Table 3

The TF-starch relationships from the starch sub-network
Starch Metabolic Gene (AGI code) Starch Metabolic Gene (Gene Name) pCor / Interaction1 TF (AGI code) TF (Gene Name) TF Family AthaMap2 Rank of TF-starch correlation in ATTED
2-kb upstream Correlation Rank in all genes (total = 22,263 ) Ranks in all TFs (total = 1,849) Rank in specific TF family/No. of TFs in a family
At1g03310 ISA2/DBE1 -0.0756 / n At5g46710 zinc-binding PLATZ NA -0.05 11356 818 2/7
At1g03310 ISA2/DBE1 0.0674 / p At2g34720 CBF-B/NF-YA CCAAT-HAP2 NA 0.03 8424 557 6/10
At1g03310 ISA2/DBE1 0.0733 / p At1g05805 bHLH bHLH N 0.165 4598 241 27/114
At1g32900 GBSS 0.0736 / p At1g73870 COL7 C2C2-CO-like NA 0.609 17 4 3/42
At1g32900 GBSS 0.0686 / p At2g21320 COL C2C2-CO-like NA 0.608 18 5 4/42
At1g76130 a-AMY2 0.0665 / p At2g31070 TCP TCP N 0.174 3347 344 7/20
At1g76130 a-AMY2 0.0758 / p At1g02340 HFR1/BHLH26 bHLH N -0.019 11812 1052 56/114
At1g76130 a-AMY2 -0.1268 / n At5g65310 HB-5 HB N -0.372 21286 1809 87/89
At2g32290 b-AMY6 0.0763 / p At1g22070 TGA3 bZIP Y 0.111 3654 225 4/69
At2g32290 b-AMY6 0.0676 / p At1g50420 SCL3 GRAS NA 0.07 4806 328 10/32
At2g32290 b-AMY6 -0.0707 / n At1g07520 scarecrow GRAS NA -0.125 18495 1527 30/32
At2g32290 b-AMY6 0.0818 / p At2g31070 TCP TCP N 0.204 2008 111 4/20
At2g39930 ISA1 0.0917 / p At5g05090 myb GARP-G2-like Y 0.242 3728 181 6/39
At2g39930 ISA1 0.0763 / p At1g05805 bHLH bHLH Y 0.356 2106 81 9/114
At2g39930 ISA1 0.0783 / p At5g39860 bHLH bHLH Y 0.255 3490 164 22/114
At2g39930 ISA1 -0.0704 / n At1g51950 IAA18 AUX-IAA NA 0.056 8010 542 14/28
At3g46970 Stp,Cyt 0.0670 / p At1g05805 bHLH bHLH Y 0.442 511 37 1/114
At4g17090 b-AMY3 0.0761 / p At2g35940 Homeo domain HB Y 0.233 2173 127 12/89
At4g17090 b-AMY3 0.0674 / p At1g19700 HB-ZIP HB Y 0.009 7815 644 41/89
At4g17090 b-AMY3 0.0916 / p At4g39780 AP2 domain AP2-EREBP Y -0.179 18803 1537 110/130
At4g17090 b-AMY3 0.0810 / p At3g58680 ethylene-responsive MBF1 NA -0.009 8743 713 1/3
At4g17090 b-AMY3 0.1093 / p At1g76590 zinc-binding PLATZ NA 0.015 7522 608 2/7
At4g17090 b-AMY3 -0.0871 / n At1g77850 B3 ARF NA 0.026 7013 569 7/18
At4g17090 b-AMY3 0.0684 / p At5g48250 B-box C2C2-CO-like NA 0.285 1615 74 9/42
At4g17090 b-AMY3 0.0671 / p At3g07650 B-box C2C2-CO-like NA 0.264 1805 92 10/42
At4g17090 b-AMY3 0.1051 / p At5g61380 TOC1 C2C2-CO-like NA 0.181 2903 191 14/42
At4g17090 b-AMY3 -0.0941 / n At5g05090 myb GARP-G2 NA 0.015 7574 611 19/39
At4g17090 b-AMY3 -0.0774 / n At1g07520 scarecrow GRAS NA -0.139 16919 1385 30/32
At4g17090 b-AMY3 -0.0757 / n At4g39410 WRKY WRKY N 0.094 4649 365 16/63
At4g18240 SS4 0.0928 / p At2g02070 AtIDD5 C2H2 Y 0.542 158 9 1/122
At4g18240 SS4 -0.0671 / n At3g21175 GATTF_20_A ZIM NA 0.225 2276 119 1/16
At4g18240 SS4 0.1016 / p At5g61380 TOC1 C2C2-CO-like NA 0.569 124 5 3/42
At4g18240 SS4 0.0720 / p At3g07650 B-box C2C2-CO-like NA 0.514 201 13 5/42
At5g11720 AGLU-like4 0.0687 / p At3g50700 C2H2 C2H2 Y 0.295 2024 87 5/122
At5g11720 AGLU-like4 0.0837 / p At5g60850 Dof C2C2-Dof Y 0.135 5244 310 6/32
At5g11720 AGLU-like4 0.0910 / p At2g18280 TULP2 TLP NA 0.213 3463 169 3/11
At5g24300 SS1 0.0961 / p At5g06770 KH-CCCH C3H NA 0.422 1194 31 3/172
At5g24300 SS1 -0.0786 / n At3g55770 LIM LIM NA -0.079 13020 995 7/13
At5g24300 SS1 0.0817 / p At3g06160 B3 ABI3-VP1 N 0.241 2965 136 4/45
At5g51820 PGM -0.0829 / n At3g55770 LIM LIM NA -0.07 11712 853 6/13
At5g64860 DPE1 0.0663 / p At2g39900 WLIM2a LIM NA 0.715 30 1 1/13

Global-expression correlations extracted from ATTED database and the correlation ranks were shown in the table.

1. pCor is partial correlation of a gene pair under the diurnal condition predicted by GGM. p and n represent a positive and negative interactions, respectively.

2. Y = Physical binding of TFs to target genes was predicted by the comparative TF family analysis; N = No physical binding of TFs was predicted; NA = no TF binding site information in AthaMap.

Ingkasuwan et al.

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

Open Data