Clusters

• homologene.H_sapiens.M_musculus.len65.activation_FINAL (n = 355):  Summary of GO annotations  Details

The Ontologizer v. 0.2 displays statistical rank scores for overrepresentation of particular GO terms in the dataset as determined by the hypergeometric distribution based on Castillo-Davis et al. (2003).

The E values shown are displayed both without correction for multiple testing and (in parentheses)corrected for multiple testing by a Bonferroni correction. This conservative correction multiplies the nominal p value by the number of tests performed, i.e. by the number of GO terms for which more than one gene (product) in the population is annotated:

• 91 GO terms for direct annotations
• 100 GO terms for total annotations
• Total number of population genes/proteins: 3174 (of which annotations were found for 1962)
• "**" is shown in the E-value column if no testing was performed because only one gene in the population was annotated to the term.

Note that we do not correct for terms for which there is no annotation in the population (overrepresentation is obviously impossible) or for which only one gene in the population is annotated (statistical testing doesn't really make sense in this case). The number of annotated genes in the study group is not taken into account for multiple-testing corrections.

The Gene Ontology Consortium provides a dynamic controlled vocabulary of biological functions. Associations between genes or gene products and GO terms are available from the Gene Ontology website. Functional annotations are divided into three categories:

• Molecular Function
• Biological Process
• Cellular Component

The terms in GO form a directed acyclic graph (DAG), such that specific terms are children of more general terms.Collaborating databases generate gene association files consisting of links between GO terms and genesor gene products. These annotations are made at the most specific level possible but genes are understood to share annotations from all ancestor terms of the specifically annotated term. The Ontologizer shows "Total Annotations" includes explicit annotations as well as inferred annotations. The explicit (direct) annotations are not shown in this page but can be seen in the XML output of the Ontologizer.

Each GO term represented by a GO_id of the form GO:nnnnnnn, where nnnnnnn is a unique zero-padded integer of seven digits, and a descriptive name. The Gene Ontology documentation offers more details.

• goslim_generic.obo(v. 1.0: from 28:03:2006 16:38)
• association file: gene_association.goa_human

These pages were generated by the Ontologizer.