape

o 3.4 Set the node border

 4 Data analysis features

o 4.1 Filter Nodes

o 4.2 Search for a node

o 4.3 Exploring Nodes

Cytoscape is an open source software platform for integrating, visualizing,

and analyzing measurement data in the context of networks. This tutorial will introduce you to:

 Combining data from two different sources: experimental data in the form of microarrray

expression data and network data in the form of interaction data.

 Visualizing networks using expression data.

 Filtering networks based on expression data.

Loading Network

 Start Cytoscape and load the network File:HumanInteractome subset.sif.  Apply the force-directed layout to organize the layout of the nodes. Select the

"Layout->Cytoscape Layouts->Force-Directed Layout" menu.

 The network should now look similar to this:

Loading expression data

 Download

File:Pellegrini et al Data.txt.zip expression data and unzip it.



Using your favorite text editor, open the file Pellegrini_et_al_Data.txt. The first few lines of the

file are as follows:

Gene Symbol

Entrez id

Probeset

CREB kd

control p value fold change Sign CREB binding

A2M 2 217757_at 42.24 57.45

0.4 1.5 yes

A2ML1 144568 1553505_at 67.95 206.47 0.11 0.58

A2ML1 144568 1564307_a_at 160.05 183.44 0.81 0.95

You should note the following information about the file: 1. The first line consists of labels.

2. All columns are separated by a single tab character.

3. The first column contains node names, and must match the names of the nodes in your

network exactly!

4. The second column contains Entrez Gene IDs.

5. The third column contains Affymetrix probe set IDs. This column is optional, and the data is

not currently used by Cytoscape, but this column may be useful for analysis in other

microarray analysis tools.

6. The remaining columns contain experimental data; average expression for experimental

and control groups, p value and fold change for the comparison, and data on whether or

not the gene binds CREB. See the manuscript for details on the data generation.

NOTE: The expression data used in this example has been pre-processed to work with the

interaction network used. The data is a composite of data files from Pellegrini et al, BMC Cancer,

2008.

 Under the File menu, select Import → Attribute from Table (Text/MS Excel).

 Click "Node" for the type of attribute to import.

 Select the file Pellegrini_et_al_Data.txt.

 Click the "Text File Import Options" check box.

 Make sure the "Tab" check box in the "Delimiter" section is selected and that no other check

box under "Delimiter" is selected. The preview should indicate that it is importing multiple

columns of data.

 Click the "Transfer first line as attribute names" check box in the "Attribute Names" section. The

preview should now show be using the first row of the input file as column names and the

import window should look like the image below.

 Click the "Import" button to import the attribute data.

Now we will use the Node Attribute Browser to browse through the expression data, as follows.

 Select a node on the Cytoscape canvas by clicking on it.

 In the Node Attribute Browser, click the Select Attributes button , and select the

attributes "fold change" and "p value" by left-clicking on them. Right-click to close the menu.

 Under the Node Attribute Browser, you should see your node listed with their expression

values, as shown.

Visualizing Expression Data Probably the most common use of expression data in Cytoscape is to set the visual attributes of the

nodes in a network according to expression data. This creates a powerful visualization, portraying

functional relation and experimental response at the same time. Here, we will walk through the

steps for doing this.

Set the node color

 Double-Click the Node Color row in the Visual Mapping Browser in the Unused Visual

Properties Section.

 This action will move Node Color to the top of the Visual Mapping Browser.

 Click the "Please select a value!" cell in the Node Color section.

 This will produce a drop-down menu of available attribute names. Select "fold change".

 Click the "Please select a mapping" cell in the Node Color section.