Genbank identifiers vs Entrez Gene ID?

Question

[anp375]

Hi,

I'm trying to work with a consensus coding sequence file and want to know what the gene ids actually are. Are they Entrezgene ids? Or genbank identifiers? Is there a difference?

Gene2GO seems to work on them. All I know is that Entrez gene ids and NCBI gene ids are the same thing.

Thanks.

[Neilfws]

Well, we'd have to see some examples to suggest what they are...

[anp375]

79854     LINC00115
148398    SAMD11
26155     NOC2L
84069     PLEKHN1
57801     HES4
9636      ISG15
54991     C1orf159
254173    TTLL10
8784      TNFRSF18
8784      TNFRSF18

Answer 1

[Neilfws]

Looks like you have a mix of Entrez Gene IDs and HGNC symbols. For example, 79854 and LINC00115 are the same gene; 79854 links to Entrez Gene, LINC00115 links to HGNC.

Entrez is the name of the system used to access NCBI databases. So you could talk about "Entrez Gene", "Entrez Taxonomy" etc. GenBank is a nucleotide database within the Entrez system, Gene is another. Some people use "NCBI" synonymously with Entrez, but best not to; NCBI is the organisation.

[anp375]

Thank you! I'm finding a lot of confusing information. One Ensembl entry called them RefSeq gene ids.

[Neilfws]

Yes, RefSeq is yet another database within Entrez, containing a curated subset of nucleotide sequence.

You might find this overview document useful.