Hello,
I am trying to extract gene symbols from UCSC gene IDs I got from some
analysis in R.
Here is the data output I got from a package DESeq in R - just the head
of the table: I just want to extract the gene symbol from the id.
id baseMean baseMeanA baseMeanB foldChange log2FoldChange
pval
22410 653048 1820.968 0.000000 3641.937 Inf Inf
2.183608e-96
22411 653067 1820.968 0.000000 3641.937 Inf Inf
2.183608e-96
22412 653219 1820.968 0.000000 3641.937 Inf Inf
2.183608e-96
22413 653220 1820.968 0.000000 3641.937 Inf Inf
2.183608e-96
22638 9503 1820.968 0.000000 3641.937 Inf Inf
2.183608e-96
22554 8277 1587.346 2.304498 3172.388 1376.60684 10.426901
3.572313e-84
1434 283120 2777.587 118.681666 5436.493 45.80735 5.517507
7.881047e-75
21708 100132399 1687.382 21.892735 3352.871 153.14994 7.258801
6.876206e-74
22485 729422 1682.980 21.892735 3344.067 152.74780 7.255008
9.705880e-74
22487 729431 1682.980 21.892735 3344.067 152.74780 7.255008
9.705880e-74
Where id refers to the USCS ID. I have 256 elements in the table so would
prefer not to do it manually!
Looks like this is a custom UCSC reference so I am unable to use online
conversion tools such as DAVID to convert. I have been able to look up gene
symbols one by one but this is tedious.
I would appreciate it if you would tell me -
1. how to extract the GENE symbols from these IDs in a high throughput
fashion
2. what exactly these identifiers are - do they refer to specific
transcripts? how do I determine that?
Thanks!
Kurinji
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