Question: Empty gene names from ensembl query using biomart
3
gravatar for kindlychung
4.8 years ago by
kindlychung60
Netherlands
kindlychung60 wrote:

Here is the code:

require(biomaRt)
ensembl = useMart("ensembl", ,dataset="hsapiens_gene_ensembl")
# filters = listFilters(ensembl)
# filters[1:5, ]
# attributes = listAttributes(ensembl)
# ensembl_attr = cbind(attributes$name, attributes$description)
# head(ensembl_attr, 15)
getBM(c("hgnc_symbol", "start_position", "end_position"), filters=c("chromosome_name", "start", "end"), values=list(16, 1100000, 1250000), mart=ensembl)

Result:

   hgnc_symbol start_position end_position
1                     1103280      1105461
2                     1111627      1113399
3        TPSB2        1227272      1230184
4                     1206560      1207124
5                     1223639      1224143
6                     1156976      1157974
7                     1159548      1160176
8      CACNA1H        1153241      1221771
9        TPSG1        1221651      1225257
10      TPSAB1        1240696      1242554
11                    1148224      1148754

 

As you can see, some gene names are missing, why is that?

 

gene • 1.6k views
ADD COMMENTlink modified 4.8 years ago by Denise - Open Targets5.0k • written 4.8 years ago by kindlychung60
3
gravatar for Denise - Open Targets
4.8 years ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets5.0k wrote:

It's because those genes have not got HGNC names. They rather have a clone based name. You may want to include Clone based VEGA gene name and/or Clone based VEGA transcript name in your Attributes.

ADD COMMENTlink written 4.8 years ago by Denise - Open Targets5.0k
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