problem with facing strange gene name in TCGA data

Question

[modarzi]

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

Answer 1

[Kevin Blighe]

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

[modarzi]

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

[Kevin Blighe]

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.