CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID GmaAffx.84643.1.S1_at

Gene name
Homology with Arabidopsis Similar to At5g61580: PFK4 (PHOSPHOFRUCTOKINASE 4) (HF=1e-19)

Module size 26 genes

NF 0.35

%ile 62.8

Co-expressed genes

Click gene/probe ID to show a list of genes that are co-expressed with the gene.

VF %ile CC Gene ID Repr. ID Gene name Func. Ev AGI code Arabidopsis gene name O.I. H.G. S.X. Other DB
0.85 92.8 0.94 GmaAffx.84643.1.S1_at BU545213 - - 1e-19 At5g61580 PFK4 (PHOSPHOFRUCTOKINASE 4) O.I. H.G. S.X.
0.54 74.8 0.96 Gma.16230.1.S1_at CD404236 - - 1e-1 At5g23330 riboflavin biosynthesis protein-related O.I. H.G. S.X.
0.52 73.1 0.95 GmaAffx.62870.1.S1_at BE346662 - - 2e-51 At3g10350 anion-transporting ATPase family protein O.I. H.G. S.X.
0.51 72.3 0.95 Gma.7276.1.S1_at CD394605 - - 2e-31 At1g45230 defective chloroplasts and leaves protein-related / DCL protein-related O.I. H.G. S.X.
0.46 65.5 0.95 GmaAffx.1301.26.S1_at CD397615 - - 4e-16 At3g53130 LUT1 (LUTEIN DEFICIENT 1) O.I. H.G. S.X.
0.44 63.3 0.94 Gma.12870.1.A1_at CD414345 - - 5e+0 At5g33421 unknown protein O.I. H.G. S.X.
0.43 60.6 0.95 Gma.1205.2.S1_at BU081316 - - 5e-32 At2g04842 EMB2761 (EMBRYO DEFECTIVE 2761) O.I. H.G. S.X.
0.39 54.5 0.94 Gma.1781.1.A1_a_at AI960136 - - 1e+0 At5g03905 hesB-like domain-containing protein O.I. H.G. S.X.
0.39 54.5 0.96 Gma.1205.2.S1_a_at BU081316 - - 5e-32 At2g04842 EMB2761 (EMBRYO DEFECTIVE 2761) O.I. H.G. S.X.
0.39 54.5 0.95 Gma.12855.1.S1_at BG045651 - - 9e-20 At5g14460 pseudouridine synthase/ transporter O.I. H.G. S.X.
0.37 51.7 0.95 Gma.613.1.S1_a_at BI424045 - - 2e-1 At1g73890 protease inhibitor/seed storage/lipid transfer protein (LTP) family protein O.I. H.G. S.X.
0.36 50.8 0.95 Gma.3336.1.S1_at BQ298636 - - 5e-23 At5g64050 ERS (GLUTAMATE TRNA SYNTHETASE) O.I. H.G. S.X.
0.36 50.8 0.95 Gma.15088.1.S1_at CD402034 - - 6e-38 At4g29670 thioredoxin family protein O.I. H.G. S.X.
0.35 48.6 0.94 GmaAffx.33373.1.A1_at BU544165 - - 5e+0 At3g06040 ribosomal protein L12 family protein O.I. H.G. S.X.
0.35 48.6 0.94 Gma.17682.1.S1_at BG839162 - - 0 Atcg00120 - O.I. H.G. S.X.
0.34 47.2 0.96 Gma.2654.1.S1_at BI425273 - - 5e-63 At2g43945 unknown protein O.I. H.G. S.X.
0.34 47.2 0.95 Gma.1390.1.S1_at BE659513 ferredoxin-dependent glutamate synthase - 6e-164 At5g04140 GLU1 (GLUTAMATE SYNTHASE 1) O.I. H.G. S.X.
0.32 43.7 0.95 Gma.9121.1.S1_at CD403401 - - 2e-34 At1g12410 CLP2 (CLP PROTEASE PROTEOLYTIC SUBUNIT 2) O.I. H.G. S.X.
0.31 42.2 0.95 Gma.1484.1.S1_at BI969651 - - 6e-1 At3g29320 glucan phosphorylase, putative O.I. H.G. S.X.
0.31 42.2 0.94 Gma.16326.1.S1_at CD401278 - - 4e+0 At5g55893 unknown protein O.I. H.G. S.X.
0.29 39.0 0.95 Gma.13391.1.A1_at CD411330 - - 2e-6 At2g38270 CXIP2 (CAX-INTERACTING PROTEIN 2) O.I. H.G. S.X.
0.27 35.7 0.95 GmaAffx.32100.1.S1_at BI471267 - - 1e+0 At2g28110 FRA8 (FRAGILE FIBER 8) O.I. H.G. S.X.
0.25 32.6 0.94 Gma.1323.2.A1_s_at CD412098 - - 2e-4 At1g06870 signal peptidase, putative O.I. H.G. S.X.
0.24 30.9 0.96 Gma.18060.1.S1_at BU578633 - - 8e-22 At3g04870 ZDS (ZETA-CAROTENE DESATURASE) O.I. H.G. S.X.
