Terms are nodes. Each node in the ontology (NeXO or GO) represents a functional group of genes or a “term”. In GO, terms are labeled with the cellular component, process, or function they represent. In NeXO, terms are labeled based on the best alignment of the data-driven ontology to the GO Cellular Component ontology.
Term relations are edges. Each edge in the ontology (NeXO or GO) represents a parent-child relation between terms. Such relations can have either of two meanings:
Browsing. Browse the NeXO or GO ontology using the mouse. Click-and-drag to pan. Use the mouse wheel (two-finger scroll) to zoom in or out of selected regions of the ontology. Click on an ontology term to select it. When a term is selected, the relations to ancestral terms are highlighted and a term summary view is presented with information about the selected term (see below). Double-click on the page background to reset the current selection and re-zoom the ontology to fit the page.
Searching for terms or genes. Search the NeXO and GO ontologies either by keyword or by gene. Results are displayed below the search box. Click on a search result to select and highlight a gene or term in the displayed ontology. Use the refresh button to clear search results and the search box.
When performing searches please keep in mind the following:
NeXO web app supports term enrichment for yeast genes. Simply enter list of genes of your interest in the text box. Default p-value cutoff is 0.01, and minimum number of genes assigned to the term is 2. Currently, SGD ID, ORF name, and gene symbol are supported as input.