Inferring transcriptional gene regulation network of starch metabolism in Arabidopsis thaliana leaves using graphical Gaussian model

Table 4 Six candidate TF genes and their ranks based on the global-expression correlations

Starch metabolic gene		TF gene		TF family	Binding Site¹	ATTED Correlation²	TF rank³	Family rank⁴
At4g18240	SS4	At2g02070	AtIDD5	C2H2	Y	0.542	9	1/122
At5g11720	AGLU- like 4	At3g50700	C2H2	C2H2	Y	0.295	87	5/122
At5g64860	DPE 1	At2g39900	WLIM2a	LIM	n.a.	0.715	1	1/13
At1g32900	GBSS	At1g73870	COL7	C2C2-CO-like	n.a.	0.609	4	3/42
At1g32900	GBSS	At2g21320	COL	C2C2-CO-like	n.a.	0.608	5	4/42
At5g24300	SS1	At5g06770	KH-CCCH	C3H	n.a.	0.422	31	3/172

1. Y = potential binding site of a TF was found at the 2,000-base upstream region of target gene by the comparative TF family analysis; n.a. = information of a binding site of that TF is not available in AthaMap http://www.athamap.de/.
2. Pearson correlation calculated from the 58 GeneChip experiments including 1,388 arrays using the weighted Pearson correlation in ATTED database http://atted.jp/.
3. Rank of TF based on the ATTED correlation of 1,849 TF genes in the database.
4. Rank of TF based on the ATTED correlation of TF genes in each specific TF family. The numerator indicates the rank and the denominator indicates the number of genes in a specific TF family.

ISSN: 1752-0509