Hello there,
Is there any paper or sites provide information about the expression of wild-type and different variants of GATA3 in ER+ breast cancer cell line? such as MCF-7, ZR-75.1 and T47-D? how can I find the mutations of GATA3 in these three cell lines?
Hello, NCBI GEO is the best. You can also find many array and RNA-seq raw data for analysis on your own platform.
https://www.ncbi.nlm.nih.gov/gds/?term=%22Breast+cancer+cell+lines%22
In addition to the site above you could check the Human Protein Atlas, very useful site in general.
https://www.proteinatlas.org/
The Human Protein Atlas does not provide information on variants while neXtProt does. For GATA3 if you go the sequence view:
https://www.nextprot.org/entry/NX_P23771/sequence
You can see all the variants: SNP and cancer-linked somatic mutations (from COSMIC). However this is quite a lot and you want only those linked to a cell line. So one solution is to export the variants in XML:
https://api.nextprot.org/entry/NX_P23771/variant.xml
And then look for those linked to a cell line (those having a cross-reference to the Cellosaurus)
Now this is not so trivial if you are not used to look/process an XML file so I looked for you and there are some somatic variants linked to cell lines, but none to breast cancer cell lines.
But this will only get you the variants that are simple amino acid modifications, so you need to check if there are also frameshift or other complex variants.
To do that go either through the Cellosaurus or directly to the Cosmic cell line project for the breast cancer cell lines that are part of it. For example for MCF-7:
http://cancer.sanger.ac.uk/cell_lines/sample/overview?id=905946
You can then scroll down (chenge the display of variant to 100 per page instead of 10) in the mutation list.
And bingo you get a mutation for GATA3:
GATA3 ENST00000379328📷Yes p.D336fs*17c.1006_1007insG Previously ReportedHeterozygousVerifiedInsertion - Frameshift10:8069554..8069555
You can than open a page on that mutation:
http://cancer.sanger.ac.uk/cell_lines/mutation/overview?id=41681
You can do that for the other cell lines that you mention.
Best regards
Amos
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