0.21 26.6 0.94 GmaAffx.84912.2.S1_at BE021707 - - 1e+0 At5g16090 - O.I. H.G. S.X.
0.15 18.7 0.94 GmaAffx.93066.1.S1_s_at CF808791 - - 7e-36 At4g29670 thioredoxin family protein O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	Ev	AGI code	Arabidopsis gene name	O.I.	H.G.	S.X.
0.85	92.8	0.94	GmaAffx.84643.1.S1_at	BU545213	-	-	1e-19	At5g61580	PFK4 (PHOSPHOFRUCTOKINASE 4)	O.I.	H.G.	S.X.
0.54	74.8	0.96	Gma.16230.1.S1_at	CD404236	-	-	1e-1	At5g23330	riboflavin biosynthesis protein-related	O.I.	H.G.	S.X.
0.52	73.1	0.95	GmaAffx.62870.1.S1_at	BE346662	-	-	2e-51	At3g10350	anion-transporting ATPase family protein	O.I.	H.G.	S.X.
0.51	72.3	0.95	Gma.7276.1.S1_at	CD394605	-	-	2e-31	At1g45230	defective chloroplasts and leaves protein-related / DCL protein-related	O.I.	H.G.	S.X.
0.46	65.5	0.95	GmaAffx.1301.26.S1_at	CD397615	-	-	4e-16	At3g53130	LUT1 (LUTEIN DEFICIENT 1)	O.I.	H.G.	S.X.
0.44	63.3	0.94	Gma.12870.1.A1_at	CD414345	-	-	5e+0	At5g33421	unknown protein	O.I.	H.G.	S.X.
0.43	60.6	0.95	Gma.1205.2.S1_at	BU081316	-	-	5e-32	At2g04842	EMB2761 (EMBRYO DEFECTIVE 2761)	O.I.	H.G.	S.X.
0.39	54.5	0.94	Gma.1781.1.A1_a_at	AI960136	-	-	1e+0	At5g03905	hesB-like domain-containing protein	O.I.	H.G.	S.X.
0.39	54.5	0.96	Gma.1205.2.S1_a_at	BU081316	-	-	5e-32	At2g04842	EMB2761 (EMBRYO DEFECTIVE 2761)	O.I.	H.G.	S.X.
0.39	54.5	0.95	Gma.12855.1.S1_at	BG045651	-	-	9e-20	At5g14460	pseudouridine synthase/ transporter	O.I.	H.G.	S.X.
0.37	51.7	0.95	Gma.613.1.S1_a_at	BI424045	-	-	2e-1	At1g73890	protease inhibitor/seed storage/lipid transfer protein (LTP) family protein	O.I.	H.G.	S.X.
0.36	50.8	0.95	Gma.3336.1.S1_at	BQ298636	-	-	5e-23	At5g64050	ERS (GLUTAMATE TRNA SYNTHETASE)	O.I.	H.G.	S.X.
0.36	50.8	0.95	Gma.15088.1.S1_at	CD402034	-	-	6e-38	At4g29670	thioredoxin family protein	O.I.	H.G.	S.X.
0.35	48.6	0.94	GmaAffx.33373.1.A1_at	BU544165	-	-	5e+0	At3g06040	ribosomal protein L12 family protein	O.I.	H.G.	S.X.
0.35	48.6	0.94	Gma.17682.1.S1_at	BG839162	-	-	0	Atcg00120	-	O.I.	H.G.	S.X.
0.34	47.2	0.96	Gma.2654.1.S1_at	BI425273	-	-	5e-63	At2g43945	unknown protein	O.I.	H.G.	S.X.
0.34	47.2	0.95	Gma.1390.1.S1_at	BE659513	ferredoxin-dependent glutamate synthase	-	6e-164	At5g04140	GLU1 (GLUTAMATE SYNTHASE 1)	O.I.	H.G.	S.X.
0.32	43.7	0.95	Gma.9121.1.S1_at	CD403401	-	-	2e-34	At1g12410	CLP2 (CLP PROTEASE PROTEOLYTIC SUBUNIT 2)	O.I.	H.G.	S.X.
0.31	42.2	0.95	Gma.1484.1.S1_at	BI969651	-	-	6e-1	At3g29320	glucan phosphorylase, putative	O.I.	H.G.	S.X.
0.31	42.2	0.94	Gma.16326.1.S1_at	CD401278	-	-	4e+0	At5g55893	unknown protein	O.I.	H.G.	S.X.
0.29	39.0	0.95	Gma.13391.1.A1_at	CD411330	-	-	2e-6	At2g38270	CXIP2 (CAX-INTERACTING PROTEIN 2)	O.I.	H.G.	S.X.
0.27	35.7	0.95	GmaAffx.32100.1.S1_at	BI471267	-	-	1e+0	At2g28110	FRA8 (FRAGILE FIBER 8)	O.I.	H.G.	S.X.
0.25	32.6	0.94	Gma.1323.2.A1_s_at	CD412098	-	-	2e-4	At1g06870	signal peptidase, putative	O.I.	H.G.	S.X.
0.24	30.9	0.96	Gma.18060.1.S1_at	BU578633	-	-	8e-22	At3g04870	ZDS (ZETA-CAROTENE DESATURASE)	O.I.	H.G.	S.X.
0.21	26.6	0.94	GmaAffx.84912.2.S1_at	BE021707	-	-	1e+0	At5g16090	-	O.I.	H.G.	S.X.
0.15	18.7	0.94	GmaAffx.93066.1.S1_s_at	CF808791	-	-	7e-36	At4g29670	thioredoxin family protein	O.I.	H.G.	S.X.

