getting gene coordinates

[bio_informatics]

Hi Members,
I have bunch of 350+ gene names. These are cancer causing gene to which drugs are approved.
I want there chromosome name, start, end information.
How do I get that?

Kindly advise.

[bruce01]

Biomart is a good place to do this sort of thing.

From the drop-downs, select "Ensembl Genes <X>", "Homo Sapiens <Y>".

Filters > Gene > ID list, copy/paste you're 350+ genes into the box.

Attributes > Gene, select your attributes of interest.

Good luck!

[bio_informatics]

Thank you for prompt reply.

I followed this, but getting a blank file [ only headers ].
Also, the HTML preview/output consists of headers.

http://useast.ensembl.org/biomart/martview/13abc9d666af86902b19c8a10de17858

Biomart is a good place to do this sort of thing.

From the drop-downs, select "Ensembl Genes <X>", "Homo Sapiens <Y>".

Filters > Gene > ID list, copy/paste you're 350+ genes into the box.

Attributes > Gene, select your attributes of interest.

Good luck!

[GenoMax]

Your gene ID's have to match the filter selection (kind of Gene ID's) you are making in BioMart. What kind of ID's do you have?

[GenoMax]

You can probably find the information at pharmGKB (https://www.pharmgkb.org/downloads/) as well.

[bio_informatics]

I have gene name(s)- CARD11, ABL2, DICER1
I was using these in GENE ID list.

Your gene ID's have to match the filter selection (kind of Gene ID's) you are making in BioMart. What kind of ID's do you have?

[bio_informatics]

This helps a lot.

This is as per version GrCh 37.

However, if I want as per 38. Are below filters(steps) correct (?) :-
UCSC table:
clade-->mammal, genome-->Human; Assembly--> Dec 2013 GrCh38; Group gene and gene predictions; track --> Refseq Genes; Table --> ref genes

This has column --> name2

You can probably find the information at pharmGKB (https://www.pharmgkb.org/downloads/) as well.

[GenoMax]

That looks right.

For BioMart search: You should select "Filters" --> "ID_Limit_list" --> "HGNC symbol" in the drop-down.

[bio_informatics]

Thank you for confirming.
HGNC Symbol path also worked.