Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration.
The Ontologizer is a Java application that can be used to perform statistical analysis for overrepresentation of Gene Ontology (GO) terms in sets of genes or proteins derived from an experiment. The Ontologizer implements the standard approach to statistical analysis based on the one-sided Fisher's exact test, the novel parent-child method, as well as topology-based algorithms. A number of multiple-testing correction procedures are provided. The Ontologizer allows users to visualize data as a graph including all significantly overrepresented GO terms and to explore the data by linking GO terms to all genes/proteins annotated to the term and by linking individual terms to child terms.


BACKGROUND
The Ontologizer application is available under the terms of the GNU GPL. It can be started as a WebStart application from the project homepage, where source code is also provided: http://compbio.charite.de/ontologizer.


METHODS
Ontologizer requires a Java SE 5.0 compliant Java runtime engine and GraphViz for the optional graph visualization tool.
Institute of Medical Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. sebastian.bauer@charite.de
Sebastian
S
Bauer
Steffen
S
Grossmann
Martin
M
Vingron
Peter N
PN
Robinson
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D030562:Databases, Protein; D020407:Internet; D008954:Models, Biological; D015233:Models, Statistical; D005810:Multigene Family; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011381:Programming Languages; D011506:Proteins / Q000145:classification* / Q000235:genetics / Q000378:metabolism; D012984:Software; D014584:User-Computer Interface
D011506:Proteins