Get current gene identifiers for the results of microarray which has obsolete gene IDs (using Illumina IDs, probe sequence etc)

Question

[vaushev]

I have results of a microarray analysis (not the raw data unfortunately), and I see that some gene symbols do not correspond to the current version of nomenclature. Of course I can submit those gene symbols to some tool which looks for synonyms and then choose the approved symbols. But ideally I would like to use more "primary" information: I mean, knowing the version of the chip, I can get Illumina IDs, probe sequences and other information. What would be the best way to use it?

Just as an example: I have in my list such genes as OKL38, FTHL11, FREQ, PIB5PA, CDC2, for those I can get Illumina Transcript_IDs (ILMN_17240, ILMN_16343, ILMN_163950, ILMN_8156, ILMN_24793) as well as Probe_IDs, and what I want to get would be the list from the current version of gene symbols: OSGIN1, FTH1P11, NCS1, INPP5J, CDK1.

Answer 1

[Jean-Karim Heriche]

Map the probe sequences to a current annotated version of the genome. Any inference from sequence-based reagents is subject to change in genome assembly and annotation. Nowadays you could even consider mapping the probes to the genomes of the samples used in the study if available.

[vaushev]

can you recommend what is better to use for mapping Illumina probes?

[Jean-Karim Heriche]

Blastn should be just fine.