From a series of lectures for the 2014 WCMC LC-MS Data Processing and Statistics for Metabolomics short-course (http://metabolomics.ucdavis.edu/courses-and-seminars/courses). Download all the material: http://sourceforge.net/projects/teachingdemos/files/Winter%202014%20LC-MS%20and%20Statistics%20Course/Winter%202014%20LC-MS%20and%20Statistics%20Course.zip/download Licens

1. Biology
Chemistry
Informatics
Biochemical and Structural
Similarity Network Mapping
Network Mapping
Goal: Generate a mapped biochemical product/substrate
and chemical similarity network
Topics:
1. Edge list generation
2. Node attributes generation
3. Network Mapping

2. Biology
Chemistry
Informatics
Biochemical and Structural
Similarity Network Mapping
Network Mapping
Steps
1. Use MetaMapR to generate:
url: https://github.com/dgrapov/MetaMapR
• Biochemical and structural similarity based edge list for all
metabolites with KEGG and PubChem identifiers.
• Network preview
• Node attributes
1. Use previously generated Pumpkin/Tomatillo analysis results to
generate node attribute mappings
2. Visualize and map network using Cytoscape

3. MetaMapR: Edge List
Biology
Chemistry
Informatics
Network Mapping
Download the generated edge list, overview and save as an .xlsx
file (for ease of import).

4. Preview Network
Biology
Chemistry
Network Mapping
Informatics

5. Node Attributes
Biology
Chemistry
Network Mapping
Informatics

6. Biology
Chemistry
Network Mapping
Informatics
Mapping Analysis results to
Node Attributes
Labels:
Shape: Direction of
metabolite
Index
change relative to
matching names
pumpkin
edge list
Color: Direction of change
Border: O/PLS/-DA
ID
for significantly changed
selected feature?
species (t-Test)
Size(a): log of the
magnitude of fold
change
Size(b): O/PLS/-DA
LV 1 loadings

7. Mapping in cytoscape
Biology
Chemistry
Network Mapping
Informatics

8. Biology
Chemistry
Informatics
Biochemical and Spectral Similarity Mapped
Network for: Differences in Pumpkin and
Tomatillo Leaf Primary Metabolites
Network Mapping
Leaf fatty acids are
decreased and phytosterols
increased in tomatillo
compared to pumpkin
Tomatillo displays a general
increases in leaf
carbohydrates with the
exception of raffinose and
trehalose, which are
importantly decreased in
tomatillo compared to
pumpkin
Helps withstand
prolonged
periods of
desiccation
intermediate for
lignin
synthesis, related
to quinic acid which
is an astringent
A trisaccharide, can
not be digested by
humans, but readily
fermented by bacteria

9. Summary
Biology
Chemistry
Network Mapping
Informatics
View all files and mappings used in the network
construction in the:
1. Data folder
• Pumpkin and Tomatillo data for network.csv
2. Network folder
• Biochemical edge list.xlsx
• Biochemical node attributes.xlsx
• Biochemical network.cys (final network)