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closeEnsembl ID incompatibility
Posted by Masyh on 27 Jul 2015 at 11:30 GMT
Some of the Ensembl Gene IDs claimed to be Hominoid Specific in this study are too old (NCBI 36 release) and need to be updated because in current Ensembl release, they are either non coding RNA genes or retired IDs. Examples are:
ENSG00000212736 #do not exist in GRCH38
ENSG00000174407 #codes for noncoding RNA in GRCH38
ENSG00000204091 #codes for noncoding RNA in GRCH37 and 38
ENSG00000221891 #annotated as Pseudogene in GRCH38
Adding gene ID update will help better understanding of the paper
RE: Ensembl ID incompatibility
Chuan-Yun-Li replied to Masyh on 28 Jul 2015 at 03:48 GMT
Many thanks for the interests in this study. As we discussed in the paper, the Ensembl accession numbers assigned to de novo genes are typically not stable, due to the difficulties in defining the coding potential, as well as the poor cross-species conservation/relatively low expression levels. It is thus not strange that some genes are annotated as non-coding genes or discarded by the current version of Ensembl. While they do represent bona fide de novo genes on the basis of the evidence as we provided in the paper.
In our recent publication on this topic (http://journals.plos.org/...), we included a supplementary table (Table S1) to provide the exact position coordinates of these de novo genes (GRCh37/hg19). Please let me know if you have further questions.