Question

Conversion of Probe ID to Gene Symbol/Name

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Prateek • 0

@b13bb491

Last seen 23 months ago

India

Series GSE138260
Agilent-034879 ADchip_1.0 033934 (Probe name version)

In the above GEO Series, I have extracted top genes for differential expression analysis. Some of the IDs are as follows:

ACUST_8984_PI426217866, ACUST_4639_PI426333075, ACUST_4167_PI426418842

Is there any Bioconductor package to convert these probe IDs to gene names or symbols? DAVID and g:Profiler gave no results.

AgilentChip • 1.5k views

ADD COMMENT • link 2.1 years ago Prateek • 0

score 1 · Answer 1 · 2022-03-27

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Gordon Smyth 50k

@gordon-smyth

Last seen 7 hours ago

WEHI, Melbourne, Australia

The authors of GSE138260 provided a probe ID to gene mapping: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL27556

ADD COMMENT • link 2.1 years ago Gordon Smyth 50k

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Thanks for your reply

This link provides me a table which contains many probe IDs most of which do not have GENE SYMBOL or NAME since I guess these are custom probes (ACUST). So I think in order to get gene name of custrom ACUST probes I have to individually BLAST the sequences of each ACUST genes to know the highest query cover match.

ADD REPLY • link 2.1 years ago Prateek • 0