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Supplemental Information
Supplemental Figure S1. Secondary regulatory network of genes associated with the
flavonoid metabolic pathway. The genes directly associated with the 12 bait candidate
genes (yellow nodes) are named as “1st rank” while “2nd rank” marks those genes that
are linked to the “1st rank”.
Supplemental Figure S2. Schematic summary of GO term enrichment analysis on
newly found genes in the secondary regulatory network associated with the flavonoid
metabolic pathway.
Supplemental Figure S3. Phylogenetic analysis of candidate genes belonging to
UGT1 family genes involved in flavonoid biosynthesis. Molecular phylogenetic tree of
the amino acid sequences of the flavonoid glycosyltransferases was analyzed using
flavonoid UGT1 phylogenic tree presented by Tohge et al., 2015. The amino acid
sequences were aligned using the multiple sequence alignment MEGA 5.1
(http://www.megasoftware.net/). Abbreviation: Fd, flavonoid; If, isoflavone; Fl, flavonol;
An, anthocyanin; Glc, glucose; Rha, rhamnose.
Supplemental Table S7. Summary of Gene Ontology (GO) term analysis of all the 58
genes in the primary regulatory network associated with the flavonoid metabolic
pathway.
GO term
Ontologya
Description
p-valueb
FDRc
GO:0006629
P
lipid metabolic process
0.0000046
0.00014
GO:0055114
P
oxidation-reduction process
0.0000026
0.00014
GO:0008610
P
lipid biosynthetic process
0.00002
0.00041
GO:0008152
P
metabolic process
0.0031
0.048
GO:0003824
F
catalytic activity
0.0000005
0.000025
GO:0016491
F
oxidoreductase activity
0.000019
0.00047
GO:0050662
F
coenzyme binding
0.00024
0.0041
GO:0016758
F
0.00049
0.0061
GO:0048037
F
0.0014
0.014
GO:0016757
F
0.002
0.017
transferase activity, transferring hexosyl
groups
cofactor binding
transferase activity, transferring glycosyl
groups
a)
P represents biological process; F represents molecular function
b)
P-value is the enrichment p-value calculated by goodness of fit test
c)
FDR: false discovery rate; is the correction of the enrichment p-value for multiple test
Supplemental Table S8. Summary of Gene Ontology (GO) term analysis of the newly
found 48 genes in the primary regulatory network associated with the flavonoid
metabolic pathway.
GO term
Ontologya
Description
p-valueb
FDRc
GO:0006629
P
lipid metabolic process
0.0000073
0.00043
GO:0055114
P
oxidation reduction
0.000041
0.0012
lipid biosynthetic
GO:0008610
P
process
0.000084
0.0016
GO:0003824
F
catalytic activity
0.00002
0.00066
GO:0016491
F
oxidoreductase activity
0.00019
0.0032
GO:0050662
F
coenzyme binding
0.0007
0.0078
GO:0048037
F
cofactor binding
0.0031
0.026
a)
P represents biological process; F represents molecular function
b)
P-value is the enrichment p-value calculated by goodness of fit test
c)
FDR: false discovery rate; is the correction of the enrichment p-value for multiple test