Examples

 

We provide two complete examples to illustrate the numerous features of GraphExplore. After loading an example, you can start to query the network and create meaningful graphical displays as we have described in the Tutorial.

 

Yeast Protein Interaction Network

 

·        Description File

·        Network File

·        Cluster File

 (Run this example using Java WebStart)

The yeast ORF/gene description file was derived from SGD (Saccharomyces Genome Database).

 

·        Issel-Tarver, L., Christie, K. R., Dolinski, K., Andrada, R., Balakrishnan, R. et al. (2002). Saccharomyces Genome Database. Methods Enzymol 350: 329–346.

 

The network file was obtained from DIP (Database of Interacting Proteins) as of March 2004.

 

·        Xenarios, I., Salwinski, L., Duan, X. J., Higney, P., Kim, S. M. et al. (2002). DIP, the database of interacting proteins: A research tool for studying cellular networks of protein interactions. Nucleic Acids Res. 30: 303-305.

 

The cluster file groups together genes in denser parts of the network.

 

Breast Cancer Gene Expression Network

 

·        Data File

·        Description File

·        Directed Network File

·        Cluster File

  (Run this example using Java WebStart)

The data is a breast cancer gene expression data with 89 samples and 12,558 genes from the paper:

 

·        Huang, E., Cheng, S.H., Dressman, H., Pittman, J., Tsou, M-H., Horng, C-F., Bild, A., Iversen, E.S., Liao, M., Chen, C-M., West, M., Nevins, J.R. and Huang, A.T. (2003). Gene expression predictors of breast cancer outcomes. Lancet 361: 1590-1596.

 

The description file corresponds with the probes on the Affymetrix HG-U95A array after removing the 67 controls. The cluster file puts together the probes that are associated with the same gene. Both the description file and the cluster file were created by Guang Yao. The directed network file was created using Adrian Dobra's HdBCS software. The software calculates the probability of an undirected symmetric association, the probability of a directed forward association (arrow) and the probability of a directed backward association for each pair of genes. The same software generates the following undirected network:

 

·        Undirected Network File

·        Cluster File

  (Run this example using Java WebStart)

Two genes are connected in this network if there is an undirected symmetric association between them. The cluster file groups together genes in denser parts of the undirected network.