About probe annotation |
Agilent provides annotation for its gene expression probes using BLAST and/or BLAT to align probes to various database transcripts. For more information on these sequence alignment tools, go to www.ncbi.nih.gov/BLAST/ and www.genomeblat.com. The exact procedure depends on the species.
Each probe is annotated to a primary transcript and secondary transcripts to assist you in probe searches.
After the transcript alignments are established, Agilent uses public domain linkages from the transcript identifiers to derive additional annotations such as title lines, gene names, gene symbols, or Gene Ontology terms. The additional annotations are derived from the primary transcript whenever possible, and from the secondary transcripts if unavailable from the primary.
Agilent computes genomic annotation for each probe by aligning the primary transcripts to the genome using BLAT, aligning the probes to the transcripts, and subsequently computing the probe alignment to the genome. Agilent employs this multi-step process to provide greater robustness when a probe spans a splice site.
The most common reason for probe 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 If a particular RefSeq transcript is withdrawn later, then the probe annotation could switch to a GenBank or Ensembl identifier.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.
You can register for e-mail notification of probe annotation changes for any microarray in your folder. If annotation is updated on any probe used on one of those microarrays, you receive notification. See Subscribe to microarray design updates.
In addition, when annotations are updated, new microarray design files are automatically generated and become available for download.
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.
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