Click More genes

Specific experiments for the module

Std2 GX %ile GSM ID Assay name GSE ID Experiment title Link to GEO
9.4 99.2 GSM245938 Leaf_LCO treated_Rep 3_48 h After Treatment GSE9730 Effect of foliar spray of lipo-chitooligosaccharide (Nod factor) on soybean leaf gene expression.
8.2 99.0 GSM245937 Leaf_LCO treated_Rep 2_48 h After Treatment GSE9730 Effect of foliar spray of lipo-chitooligosaccharide (Nod factor) on soybean leaf gene expression.
7.9 99.0 GSM245935 Leaf_Water Control_Rep 3_48 h After Treatment GSE9730 Effect of foliar spray of lipo-chitooligosaccharide (Nod factor) on soybean leaf gene expression.
7.8 99.0 GSM238048 Soybean-Mandarin-3-RMA GSE9374 Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
7.7 99.0 GSM245936 Leaf_LCO treated_Rep 1_48 h After Treatment GSE9730 Effect of foliar spray of lipo-chitooligosaccharide (Nod factor) on soybean leaf gene expression.
7.7 99.0 GSM238050 Soybean-Mandarin-6-RMA GSE9374 Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
7.6 98.9 GSM238049 Soybean-Mandarin-4-RMA GSE9374 Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
7.5 98.9 GSM238051 Soybean-Mandarin-7-RMA GSE9374 Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
7.4 98.9 GSM238030 Soybean-2601R-2-RMA GSE9374 Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
7.3 98.9 GSM245934 Leaf_Water Control_Rep 2_48 h After Treatment GSE9730 Effect of foliar spray of lipo-chitooligosaccharide (Nod factor) on soybean leaf gene expression.
7.3 98.9 GSM209589 resistant_48hours_rep2 GSE8432 Expression survey of Rpp1 soybean line PI200492 resistant to P. pachyrhizi
7.2 98.9 GSM238047 Soybean-Mandarin-1-RMA GSE9374 Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
6.9 98.8 GSM245933 Leaf_Water Control_Rep 1_48 h After Treatment GSE9730 Effect of foliar spray of lipo-chitooligosaccharide (Nod factor) on soybean leaf gene expression.
6.9 98.8 GSM238061 Soybean-S03W4-5-RMA GSE9374 Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
6.7 98.7 GSM238034 Soybean-2601R-6-RMA GSE9374 Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
6.7 98.7 GSM209590 susceptible_48hours_rep2 GSE8432 Expression survey of Rpp1 soybean line PI200492 resistant to P. pachyrhizi
6.6 98.7 GSM209581 susceptible_48hours_rep1 GSE8432 Expression survey of Rpp1 soybean line PI200492 resistant to P. pachyrhizi
6.6 98.7 GSM238043 Soybean-Bayfield-5-RMA GSE9374 Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
6.3 98.6 GSM209599 susceptible_48hours_rep3 GSE8432 Expression survey of Rpp1 soybean line PI200492 resistant to P. pachyrhizi
6.3 98.6 GSM238032 Soybean-2601R-4-RMA GSE9374 Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
6.3 98.6 GSM238056 Soybean-PS46R-5-RMA GSE9374 Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
6.2 98.6 GSM238036 Soybean-Bayfield-1-RMA GSE9374 Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
6.1 98.5 GSM238054 Soybean-PS46R-3-RMA GSE9374 Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
6.1 98.5 GSM209598 resistant_48hours_rep3 GSE8432 Expression survey of Rpp1 soybean line PI200492 resistant to P. pachyrhizi
6.0 98.5 GSM238041 Soybean-Bayfield-4-RMA GSE9374 Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
5.9 98.5 GSM238060 Soybean-S03W4-4-RMA GSE9374 Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
5.9 98.5 GSM238059 Soybean-S03W4-3-RMA GSE9374 Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
5.9 98.5 GSM238053 Soybean-PS46R-2-RMA GSE9374 Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
5.9 98.5 GSM238058 Soybean-S03W4-2-RMA GSE9374 Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
