Rice FOX Database



Trait hierarchical cluster analysis

The trait hierarchical cluster analysis (HCA) tool is a web-based application and facilitates identification of the relationships of mutant traits. In order to enable HCA by mutant trait, all screening results that the RiceFOX database contains were converted from trait vocabularies to numeric values (Conversion table). The numerically-converted trait information can be applied to the HCA by optional distance and clustering methods, screening items, and related genes. Therefore, this clustering tool aids the understanding of relationships among the traits of interest.

The procedure is divided into two main steps. In the first step, in order to retrieve the observation records of the rice FOX Arabidopsis mutants, users select the generation (T1/T2), search condition (and/or), and screening items that are of interest. Next, in order to cluster the retrieved mutant line records in the first step, users choose the clustering method (average, single, complete, ward, mcquitty, median, and centroid) and distance method (manhattan, euclidean, maximum, binary, and minkowski), and then select the screening items that are to be calculated by HCA execution.


Step 1

Collection of the observation records of the rice FOX mutants.
In order to collect the observation records of the rice FOX Arabidopsis mutants, users select the generation (T1/T2), search condition (and/or) and screening items.



Generation
Search
Phenotype
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Adult plant
Growth
fast slow
others
Plant height
tall short
Flowering
early late
Root
Number
many few
Others
Rosette leaf
Shape
large small
long short
wide narrow
epinastic hyponastic
spiral
Color
dark pale
variegated
Number
many few
Others
Cauline leaf
Shape
large small
long short
wide narrow
epinastic hyponastic
spiral
Color
dark pale
variegated
Number
many few
Others
Stem
Shape
thick thin
long internode short internode
spiral zigzag
Color
dark pale
Number
many few
Others
Flower
Shape
large small
pistil
stamen
petal
sepal
Others
Silique
Shape
large small
long short
wide narrow
Others
Seed
Shape
large small
long short
wide narrow
Color
dark pale
Number
many few
Hormones
Others
increase total CK decrease total CK
increase total Auxin decrease total Auxin
increase ABA decrease ABA
increase total GA decrease total GA
Elements
Others
K
Ca
S
P
Fe
Zn
Mn
Mg
Si
Pigments
Others
positive
Photosynthesis
Others
high light stress
chlorophyll fluorescence
UV signal
Others
positive
Metabolite
GC-TOF/MS profile
change
FT-NIR fingerprint
change
SA sensitivity
Others
hypersensitive
Resistance to pathogen
bacteria
resistant
High-salinity tolerance
Others
positive
Thermotolerance
Others
positive
UV stress tolerance
Others
positive