Question: Gene symbol for original TCGA data ...help!
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gravatar for elizabethR
7 months ago by
elizabethR40
elizabethR40 wrote:

Hi all

I have been on maternity leave for a year prior to which I was analysing TCGA RNASeq cancer data, which I downloaded, collated and analysed. I have been trying to run some new analyses now IM back at work but the gene symbol names have changed that Im looking at! I tried to run GSEA in WebGestalt and found a lot that couldnt be mapped and I assume this is because some gene symbols have changed. Now I am in a conundrum. I cant merely access a file of different gene ID types because these contain the new gene symbol IDs so I cannot programme it to look them up.

Has any one had this problem? And if so how did you overcome it? I was thinking Id need an archive gene ID conversion file so I could change the gene ID from gene symbol to something like ensembl and run that instead in my GSEA. Id like to avoid redownloading and reprocessing the data if possible!

Many thanks in advance

genesymbol tcga • 462 views
ADD COMMENTlink modified 7 months ago • written 7 months ago by elizabethR40

Can you post examples of what you are referring to? TCGA data moved to the new portal while you were gone and perhaps that may have something to do with this.

ADD REPLYlink written 7 months ago by genomax46k

Yes, FAM38A is now Piezo1 for instance. When I ran the data through WebGestalt it couldnt map 1338 of the genes and eyeballing them it looks like their gene symbols have changed.

ADD REPLYlink written 7 months ago by elizabethR40
2
gravatar for genomax
7 months ago by
genomax46k
United States
genomax46k wrote:

I think your best bet is to use the multi-symbol gene name checker tool provided by HGNC. That should help map all old gene names.

ADD COMMENTlink written 7 months ago by genomax46k
0
gravatar for elizabethR
7 months ago by
elizabethR40
elizabethR40 wrote:

Thank you that's incredibly helpful!

ADD COMMENTlink written 7 months ago by elizabethR40
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