Sentence examples for gene ontology tree from inspiring English sources
First, we classified genes that are regulated at all time points by collecting information from Web-based sources (GOTM, gene ontology tree machine at http://bioinfo.vanderbilt.edu/gotm; SOURCE at http://source.stanford.edu/cgi-bin/source/sourceSearch; Gene and PubMed at http://www.ncbi.nlm.nih.gov/).nih.gov/
The results were visualized as a gene ontology tree in order to show the relationship among the enriched GO categories (Figure 4).
We also mapped each gene in a gene ontology tree.
Color indicates term uniqueness while size represents the log size of the term group in the gene ontology tree.
Briefly, we (i) aggregated the contributions of each GO term based on ancestor terms in the gene ontology tree to give a semantic value for the term; and (ii) we calculated the semantic similarity of each pair of GO terms based on these values (detailed method in (Wang et al., 2007)).
The GO (gene ontology) trees were built using only UniProt annotations that were the best match for a Unitrans (E-value ≤ 1e-40) where at least 60% of the individual ESTs in the Unitrans also matched that protein with an E-Value ≤ 1e-10.
For chromosome mapping analysis, we used the Gene Ontology Tree Machine, WebGestalt web-tool (Vanderbilt University, The Netherlands, http://bioinfo.vanderbilt.edu/gotm/) [35] and the Matlab ® (The Mathworks Inc).
We used the Gene Ontology Tree Machine (GOTM - http://bioinfo.vanderbilt.edu/gotm/) to measure the enrichment in GO categories of the genes located within the CNVs showing population differences in comparison with the rest of genes of the human genome and the subset of genes located within known CNVs.
In the Gene Ontology (GO) tree, enriched Gene Ontology biological processes are represented by connected nodes with an associated statistical significance (P values derived from a hypergeometric hypothesis test in BiNGO).
To determine whether these 10 DISC1 and 14 DISC1 pathway variants identified convergent biological pathways, the gene ontology (GO) tree machine [27] was used to test for over abundance of similar functions (Table S4).
