96 5 Survey of Ontologies in Bioinformatics
web-based tool for rapidly listing genes in GO categories (Dennis, Jr. et al.
2003).
GOTM genereg.ornl.gov/gotm
The GOTree Machine is a web-based platform for interpreting microarray
data or other interesting gene sets using GO (Zhang et al. 2004).Figure 5.2 A GO network graph generated using the NetAffx Gene Ontology Min-
ing Tool.As an example of the use of GO, consider PTD, defined as a delivery oc-
curring before the completion of 37 weeks of gestation. PTD is the major
determinant of infant mortality, yet the molecular mechanisms of this disor-
der remain largely unknown. To better understand gene expression changes
associated with PTD at the transcriptional level, we extracted total RNA
samples using the PAXgene Blood RNA kit from whole-blood samples ob-
tained from black mothers who had PTD (n=8, cases) and ethnicity-matched
mothers with term deliveries (n=6, controls) at the Boston Medical Center.
Gene expression profiling was carried out using the Affymetrix HU133A
GeneChip. Among the 6220 genes that were detected as being expressed, we