AMON on Helix

Quick Links

AMON (Annotation of Metabolite Origins via Networks) is an open-source bioinformatics application that can be used to
(1) annotate which compounds in the metabolome could have been produced by bacteria present or the host;
(2) evaluate the pathway enrichment of host verses microbial metabolites, and
(3) to visualize which compounds may have been produced by host versus microbial enzymes in KEGG pathway maps.

References:

M. Shaffer, K. Thurimella, K. Quinn, K. Doenges, X. Zhang, S. Bokatzian, N. Reisdorph and C. A. Lozupone
AMON: annotation of metabolite origins via networks to integrate microbiome and metabolome data
BMC Bioinformatics 2019, 20: 614. https://doi.org/10.1186/s12859-019-3176-8

Documentation

AMON on GitHub

Important Notes

Module Name: AMON (see the modules page for more information)

Interactive job

This application can only be run on Helix, and not on Biowulf.

[user@biowulf]$ ssh Helix 
[user@helix]$ APPS=/usr/local/apps 
[user@helix]$ export PATH=$APPS/AMON/1.0.0/bin:$PATH 
[user@helix]$ export LD_LIBRARY_PATH=$APPS/AMON/1.0.0/lib:$LD_LIBRARY_PATH 
[user@helix]$ export PYTHONPATH=$APPS/AMON/1.0.0/lib/pythin3.6/site-packages:$PYTHONPATH 
[user@helix]$ export AMON_DATA=$APPS/AMON/1.0.0/sample_data

Copy sample data to the current folder:

[user@helix]$ cp $AMON_DATA/* .

Run the AMON application on the sample data:

[user@helix]$ amon.py -i ko_list.txt -o test

Review the results stored in the output folder test:

[user@helix]$ ls test
AMON_log.txt            gene_set_1_compound_pathway_enrichment.tsv  origin_table.tsv
enrichment_heatmap.png  kegg_mapper.tsv
[user@helix]$  head test/kegg_mapper.tsv
        0
C02631  blue
K13489  blue
C03287  blue
K00926  blue
C20423  blue
K08224  blue
K00800  blue
K00162  blue
K01505  blue
[user@helix]$ head -n 10 test/gene_set_1_compound_pathway_enrichment.tsv
        pathway size    overlap probability     adjusted probability
Purine metabolism       95      70      1.5357411062115152e-24  3.2404137341062968e-22
Methane metabolism      86      63      4.696075577134766e-22   4.954359733877178e-20
Aminoacyl-tRNA biosynthesis     52      44      1.0032329802784207e-20  7.05607196129156e-19
Folate biosynthesis     57      45      1.1333844794425998e-18  5.978603129059714e-17
Pentose phosphate pathway       35      32      3.680767932496869e-18   1.5532840675136786e-16
Lipopolysaccharide biosynthesis 54      42      4.0149350164351284e-17  1.4119188141130203e-15
Glycolysis / Gluconeogenesis    31      28      7.816512870575171e-16   2.3561203081305158e-14
Central carbon metabolism in cancer     37      31      4.8353494377765e-15     1.2753234142135519e-13
Phosphotransferase system (PTS) 57      41      1.266083970361715e-14   2.968263530514687e-13

Visualize the output heat map:

[user@helix]$ show_image.py test/enrichment_heatmap.png

End the interactive session:

[user@helix ~]$ exit
[user@biowulf ~]$