CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At2g40840

Gene name DPE2 (DISPROPORTIONATING ENZYME 2)

Module size 8 genes

NF 0.61

%ile 82.1

Co-expression network

: Transcription factor, : Binding protein, : Enzyme protein, : Other protein
: VF over 0.50, : over 0.25, : below 0.25

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. O.I. H.G. S.X. Other DB
1.00 100.0 1.00 At2g40840 818682 DPE2 (DISPROPORTIONATING ENZYME 2) Encodes a cytosolic protein with transglucosidase and amylomaltase activity. It is an essential component of the pathway from starch to sucrose and cellular metabolism in leaves at night. The protein binds to heteroglycans and utilizes glucose, mannose and xylose as acceptors. Fucose and galactose can also act as acceptors but less efficiently than the previous three. It was also was also recently reported to act on maltodextrins. On the other hand, arabinose and fructose were not efficiently used. Its role probably includes metabolizing maltose exported from the chloroplast. Studies using maltose extracted from the double mutant be2-1 be3-2 showed that this enzyme is preferentially active of β-maltose. O.I. H.G. S.X.
0.71 84.2 0.89 At3g52180 824383 SEX4 (STARCH-EXCESS 4) Encodes a plant-specific protein phosphatase that contains a protein tyrosine phosphatase (PTP) catalytic domain and a kinase interaction sequence (KIS) domain. This protein interacts with the plant SnRK AKIN11. Binds starch. Localized in the chloroplast. O.I. H.G. S.X.
0.67 81.6 0.90 At1g10760 837619 SEX1 (STARCH EXCESS 1) Encodes an α-glucan, water dikinase required for starch degradation. Involved in cold-induced freezing tolerance. Mutations that eliminate the GWD protein or affect the dikinase domain of the enzyme dramatically reduce both the amount of phosphate in the amylopectin and the rate of starch degradation. Mature leaves of these mutants accumulate amounts of starch up to seven times greater than those in wild-type leaves. NMR analysis of the mutants, suggests that the gene is specifically involved in the phosphorylation of the glucosyl residues of starch at the C6 position. O.I. H.G. S.X.
0.67 81.6 0.91 At3g46970 823850 PHS2 (ALPHA-GLUCAN PHOSPHORYLASE 2) Encodes a cytosolic alpha-glucan phosphorylase. In vitro, the enzyme has a preference for branched polysaccharides, such as glycogen. O.I. H.G. S.X.
0.55 70.6 0.90 At3g29320 822590 glucan phosphorylase, putative Encodes a plastidic alpha-glucan phosphorylase. In vitro, the enzyme has a preference for maltooligosaccharides, such as maltoheptaose. O.I. H.G. S.X.
0.50 65.3 0.89 At2g21380 816676 kinesin motor protein-related F:protein binding, microtubule motor activity, zinc ion binding, ATP binding;P:microtubule-based movement;C:microtubule associated complex, chloroplast;MOBFPAV O.I. H.G. S.X.
0.40 50.8 0.91 At1g03310 839531 isoamylase, putative / starch debranching enzyme, putative Encodes a protein with strong similarity to isoamylase (EC:3.2.1.68) however lacks critical residues known to be important for activity. Appears to co localize with ISA1 in the chloroplast isoamylase complex. Mutations in this gene cause the loss of detectable isoamylase activity and the disruption of normal starch structure. It has been postulated that AtISA2 interacts with AtISA1 to form the Iso1 complex. O.I. H.G. S.X.
0.27 26.2 0.89 At5g64860 836609 DPE1 (DISPROPORTIONATING ENZYME) Encodes a maltotriose-metabolizing enzyme with chloroplastic α-1,4-glucanotransferase activity. Mutant has altered starch degradation. O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
1.00	100.0	1.00	At2g40840	818682	DPE2 (DISPROPORTIONATING ENZYME 2)	Encodes a cytosolic protein with transglucosidase and amylomaltase activity. It is an essential component of the pathway from starch to sucrose and cellular metabolism in leaves at night. The protein binds to heteroglycans and utilizes glucose, mannose and xylose as acceptors. Fucose and galactose can also act as acceptors but less efficiently than the previous three. It was also was also recently reported to act on maltodextrins. On the other hand, arabinose and fructose were not efficiently used. Its role probably includes metabolizing maltose exported from the chloroplast. Studies using maltose extracted from the double mutant be2-1 be3-2 showed that this enzyme is preferentially active of β-maltose.	O.I.	H.G.	S.X.
0.71	84.2	0.89	At3g52180	824383	SEX4 (STARCH-EXCESS 4)	Encodes a plant-specific protein phosphatase that contains a protein tyrosine phosphatase (PTP) catalytic domain and a kinase interaction sequence (KIS) domain. This protein interacts with the plant SnRK AKIN11. Binds starch. Localized in the chloroplast.	O.I.	H.G.	S.X.
0.67	81.6	0.90	At1g10760	837619	SEX1 (STARCH EXCESS 1)	Encodes an α-glucan, water dikinase required for starch degradation. Involved in cold-induced freezing tolerance. Mutations that eliminate the GWD protein or affect the dikinase domain of the enzyme dramatically reduce both the amount of phosphate in the amylopectin and the rate of starch degradation. Mature leaves of these mutants accumulate amounts of starch up to seven times greater than those in wild-type leaves. NMR analysis of the mutants, suggests that the gene is specifically involved in the phosphorylation of the glucosyl residues of starch at the C6 position.	O.I.	H.G.	S.X.
0.67	81.6	0.91	At3g46970	823850	PHS2 (ALPHA-GLUCAN PHOSPHORYLASE 2)	Encodes a cytosolic alpha-glucan phosphorylase. In vitro, the enzyme has a preference for branched polysaccharides, such as glycogen.	O.I.	H.G.	S.X.
0.55	70.6	0.90	At3g29320	822590	glucan phosphorylase, putative	Encodes a plastidic alpha-glucan phosphorylase. In vitro, the enzyme has a preference for maltooligosaccharides, such as maltoheptaose.	O.I.	H.G.	S.X.
0.50	65.3	0.89	At2g21380	816676	kinesin motor protein-related	F:protein binding, microtubule motor activity, zinc ion binding, ATP binding;P:microtubule-based movement;C:microtubule associated complex, chloroplast;MOBFPAV	O.I.	H.G.	S.X.
0.40	50.8	0.91	At1g03310	839531	isoamylase, putative / starch debranching enzyme, putative	Encodes a protein with strong similarity to isoamylase (EC:3.2.1.68) however lacks critical residues known to be important for activity. Appears to co localize with ISA1 in the chloroplast isoamylase complex. Mutations in this gene cause the loss of detectable isoamylase activity and the disruption of normal starch structure. It has been postulated that AtISA2 interacts with AtISA1 to form the Iso1 complex.	O.I.	H.G.	S.X.
0.27	26.2	0.89	At5g64860	836609	DPE1 (DISPROPORTIONATING ENZYME)	Encodes a maltotriose-metabolizing enzyme with chloroplastic α-1,4-glucanotransferase activity. Mutant has altered starch degradation.	O.I.	H.G.	S.X.

