How to annotate GEO data that uses GPL13112 Illumina HiSeq 2000 (Mus musculus) platform?

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6.0 years ago

FallingBabyEagle • 0

Hello, I've downloaded some text files from GEO, and I'm hoping to annotate these. Could someone point me in the right direction?

gene count • 3.2k views

ADD COMMENT • link 6.0 years ago by FallingBabyEagle • 0

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What do you mean by "hoping to annotate these"?

ADD REPLY • link 6.0 years ago by GenoMax 141k

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The text files have ensembl gene ID for mouse, and gene counts. I want to know what genes they are, without having to look them up individually. I don't wanna look up 26000 rows.

ADD REPLY • link 6.0 years ago by FallingBabyEagle • 0

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Can you post a few rows to show what the output looks like?

ADD REPLY • link 6.0 years ago by GenoMax 141k

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ENSMUSG00000000001  4827
ENSMUSG00000000003  0
ENSMUSG00000000028  201
ENSMUSG00000000031  20
ENSMUSG00000000037  125
ENSMUSG00000000049  3
ENSMUSG00000000056  947
ENSMUSG00000000058  1167
ENSMUSG00000000078  2009
ENSMUSG00000000085  1497
ENSMUSG00000000088  2535

ADD REPLY • link updated 6.0 years ago by GenoMax 141k • written 6.0 years ago by FallingBabyEagle • 0

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You can use biomaRt (https://bioconductor.org/packages/release/bioc/html/biomaRt.html ) or BioMart via the web interface to convert those ID's to gene symbols.

ADD REPLY • link 6.0 years ago by GenoMax 141k

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@genomax Thank you so much. I'll give that a go. Have a great day, everyday hero.

ADD REPLY • link 6.0 years ago by FallingBabyEagle • 0

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