New Year, New Features — Retired Gene Support

Welcome back to our New Year, New Features Series, where we’re kicking off 2011 with a bounty of new goodies for all BioGPS users. This week we’re announcing support for…

Retired Gene IDs

The annotation about any given gene is constantly updated as our knowledge of the genome expands. We regularly update the underlying gene annotation data behind BioGPS, roughly once per month. At the time of writing, our data is sync’ed with NCBI‘s 2010/11/12 data snapshot and Ensembl release 60. Another sync is in the works now and will be live by the end of January.

While we enjoy up-to-date knowledge about genes, there’s one drawback that can catch researchers unaware. Every time annotation data is updated, a small portion of gene IDs get “retired.” Either they are replaced by another ID (i.e. merged with another record) or discontinued completely. What happens if your valuable candidate gene list contains a retired gene ID? Or you bookmarked a BioGPS gene report page months ago, but you’re afraid the link might not work anymore?

We now support all retired gene IDs, provided that they have a replacement. Plug your candidate list into BioGPS Search and the results will automatically translate to the new IDs. For example, a query for retired id “7129” will return gene PTX3 (gene id: 5806) as the result.

We’ve given gene reports the same treatment. When a gene report URL contains a retired ID, BioGPS now shows the replaced gene, along with an alert to let you know about the change. For example, the report for gene 980 (CDAN2) will display the same content as gene 10483 (SEC23B), since gene “980” was replaced by “10483”.

We hope this alleviates some of the headaches when working with older gene lists. Keep in mind that these new features only work for retired gene IDs that have replacements. Discontinued genes are permanently removed, as they are meant to be.

Stay tuned!

This is feature #3 in our new weekly series: New Year, New Features. There’s so much to tell, we’re giving each goody its own article, so sign up for the email, subscribe to our RSS feed or follow us on Twitter to get the latest. See you next week!


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