Tools for conversion of probe IDs


Whichever tool you use, remember to take note of the underlying mapping of probes to bioentities (i.e. transcripts/genes/proteins) that is used. While probe sequences don’t change, genome assemblies (e.g. chromosomal sequences) and annotation of bioentities are both subject to change over time. You may find that a certain probe which mapped to gene X six months ago is now mapped to gene Y because gene X has been made obsolete, or its exon-intron structure has changed in light of new supporting evidence.

If you have a small list of probe IDs, you can use the conversion tool in the Ensembl Genome Browser (13). For some common microarray platforms (Affymetrix, Agilent and Illumina), Ensembl regularly maps the probes/probe sets against the latest set of transcript models. To search, simply use individual probe identifiers as search terms in Ensembl (e.g. Agilent probe ID A_14_P109686). Alternatively, different web tools offer probe conversion, such as DAVID (14).

If you have a long list of probe IDs, R/Bioconductor (15) offers a range of annotation packages (16) that can be used to convert probe IDs during the microarray analysis workflow.