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I am trying to figure out how to link Gene Entrez ID with Gene Symbol, for TCGA dataset.

So far, I have found this ftp directory with Gene info updated daily.

But, for Entrez ID 728661, I have found two different mappings:

  • here symbol is RP11-345P4.4;
  • here, and in gene info downloaded from ftp above, symbol is SLC35E2B while RP11-345P4.4 is in the field 'locus tag'.

Since I am a newbie I am bit confused about this thing. And, while I think they can be synonyms, I need to know if there is a best practice to use in this case, and if I need to implement some script on my own to do it automatically.

Thanks

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  • $\begingroup$ To be sure, if I understand you right: You want to have a list with the Gene ID in one column and the corresponding Gene symbol in the next? $\endgroup$ – Chris♦ Feb 20 '14 at 16:56
  • $\begingroup$ It is best to use the Standard Gene Symbol (HGNC) or Refseq IDs. Some Refseq IDs may be of this form NM_xxxx.x (where x is a number). In such cases remove the . and the following number. Sometimes same transcript can have more than one refseq ids- in such cases use the shorter id (not a universal rule though). $\endgroup$ – WYSIWYG Feb 21 '14 at 8:24
  • $\begingroup$ @Chris yes, I want the unique mapping between the two ID, is it possible? $\endgroup$ – gc5 Feb 21 '14 at 12:54
  • $\begingroup$ @WYSIWYG Thanks, I think I am going to use the HGNC symbol. Could you please explain, if you know it, why the two symbols differs? HGNC is the standard for Gene Symbols? Thanks $\endgroup$ – gc5 Feb 21 '14 at 12:54
  • $\begingroup$ Do you have this list with the IDs? If so, you can use Biomart from Ensembl to convert it. $\endgroup$ – Chris♦ Feb 21 '14 at 13:17

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