Question: GO annotation missing in org.EcSakai.eg.db?
0
gravatar for Guangchuang Yu
4.2 years ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:

Referring to the issue, https://github.com/GuangchuangYu/clusterProfiler/issues/16, it seems that the annotation package, org.EcSakai.eg.db, has no GO annotation.

 

ADD COMMENTlink modified 4.2 years ago by James W. MacDonald51k • written 4.2 years ago by Guangchuang Yu1.1k
Answer: GO annotation missing in org.EcSakai.eg.db?
0
gravatar for James W. MacDonald
4.2 years ago by
United States
James W. MacDonald51k wrote:

The GO annotations are based on the gene2go file from NCBI, and if you look at the species for which there are mappings between Entrez Gene ID and GO ID, there is only one E. coli strain, the K12, which has a taxon ID of 511145:

511145    |    Escherichia coli MG1655    |        |    synonym    |
511145    |    Escherichia coli str. K-12 substr. MG1655    |        |    scientific name    |
511145    |    Escherichia coli str. K12 substr. MG1655    |        |    equivalent name    |
511145    |    Escherichia coli str. MG1655    |        |    equivalent name    |
511145    |    Escherichia coli strain MG1655    |        |    equivalent name    |

There may be GO terms for the Sakai strain, but they are not in the gene2go table, and hence are not in the org.EcSakai.eg.db package.

ADD COMMENTlink written 4.2 years ago by James W. MacDonald51k

Thanks for your reply. Now it's very clear.

ADD REPLYlink written 4.2 years ago by Guangchuang Yu1.1k
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