mutation_table

[Instructions]

mutation_table : create table of mutations. Given a list of gene symbols, query the selected datasets for all samples containing a mutation in the given genes. Concatenates mutations in the same gene.

HUGO : list gene symbols separated by spaces. (required) eg. KRAS TP53 CDKN2A
MUTATION : source of mutations to query. (required) (default ALL)
For cell lines, use ALL to list mutations from CCLE, SANGER, and COSMIC.
Cell Lines : restrict results to the given samples. eg. KASUMI2

Cell Type : add columns for tumor type and tissue type. (optional) (default unchecked)

Notation:

* = STOP mutation
- = fusion product, ie. BCR-ABL = fusion of BCR and ABL genes. Note that the order of genes does not necessarily match the true order of the actual fusion product. Also, often times the fusion will appear twice (eg BCR-ABL and ABL-BCR) which may distort mutation frequencies if you just count number of mutations instead of summarizing by sample. Also fusion information is incomplete and often entered from literature or specific studies on only a few genes or suspected samples.