LC-N2G
Data Preprocessing
Gene Cluster
Gene Nutrition Visualization
Browse your gene expression input file (.csv, row sample)
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Browse your nutrition input file (.csv, row sample)
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Download demo nutrition data
Download demo gene data
Filter out gene expression (cpm) below:
Filter out gene expression (cpm) above:
Filter out gene expression (cpm) sd below :
Transformation method
cpm
log2 cpm
none
Filter out gene expression (cpm) maxium absolute correlation with nutrition variables below:
Analysis
Paramerters for clustering using gene-gene relationship:
Cluster method:
Cluster by gene expression
Cluster by gene-gene correlation (WGCAN)
Parameters for clustering using gene-nutrition relationship:
Cluster method:
Cluster by gene-nutrition covariance
Cluster by gene-nutrition correlation
Other Parameters for clustering
Mix coefficient for two kind of cluster method (0 for gene-gene relationship,1 for gene-nutrition relationship)
Scaling method for distance matrix:
No scaling
Linear transformation scaling
Exponential transformation scaling
Tree cutting method:
Dynamic tree cut
By threshold
Desired number of groups
Threshold of correlation for network visualization for clustering result:
Analysis
Dendro
Table
Summary
Parameters for z-axis
z-axis chosen by:
Cluster
Gene name
z-axis (gene):
zscore for z-axis:
Parameters for minimum local consistency nutrition variables selection
Nutrition variables considered
P in diet
C in diet
F in diet
Cellulose in diet
Dry weight food eaten
Cellulose intake
P eaten
C eaten
F eaten
Energy intake
SFA
PC1
PC2
PC3
PC4
Analysis
Parameters for 2D visualization of Nutrigenetics
zscore for xy-axis:
Analysis