Concepts

Mutation Type

A classification of mutations into single-base-substitution (SBS), doublet-base-substitution (DBS), insertion/deletion (INDEL)

Category Type

A classification of mutations of a specific mutation type into categories. For example, by considering 6 mutation classes of single-base-substitutions C>A, C>G, C>T, T>A, T>C, T>G as well as 5' and 3' flanking bases, we obtain the SBS_96 category type. This maps to the SBS_96_category_name and SBS_96_category_list functions in the mutation-signatures-data categories.py file.

Signature

A distribution over mutation categories from a specific category type. For example Signature 1 from COSMIC (which maps to the SBS_96 category type).

Signature Group

A set of signatures from a source. For example the COSMIC signature group consists of 30 signatures. A signature group can consist of signatures spanning multiple category types.

Cancer Type and Oncotree Code

A cancer type is simply a name. Ideally this name maps to an Oncotree Code found in the Oncotree tool.

Pathways Group

A set of pathways. For example the DNA Damage Repair pathways group might include the Nucleotide Excision Repair pathway and Base Excision Repair pathway (among others).

Pathway

A set of genes. For example the Nucleotide Excision Repair pathway might include the genes ERCC2 and POLD1.