I have a list of 80 ensembl ids(gene stable ids) for which BioMart is not generating gene names.

Question

[devina1404]

I have a list of 80 ensembl ids(gene stable ids) for which BioMart is not generating gene names. What could be the reason?It'll be nice if you could help me resolve the issue. And where could I get gene names for all 80 of them in one go.

ENSG00000006075
ENSG00000031544
ENSG00000152487
ENSG00000166157
ENSG00000171129
ENSG00000182851
ENSG00000183657
ENSG00000197262
ENSG00000197704
ENSG00000201678
ENSG00000204828
ENSG00000205020
ENSG00000205021
ENSG00000215394
ENSG00000221051
ENSG00000221319
ENSG00000221356
ENSG00000224201
ENSG00000224930
ENSG00000225946
ENSG00000226505
ENSG00000229489
ENSG00000229645
ENSG00000232224
ENSG00000232694
ENSG00000233147
ENSG00000233438
ENSG00000234453
ENSG00000234531
ENSG00000235878
ENSG00000237647
ENSG00000237726
ENSG00000238890
ENSG00000239776
ENSG00000240820
ENSG00000241781
ENSG00000241847
ENSG00000242463
ENSG00000242924
ENSG00000252306
ENSG00000252703
ENSG00000255124
ENSG00000255651
ENSG00000256391
ENSG00000256515
ENSG00000257061
ENSG00000259785
ENSG00000259888
ENSG00000260396
ENSG00000261788
ENSG00000261827
ENSG00000261925
ENSG00000263391
ENSG00000263422
ENSG00000263569
ENSG00000263820
ENSG00000264604
ENSG00000264756
ENSG00000265130
ENSG00000265676
ENSG00000265710
ENSG00000265741
ENSG00000266089
ENSG00000266701
ENSG00000266911
ENSG00000266949
ENSG00000267093
ENSG00000267167
ENSG00000267230
ENSG00000268275
ENSG00000268470
ENSG00000268852
ENSG00000269908
ENSG00000270145
ENSG00000270235
ENSG00000270246
ENSG00000271835
ENSG00000272349
ENSG00000272448
ENSG00000272828
ENSG00000273019

[Santosh Anand]

Tagging Emily_Ensembl BTW, the rna-seq tag is useless. If you don't put the right tags (Biomart and Ensembl), it might miss the attention of people expert in that domain

[microfuge]

These ids seem to of the older version of ensemble, if I am not wrong. One way would be to use biomart from archive of old ensemble releases (http://www.ensembl.org/info/website/archives/index.html)

Answer 1

[Jean-Karim Heriche]

Actually it looks like these genes were last seen on GRCh37. This demonstrates why one should always keep track of underlying genome and database versions when using any kind of identifier. Note that some genes may not exist anymore in GRCh38 and that older names associated with these genes may also not be current.

[h.mon]

You are right in that these genes are probably defunct (changed id, ceased to exist, etc). However, OP should state genome source, as I could find remnants of old annotations for other organisms than human for some genes. For example, the first (ENSG00000006075) identifier seemed to be found on human and mouse genomes:

http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000006075

http://www.ensembl.org/Mus_musculus/Gene/Summary?g=ENSG00000006075

http://ensemblgenomes.org/id/ENSG00000006075

Is ENSGwhatever a generic identifier for gene, independent of species?

[Emily]

ENSG is a human gene. ENSMUSG is a mouse gene. More info here.

Answer 2

[EagleEye]

You will find information for those in archived version from Ensembl.

Search in BioMart for HG19/GRCh37 lastest annotation (Ensembl 75)

Here is the results for your genes listed.

Answer 3

[xidianbill]

Ensembl will remove some gene id in different version. I think you should choose the right version when initialize the biomart.