Annotation changes

The most common reason for annotation changes is the addition or removal of a sequence from a public database.

For example, if a probe aligns to a RefSeq transcript, then eArray uses that annotation. If a particular RefSeq transcript is withdrawn later, then the probe annotation could switch to a GenBank or Ensembl identifier.

Changes to the primary transcript annotation often cause several additional annotations to change, as they are derived by linkage to the primary transcript annotation. In addition, probe annotations can change when public databases change assignments of gene names, gene symbols, GO terms, and the like.

Agilent updates its probe annotation approximately every 3–4 months. For most application types, the eArray system contains only the most recent annotations.

microRNA annotation changes

Agilent updates microRNA probe annotation when new versions of the Sanger database become available. Several types of changes can occur:

Change in microRNA name – If this type of change occurs, the primary accession for the probe will reflect the name in the latest version of the Sanger database. In the Accessions field, previous names will appear, each appended with the last version of the database in which they appeared. Example: miR-hsa-###_v9.1
Change in microRNA sequence, resulting in new probe sequences – If this type of change occurs, the new probes will be annotated with the microRNA name. The old probes will be annotated with the microRNA name, appended with the last version of the database in which that sequence appeared.
Deletion of a microRNA from the database – The probes associated with the deleted microRNA will be annotated with the old name, appended with the last version of the database in which that microRNA appeared.