working with mgMap - PeltzLab-Stanford/mMap GitHub Wiki

Move input file to the mgmap folder and run the following command:

For input file with genomics coordinates of mutations

• python3 mgmap.py -nc inputfile

For input file with protein level residue alterations

• python3 mgmap.py -g inputfile

Expected output should contain the following files:

1 – file with (i) proteins or gene names (depending on the input file) with (ii) mutations of interest, (iii) functional or regulatory regions where these mutations can be mapped, (iv) conservation of each mutated residue position see here.

• graph showing the number of mutations per gene/protein and conservation of each mutated positions

• files containing the output for the following analyses:

2 – GO term enrichment test
3 – biological pathways enrichment test example
4 – biological processes enrichment test example
5 – significantly mutated protein functional or genome regulatory regions example
6 – protein network analysis
7 – single cell expression data of proteins/genes with mutations example
8 – PubMed based literature search for gene-disease terms For genes/proteins with mutations, previously known entries for mouse phenotype(s). example

• All the files (text and png) are saved in the output folder with the same name as input file.
• For the better seamless view, we also generate an elegant html page contains all the visualizations.