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/ webcite.

2. Pearson correlation calculated from the 58 GeneChip experiments including 1,388 arrays using the weighted Pearson correlation in ATTED database http://atted.jp/ webcite.

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.

Ingkasuwan et al.

Ingkasuwan et al. BMC Systems Biology 2012 6:100   doi:10.1186/1752-0509-6-100

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