The Ontologizer: A Tool for Statistical Analysis and Visualization of High-Throughput Biological Data Using Gene Ontology
Mac OS X users, who experienced problems starting Ontologizer, may want to disable Java7 support for starting Webstart applications until the problem is solved. See http://support.apple.com/kb/HT5559 for instructions. Thanks to Christine Oger for finding this work-arround.
Following analysis with one of the above methods and optionally a multiple-testing correction procedure, the Ontologizer rows of terms together with their p-values or marginal probabilities, annotation counts and other information. Relevance of a term is indicated by color coding according to the sub ontology to which the term belongs, whereby the intensity of the color correlates with the maginitude of relevance.
Users can click on any term in the table to display properties and results related to the term such as its parents and children, its description, and a list of all genes annotated to the term in the study set. This information is presented as a hypertext in the lower panel with links to parent and child terms. The Ontologizer also provides a tightly integrated graphical display of the results using GraphViz.
The following pages present a brief introduction to the Gene Ontology, the standard "term-for-term" approach to statistical analysis, and the the parent child approach.