Question: Genbank identifiers vs Entrez Gene ID?
0
gravatar for anp375
3.8 years ago by
anp375150
anp375150 wrote:

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.

entrezgene genbank ccds bioperl • 10k views
ADD COMMENTlink modified 3.8 years ago by Neilfws48k • written 3.8 years ago by anp375150

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

ADD REPLYlink written 3.8 years ago by Neilfws48k
79854
148398
26155
84069
57801
9636
54991
254173
8784

8784

LINC00115
SAMD11
NOC2L
PLEKHN1
HES4
ISG15
C1orf159
TTLL10
TNFRSF18
TNFRSF18
ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by anp375150
4
gravatar for Neilfws
3.8 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

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.

ADD COMMENTlink written 3.8 years ago by Neilfws48k

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

ADD REPLYlink written 3.8 years ago by anp375150

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

You might find this overview document useful.

ADD REPLYlink written 3.8 years ago by Neilfws48k
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