5.8 98.4 GSM238039 Soybean-Bayfield-3-RMA GSE9374 Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
9.4	99.2	GSM245938	Leaf_LCO treated_Rep 3_48 h After Treatment	GSE9730	Effect of foliar spray of lipo-chitooligosaccharide (Nod factor) on soybean leaf gene expression.
8.2	99.0	GSM245937	Leaf_LCO treated_Rep 2_48 h After Treatment	GSE9730	Effect of foliar spray of lipo-chitooligosaccharide (Nod factor) on soybean leaf gene expression.
7.9	99.0	GSM245935	Leaf_Water Control_Rep 3_48 h After Treatment	GSE9730	Effect of foliar spray of lipo-chitooligosaccharide (Nod factor) on soybean leaf gene expression.
7.8	99.0	GSM238048	Soybean-Mandarin-3-RMA	GSE9374	Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
7.7	99.0	GSM245936	Leaf_LCO treated_Rep 1_48 h After Treatment	GSE9730	Effect of foliar spray of lipo-chitooligosaccharide (Nod factor) on soybean leaf gene expression.
7.7	99.0	GSM238050	Soybean-Mandarin-6-RMA	GSE9374	Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
7.6	98.9	GSM238049	Soybean-Mandarin-4-RMA	GSE9374	Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
7.5	98.9	GSM238051	Soybean-Mandarin-7-RMA	GSE9374	Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
7.4	98.9	GSM238030	Soybean-2601R-2-RMA	GSE9374	Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
7.3	98.9	GSM245934	Leaf_Water Control_Rep 2_48 h After Treatment	GSE9730	Effect of foliar spray of lipo-chitooligosaccharide (Nod factor) on soybean leaf gene expression.
7.3	98.9	GSM209589	resistant_48hours_rep2	GSE8432	Expression survey of Rpp1 soybean line PI200492 resistant to P. pachyrhizi
7.2	98.9	GSM238047	Soybean-Mandarin-1-RMA	GSE9374	Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
6.9	98.8	GSM245933	Leaf_Water Control_Rep 1_48 h After Treatment	GSE9730	Effect of foliar spray of lipo-chitooligosaccharide (Nod factor) on soybean leaf gene expression.
6.9	98.8	GSM238061	Soybean-S03W4-5-RMA	GSE9374	Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
6.7	98.7	GSM238034	Soybean-2601R-6-RMA	GSE9374	Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
6.7	98.7	GSM209590	susceptible_48hours_rep2	GSE8432	Expression survey of Rpp1 soybean line PI200492 resistant to P. pachyrhizi
6.6	98.7	GSM209581	susceptible_48hours_rep1	GSE8432	Expression survey of Rpp1 soybean line PI200492 resistant to P. pachyrhizi
6.6	98.7	GSM238043	Soybean-Bayfield-5-RMA	GSE9374	Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
6.3	98.6	GSM209599	susceptible_48hours_rep3	GSE8432	Expression survey of Rpp1 soybean line PI200492 resistant to P. pachyrhizi
6.3	98.6	GSM238032	Soybean-2601R-4-RMA	GSE9374	Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
6.3	98.6	GSM238056	Soybean-PS46R-5-RMA	GSE9374	Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
6.2	98.6	GSM238036	Soybean-Bayfield-1-RMA	GSE9374	Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
6.1	98.5	GSM238054	Soybean-PS46R-3-RMA	GSE9374	Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
6.1	98.5	GSM209598	resistant_48hours_rep3	GSE8432	Expression survey of Rpp1 soybean line PI200492 resistant to P. pachyrhizi
6.0	98.5	GSM238041	Soybean-Bayfield-4-RMA	GSE9374	Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
5.9	98.5	GSM238060	Soybean-S03W4-4-RMA	GSE9374	Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
5.9	98.5	GSM238059	Soybean-S03W4-3-RMA	GSE9374	Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
5.9	98.5	GSM238053	Soybean-PS46R-2-RMA	GSE9374	Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
5.9	98.5	GSM238058	Soybean-S03W4-2-RMA	GSE9374	Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
5.8	98.4	GSM238039	Soybean-Bayfield-3-RMA	GSE9374	Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans

