5.1 Bio-Ontologies 95
and the second is a compact, dynamically interactive directed acyclic graph.
Genes displayed in GoMiner are linked to major public bioinformatics re-
sources.
NetAffx GO Mining Tool
http://www.affymetrix.com/analysis/index.affx
This tool permits web-based, interactive traversal of the GO graph in the
context of microarray data (Cheng et al. 2004). It accepts a list of Affymetrix
probe sets and renders a GO graph as a heat map colored according to signif-
icance measurements. The rendered graph is interactive, with nodes linked
to public websites and to lists of the relevant probe sets. The GO Mining
Tool provides visualization combining biological annotation with expression
data, encompassing thousands of genes in one interactive view. An example
of using the NetAffx GO Mining Tool in a preterm delivery (PTD) microarray
study is shown in figure 5.2. In this figure, it can be seen that the root GO
term (level-1 node) “response to external stimulus” has five child GO terms:
“response to extracellular stimulus,” “response to abiotic stimulus,” “taxis,”
“detection of external stimulus,” and “response to biotic stimulus.” Three of
these level-2 nodes — “response to abiotic stimulus,” “detection of external
stimulus,” and “response to biotic stimulus” — have child GO terms (i.e.,
level-3 nodes). Also, a child node can have multiple parent nodes in the GO
graph. For example, the “detection of abiotic stimulus” GO term (a level-3
node) has two parent nodes: “response to abiotic stimulus” and “detection
of external stimulus.”
FatiGO fatigo.bioinfo.cnio.es
This tool extracts GO terms that are significantly over or underrepresented in
sets of genes within the context of a genome-scale experiment (Al-Shahrour
et al. 2004).
GOAL microarrays.unife.it
The GO Automated Lexicon is a web-based application for the automated
identification of functions and processes regulated in microarray and serial
analysis of gene expression experiments based on GO terms (Volinia et al.
2004).
Onto-Tools vortex.cs.wayne.edu/Projects.html
This is a collection of tools for a variety of tasks all of which involve the use
of GO terminology (Draghici et al. 2003),
DAVID david.niaid.nih.gov
The Database for Annotation, Visualization and Integrated Discovery is a