Annotating Rat Celera Identifers

Question

[Duff]

I've been tasked with re-analysing some AB rat whole genome array data from a study done some years ago. The probes on the array are based on Celera Rat transcripts (example id - rCG62155).

Does anybody have a good suggestion for annotating these to genes for downstream (eg GO etc) analysis? A few of the transcripts map to proteins (and from these to genes) via the Entrez protein database but many seem to lack annotation (or perhaps are not annotated at all).

I've got hold of the array metadata and even on this most of the probes don't seem to have any annotation.

Any advice would be gratefully received.

Thanks

duff

Answer 1

[Andrew Su]

If you've got the probe sequences, I would say you should start with a sequence-level alignment to either the current rat genome assembly or to the current rat transcriptome. Many of the genes that were identified from Celera are now obsolete (bad predictions, pseudogenes, etc.), so it doesn't make sense to try to map on the level of gene/transcript/protein identifiers.

The alignments will tell you, but I would guess that the probes that lack annotation even in the original metadata files will still not have meaningful annotations relative to the current assemblies. At least this is my experience from reannotating custom-designed Affy chips based on Celera predictions for human and mouse...

good luck...

[Duff]

Thanks Andrew.

I thought that might be the answer.