Inter-species module comparison

Select a plant to compare co-expressed genes between species.
Arabidopsis_thaliana
Hordeum_vulgare
Oryza_sativa
Populus_trichocarpa
Triticum_aestivum
Vitis_vinifera
Zea_mays

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Gene ID	GmaAffx.84643.1.S1_at
Gene name
Homology with Arabidopsis	Similar to At5g61580: PFK4 (PHOSPHOFRUCTOKINASE 4) (HF=1e-19)
Module size	26 genes
NF	0.35
%ile	62.8

Co-expression analysis

Gene ID GmaAffx.84643.1.S1_at Gene name Homology with ArabidopsisSimilar to At5g61580: PFK4 (PHOSPHOFRUCTOKINASE 4) (HF=1e-19) Module size 26 genes NF 0.35 %ile 62.8

Co-expressed genes

Click More genes

Specific experiments for the module

Inter-species module comparison

Select a plant to compare co-expressed genes between species.Arabidopsis_thalianaHordeum_vulgareOryza_sativaPopulus_trichocarpaTriticum_aestivumVitis_viniferaZea_mays

Gene ID GmaAffx.84643.1.S1_at

Gene name
Homology with Arabidopsis Similar to At5g61580: PFK4 (PHOSPHOFRUCTOKINASE 4) (HF=1e-19)

Module size 26 genes

NF 0.35

%ile 62.8

Select a plant to compare co-expressed genes between species.
Arabidopsis_thaliana
Hordeum_vulgare
Oryza_sativa
Populus_trichocarpa
Triticum_aestivum
Vitis_vinifera
Zea_mays