The default genomic locations of mouse genes from MyGene.info are always based on the current genome assembly of GRCm38 (or mm10). Although mm10 has been released in early 2012, there are still needs today to query gene annotations based on GRCm37 (or mm9), the previous mouse genome assembly, in order to handle some legacy data.
Just like what we did for human genes a while ago, supporting hg19 while upgrading to hg38, we now announce that mm9 is supported by MyGene.info for mouse genes, in addition to default mm10 we already support. Similar to our hg19 support, you can now get genomic locations and exon coordinations based on mm9 for mouse genes. And you can also query genes using mm9-based genomic intervals. Below are a few examples:
- To get the genomic location of a given gene based on mm9:
# http://mygene.info/v2/gene/12566?fields=genomic_pos_mm9
In [1]: mg.getgene(12566, fields='genomic_pos_mm9')
Out[1]:
{'_id': '12566',
'genomic_pos_mm9': {
'chr': '10',
'start': 128134995,
'strand': -1,
'end': 128142107}
}
- To get the exon coordinates based on mm9:
# http://mygene.info/v2/gene/12566?fields=exons_mm9
In [2]: mg.getgene(12566, fields='exons_mm9')
Out[2]:
{'_id': '12566',
'exons_mm9': {'NM_183417': {
'cdsstart': 128136161,
'txstart': 128134994,
'cdsend': 128141883,
'txend': 128142107,
'chr': '10',
'strand': -1,
'exons': [[128134994, 128136266],
[128136527, 128136731],
[128137031, 128137175],
[128138398, 128138500],
[128139468, 128139639],
[128140762, 128140883],
[128140981, 128141059],
[128141767, 128142107]]},
'NM_016756': {
'cdsstart': 128136161,
'txstart': 128134994,
'cdsend': 128141883,
'txend': 128142107,
'chr': '10',
'strand': -1,
'exons': [[128134994, 128136266],
[128136527, 128136731],
[128138398, 128138500],
[128139468, 128139639],
[128140762, 128140883],
[128140981, 128141059],
[128141767, 128142107]]}}
}
- To make genomic interval query based on mm9, you just need to add mm9. prefix:
# http://mygene.info/v2/query?q=mm9.chr12:57795963-57815592&species=mouse
In [3]: mg.query('mm9.chr12:57,795,963-57,815,592', species='mouse')
Out[3]:
{'took': 9,
'hits': [{'_score': 8.126015,
'name': 'paired box 9',
'_id': '18511',
'entrezgene': 18511,
'symbol': 'Pax9',
'taxid': 10090},
{'_score': 8.086747,
'name': 'solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21',
'_id': '217593',
'entrezgene': 217593,
'symbol': 'Slc25a21',
'taxid': 10090}],
'max_score': 8.126015,
'total': 2}
As we mentioned above, mm10 is still the default genome assembly for mouse genes, so all of the following queries will return data based on mm10:
# http://mygene.info/v2/gene/12566?fields=genomic_pos
In [4]: mg.getgene(12566, fields='genomic_pos')
# http://mygene.info/v2/gene/12566?fields=exons
In [5]: mg.getgene(12566, fields='exons')
# http://mygene.info/v2/query?q=chr12:57795963-57815592&species=mouse
In [6]: mg.query('chr12:57,795,963-57,815,592', species='mouse')