Gene ontology to genes¶

The Gene ontology to genes report builder generates a list of genes associated with the selected Gene Ontology (GO) code(s). The list of genes can be restricted to those overlapping with all the GO codes selected or those found in any one of the selected GO codes.

Example use case¶

The user wishes to generate a list of candidate genes related to pathways involving riboflavin. In the pop-up window, the user types “riboflavin” into the go_code field to filter a drop-down list of GO codes, and selects all of the GO codes that include “riboflavin” in the description.

Description of the algorithm¶

This query maps the Gene Ontology (GO) IDs selected and their associated gene symbols to the Ensembl reference set of gene symbols. The resulting grid consists of only gene symbols related to GO IDs that match the user’s input GO IDs. For matching gene symbols, the GO and OMIM annotations are reported in the output table.

Interpreting the output¶

The output is a GOR report listing matching GO IDs and their gene symbols annotated with the GO and OMIM annotations.

Column descriptions¶

Report output columns and descriptions¶
Group	Column	Description
gene	aliases	The aliases of the given gene as defined by Ensembl
	end	The end base pair position of the gene
	paralog_stable_ids
	Paralogs	The paralogs of the given gene as defined by Ensembl
	stable_id
	start	The start base pair position of the gene (zero based, i.e., the position of the base pair before the first base pair in the gene)
	Symbol	Based on HGNC when it exists, otherwise it is the Ensembl internal alias
GO	Descriptions	Gene Ontology category descriptions
	Ids	Gene Ontology identifier
	matching_IDs	The corresponding gene ontology ID
	Ontologies	Which of the three domains of molecular biology it belongs to: biological_process, cellular_component, or molecular_function
HGNC	approved_name
	approved_symbol
	ID
OMIM	Descriptions	OMIM disease descriptions for the gene
	ids	The OMIM ID of the gene
Other columns	Accession_Numbers
	Chrom
	entrez_id
	Pubmed_IDs
	RefSeq_IDs
	UniProt_ID