Figure 3.

Analysis of Ontology term distribution. The top 20 best discriminating gene ontology terms in each cluster were sorted for over-representation (RED) and under-representation (Green) and compared to the top 10 discriminating TFBSs for each cluster as determined by ANOVA (Figure 2). The top 10 over-represented (Red) and under-represented (Green) TFBSs for each cluster are shown. The transcription factors that recognize the TFBSs were grouped and then analyzed for asymmetric distribution of ontology terms using GoMiner (TF ontology terms, right). Transcription factor genes that are known to bind the over-represented TFBSs (TF Genes, enriched) are shown enclosed in boxes. Transcription factor ontology terms that overlap the gene cluster ontology terms within 2 branches of the ontology clade are shown in bold. Those terms with exact matches in the gene cluster ontologies are indicated with an asterisk. The numbers in parentheses indicate the total number of ontology terms associated with each respective cluster. The numbers in brackets indicated those ontology terms with a significance measurement p-value < 0.05 (Fisher Exact T-test). Representative genes from Clusters one, six and thirteen are shown in supplemental Table 3.

McNutt et al. BMC Bioinformatics 2005 6:259   doi:10.1186/1471-2105-6-259
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