Gene/protein ID converter

This report builder maps/converts gene and protein IDs from one reference source to all others (e.g., Ensembl, RefSeq, HUGO, etc.). It also provides the gene/protein names and IDs in a set of user-provided genomic regions.

Example use case

Given a list of genes, the user wants to obtain the corresponding stable IDs from Enembl or Entrez sources.

To run the report builder, the ID/name type must first be selected in the input_id field (this is a required field).

For mapping/converting only a selected set of input gene/protein IDs or gene/protein IDs from particular genomic regions, the IDs or regions can be provided using either the input_file or input_grid fields.

Inputs include the following: BED file or genomic coordinates, gene symbol, HGNC symbol, Ensembl gene IDs, RefSeq IDs, Entrez IDs, HUGO gene symbols and Uniprot IDs. Note that the input_id field recognizes the first column of a grid unless “BED - custom regions” is selected, in which case the input file must be in BED format (chromosome, region starting position, region end position).

Description of the algorithm

Input IDs or coordinates are mapped with reference data sources including Ensembl, RefSeq, Entrez, HGNC and Uniprot to generate an output which includes the input ID and the corresponding IDs from the reference data files.

Interpreting the output

The output includes the input IDs or coordinates with the corresponding Ensembl or RefSeq gene symbols, Ensembl gene stable IDs, RefSeq IDs, Entrez Gene IDs, HGNC approved gene symbols, gene aliases, and Uniprot IDs.

Column descriptions

Report output columns and descriptions

Group	Column name	Description
Gene	aliases	The aliases of the given gene as defined by Ensembl or RefSeq
	End	The end base pair position of the gene
	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	The gene symbol from Ensembl or RefSeq (if symbols from both sources do not match, they will be separated in different rows)
Other columns	Chrom	The chromosome where the gene (gene symbol) resides
	Coordinate_source	Reference data source: Ensembl or RefSeq
	Ensembl_ID	The Ensembl stable ID for the gene
	entrez_id	The Entrez Gene ID
	HGNC_approved_symbol	The HGNC (HUGO Gene Nomenclature Committee) symbol
	RefSeq_ID	The RefSeq transcript (NM, NR, XM, XR, YP) or genomic (NC, NG) IDs
	Uniprot_ID	The Uniprot protein ID