Database for cell lines, genes and proteins associated with them

Question

[SHN]

Hello All,

Does anyone have a recommendation for a database with the name of cell-lines, disease, genes and proteins associated with them?

Thank you for you're response

[Nitin Narwade]

I am not sure about all the cell lines, but there is a database for cancer cell lines, called MetaMap. It has transcriptomic, proteomics, genomics, metastatic potential and penetrance data for 500 cell lines.

UPDATE: There is The Human Protein Atlas, it has lots of information including cell lines.

Regards,

Nitin N.

Answer 1

[Mitchell.frederick]

The CCLE database from the Broad DepMap portal has RNA, mutations, and copy number on over 1000 annotated cancer cell lines spanning more than 30 cancer types

[SHN]

Thank you for the information. Can I download immunology associated cell-lines from the same database?

Answer 2

[Amos Bairoch]

I am not sure what you mean by "the name of cell-lines, disease, genes and proteins associated with them?" What do you mean by "genes and proteins involved with them"? One interpretation is that you mean the genes involved in a disease for a cell line established from a patient involved in that disease. In that case you can use the Cellosaurus and using the API (https://api.cellosaurus.org/) retrieve the sequence variations reported for a specific disease in the cell lines annotated with that disease.

For example:

https://api.cellosaurus.org/search/cell-line?q=di:Orphanet_586%20sequence-variation:mutation&fields=id,sy,ac,sequence-variation&format=json

Will get you in Json format all the cell lines from patients suffering from cystic fibrosis (Orphanet_586) having at least one sequence variant annotated and it retrieve the cell line name, synonyms, accession and the sequence variations.

There are currently almost 28000 cell lines with annotated sequence variations in the Cellosaurus. What you should know is that for cancer cell lines the sequence variations annotated are a small subset of all somatic mutations found in these cell lines, ie those known to be oncogenic. If you need to access all sequence variations for a big set of cancer cell lines, than DepMap will provide this.