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Selecting the Gene Database Type



Genes can be identified by a large number of different synonyms and looked up in a number of different databases. In order to provide database lookup of genes GeneLinkerô needs to know what database the imported gene identifiers refer to.

GeneLinkerô recognizes four different types of gene identifiers, corresponding to four different gene databases. These are:

1. Affymetrix identifiers:  Referred to as probe set identifiers in Affymetrix literature. This is the Gene Database type to choose when you are importing data which originated on Affymetrix chips.

Examples: 100_g_at    41848_f_at    AFFX-BioB-3_at

See Affymetrix Identifiers for more information.

2. GenBank identifiers: GenBank accession numbers which refer to the GenBank sequence database maintained by NCBI.

Examples: AF111785    NM_002128    X12597

See GenBank Identifiers for more information.

3. UniGene identifiers: Cluster numbers which refer to the UniGene database maintained by NCBI.

Examples: Hs.172028    Mm.3037    Rn.36437

See UniGene Identifiers for more information.

4. Custom identifiers: If your gene or spot identifiers do not fall into one of the categories above, we recommend you designate them as Custom identifiers. You may be able to instruct GeneLinkerô how to look up Custom identifiers by changing a setting in your User Preferences. See Changing Your User Preferences for more information.


Note: gene identifiers have a length restriction of 25 characters. This means that on import of a dataset or a gene list, identifiers that are longer than 25 characters are truncated.


Related Topics:

How to Import Expression Data

Importing One File Containing All Samples

Importing Multiple Files With One Sample Each

Lookup Gene