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
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,
The cluster
file groups
together genes in denser parts of the network.
Breast
Cancer Gene
Expression Network
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:
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.