problem with facing strange gene name in TCGA data

Hi,

After Batch corection through TCGA batch effect ewbsite, I downloaded corrected RNA-seq data. when I look at this data, the ID of first few genes are strange. does anybody knows why?

gene

?|100130426
?|100133144
?|100134869
?|10357
?|10431
?|136542
?|155060
?|26823
?|280660
?|317712
?|340602
?|388795
?|390284
?|391343
?|391714
?|404770
?|441362
?|442388
?|553137
?|57714
?|645851
?|652919
?|653553
?|728045
?|728603
?|728788
?|729884
?|8225
?|90288

tcga rna-seq batch-effect

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updated 2.3 years ago by Ram

• written 7.9 years ago by modarzi

1 answer

These are Entrez gene IDs. They are likely labelled that way because, when the TCGA data was being annotated, these genes did not have any assigned name and / or may not have even been validated.

Kevin

• 1 views • link

written 7.9 years ago by Kevin Blighe

Dear Dr. Blighe

Hello,

Thanks for your comment. Now, what should I do with these genes? can I use them in my analysis or have I to delete them? I appreciate if you share your comment with me.

Best Regards,

Moha

• 1 views • link

written 7.9 years ago by modarzi

Most of them likely have had official gene symbols assigned since the TCGA project. You can look up each of them and assign them their new name.

• 1 views • link

written 7.9 years ago by Kevin Blighe