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

Ingkasuwan, Papapit; Netrphan, Supatcharee; Prasitwattanaseree, Sukon; Tanticharoen, Morakot; Bhumiratana, Sakarindr; Meechai, Asawin; Chaijaruwanich, Jeerayut; Takahashi, Hideki; Cheevadhanarak, Supapon

doi:10.1186/1752-0509-6-100

Table 3 The TF-starch relationships from the starch sub-network

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

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.

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