PMC

(a) A GO Term report, using the term “smoothened signaling pathway” as an example. (b) The GO section of a Gene report. The gene Ubr3 is shown here as an example.

(a) The FlyBase Batch Download interface, using the FlyBase Gene IDs (FBgns) exported from the ACTINS Gene Group as an example. (b) The Batch Download interface for selecting data fields for download (only the top section is shown).

(a) The Gene Ontology (GO) tab of the QuickSearch tool. (b) The Vocabularies tool page, which offers two search options: a search term box (top) and a browsing window to select top-level GO terms (bottom).

(a) The Protein Domains tab of the QuickSearch tool. (b) The “Families and Domains and Molecular Function” section of a Gene report, which includes information on protein domains and Gene Group membership. The gene CASK is shown as an example.

A Venn diagram showing the overlap between genes annotated with the GO term ‘protein kinase activity’ (GO:0004672) or its child terms, the InterPro term ‘Protein kinase domain’ (IPR000719) and the ‘PROTEIN KINASE’ Gene Group. The diagram was generated using Venny 2.1.

(a) The Gene Groups tab of the QuickSearch tool. (b) Gene Groups are available as a browsable list. Groups are displayed as a nested hierarchy, with the top-level groups arranged in alphabetical order. The top section of the list is shown from ACETYLCHOLINE RECEPTORS to AUTOPHAGY-RELATED GENES. (c) A Gene Group report, using the ACTINS Gene Group as an example.

(a) A hit-list of genes. In this example, the hit-list is populated with genes exported from the ION CHANNELS Gene Group. The “Analyze” drop-down menu is shown. (b) A results analysis of individual Biological Process GO terms associated with genes from the ION CHANNELS Gene Group. (Only the top 15 most frequently associated GO terms are shown). (c) A QueryBuilder results page, showing a 2-leg query (top). First query: IDs imported from the ION CHANNELS Gene Group; second query: GO term search for “sensory perception.” A results button, with the number of genes returned from the query, is displayed at the bottom—clicking this generates a new gene hit-list.