Skip to content

3 KEGG Custom Modules analyses

Jump to bottom
Matteopaluh edited this page Feb 14, 2023 · 3 revisions

KEMET allows for custom Modules to be added alongside the manually curated ones included in the KEGG MODULES database as listed here.

KEMET Modules files (.kk files at KEMET/KEGG_MODULES/kk_files/) use a specific format, which is generated with few modifications from the original KEGG MODULES entries (.txt files at KEMET/KEGG_MODULES/).
Custom files are to be included with other .kk files in the local KEMET folder, in KEMET/KEGG_MODULES/kk_files/.

Any user can include other modules by generating a file with .kk extension and other formatting specs, listed below. As an example, module M00023 is shown and format choices are commented.

M00023_Tryptophan biosynthesis, chorismate => tryptophan
K01657, K01658, K13503, K13501, K01656, K13497
K00766, K13497
K01817, K24017, K13498, K13501
K01656, K01609, K13498, K13501
K01695, K01696, K06001, K01694
COMPLEXES_LIST
K01657+K01658, K01695+K01696, K01695+K06001

Custom .kk files format

1st line (header indications - appears in the report files):
<Module_ID> (same as file name), an underscore character (_), <longer_module_name> to ease in understanding the report tables.

2nd until end/extra lines:
Each line contains sequential KEGG orthologs alternatives for a single step (see example above), separated by a comma and a space (, ).

Extra lines (in case of more complex reaction relations):

  • Adding a "COMPLEXES_LIST" tag at the end of the file enables multi-genes relations informations to be coded in the file, in the following line (e.g. K01657+K01658 for the first step of the module in the above exemple).

  • Adding an "OPTIONAL_LIST" tag at the end of the file, as in M00544 includes KOs which are not mandatory for a Module step to be considered complete, but KO presence/absence is still indicated in the report files.

  • Adding two or more "/" tags before KO lists indicates different sub-modules, which count towards the completeness in a "cumulative" fashion.
    i.e. if 2 of such submodules are missing 1 KO each, the Module has 2 block missing (see M00935 as a format example).

  • Adding two or more "//" tags before KO lists indicates different sub-modules, which present alternative paths (with a different number of steps) towards module completeness and as such count towards completeness in an "alternative" fashion.
    i.e. if 2 of such submodules are missing 1 KO each, with the first being 8 blocks long and the second 9 blocks long, the Module will ultimately be counted as a 1 block missing with 7/8 steps (see M00026 as a format example).

Clone this wiki locally