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