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Ontologizer, Version 2

Robinson, Peter peter.robinson at
Fri May 13 04:40:39 PDT 2005

Dear GO friends,

I am writing to inform potential users of a new version of the Ontologizer:

The Ontologizer analyzes 1-n lists of genes (e.g., clusters from microarray data) and produces an overview of annotations counts together with a statistical analysis of overrepresentation of terms based on the hypergeometric distribution (Thanks to Cristian Castillo-Davis and GeneMerge for much help on this!). For each cluster, a gene-by-gene list of explicit annotations is shown on a separate page. 

The Ontologizer is a Java 1.5 application. Users need to download 1) the gene_ontology.obo file, 2) the file for the appropriate organism and 3) provide lists of genes (one to a line or as FASTA) and 4) an optional population file (e.g., all genes on a chip). The Ontologizer produces a set of interlinked HTML files with the results of analysis. There are some examples on the homepage for C elegans, M musculus, yeast, and Drosophila.

best regards,
Peter Robinson

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