Lab2  Biological network analysis with Cytoscape

1. Install Cytoscape on your computer

http://www.cytoscape.org/

Learn to use Cytoscape according to the manual or tutorial

2. Import the example network: galfiltered.sif 

(To learn the detail of this network, please read the Science paper.)

  Layout the network galfiltered

  Node/edge attribute

Topology parameters using NetworkAnalyzer

Integrate gene expression data

3. Finding and Filtering Nodes and Edges

4. Annotation with GO ontology

5. Find clusters using MCODE plugin

6. How to manage or install other plugins.

Assignment:

1. Show the galfiltered network with node color represented by gene expression level.

2. Find those nodes having closeness>0.3 and expression level>0.5, illustrate a table including ID, annotion, value of these nodes.

3. Import network from Reactome and IntAct database, calculate the topology parameters.

4. Import and visualize Yeast metabolic models (iMM904(from BIGG) and Yeast7.6(from Yeast consensus network), see Lab1). Which enzymes or metabolites are important candidates based on your understanding?

5. Choose plugins in 'Network Inference' and 'Functional modules detection'(each respectively), and use sample session(sampleData/sessions/TCGA or Yeast or....sif) to carry out.

Please send the report to molle_faust@hotmail.com before Apr.21st 23:59. (Label the file name with Lab2_Name_ID)