Click More genes

Link to AtGenExpress Visualization Tool

Specific experiments for the module

Std2 GX %ile GSM ID Assay name GSE ID Experiment title Link to GEO
27.7 99.7 GSM131322 AtGen_6-3422_Saltstress-Roots-6.0h_Rep2 GSE5623 AtGenExpress: Stress Treatments (Salt stress)
17.8 99.5 GSM131318 AtGen_6-3322_Saltstress-Roots-3.0h_Rep2 GSE5623 AtGenExpress: Stress Treatments (Salt stress)
17.0 99.5 GSM131321 AtGen_6-3421_Saltstress-Roots-6.0h_Rep1 GSE5623 AtGenExpress: Stress Treatments (Salt stress)
16.2 99.5 GSM131317 AtGen_6-3321_Saltstress-Roots-3.0h_Rep1 GSE5623 AtGenExpress: Stress Treatments (Salt stress)
16.2 99.5 GSM290758 root - 01% oxygen - 48h - A GSE11558 transcript profiling of the adaptive response to decreases in oxygen concentration in the roots of Arabidopsis plants
15.5 99.5 GSM311293 Laser capture microdissected (LCM) chalazal seed coat at the linear-cotyledon stage, biological replicate 1 GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
14.9 99.4 GSM284396 Arabidopsis GPSc2 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
12.5 99.3 GSM311282 Laser capture microdissected (LCM) chalazal seed coat at the pre-globular stage, biological replicate 2 GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
11.6 99.3 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.1 99.2 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.0 99.2 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.7 99.2 GSM184556 Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
10.5 99.2 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.4 99.2 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
10.3 99.2 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
9.8 99.1 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
9.7 99.1 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.7 99.1 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.4 99.1 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
9.4 99.1 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
9.4 99.1 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
9.3 99.1 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
9.3 99.1 GSM205156 protoplast_controlDNA_rep1 GSE8257 Identification of KIN10-target genes in Arabidopsis mesophyll cells
8.9 99.0 GSM75521 slr-1 6h NAA replicate 2 GSE3350 SLR/IAA14-dependent auxin induced lateral root initiation
8.6 99.0 GSM311289 Laser capture microdissected (LCM) cellularized endosperm at the linear-cotyledon stage, biological replicate 1 GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
27.7	99.7	GSM131322	AtGen_6-3422_Saltstress-Roots-6.0h_Rep2	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
17.8	99.5	GSM131318	AtGen_6-3322_Saltstress-Roots-3.0h_Rep2	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
17.0	99.5	GSM131321	AtGen_6-3421_Saltstress-Roots-6.0h_Rep1	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
16.2	99.5	GSM131317	AtGen_6-3321_Saltstress-Roots-3.0h_Rep1	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
16.2	99.5	GSM290758	root - 01% oxygen - 48h - A	GSE11558	transcript profiling of the adaptive response to decreases in oxygen concentration in the roots of Arabidopsis plants
15.5	99.5	GSM311293	Laser capture microdissected (LCM) chalazal seed coat at the linear-cotyledon stage, biological replicate 1	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
14.9	99.4	GSM284396	Arabidopsis GPSc2	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
12.5	99.3	GSM311282	Laser capture microdissected (LCM) chalazal seed coat at the pre-globular stage, biological replicate 2	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
11.6	99.3	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.1	99.2	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.0	99.2	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.7	99.2	GSM184556	Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
10.5	99.2	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.4	99.2	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
10.3	99.2	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
9.8	99.1	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
9.7	99.1	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.7	99.1	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.4	99.1	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
9.4	99.1	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
9.4	99.1	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
9.3	99.1	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
9.3	99.1	GSM205156	protoplast_controlDNA_rep1	GSE8257	Identification of KIN10-target genes in Arabidopsis mesophyll cells
8.9	99.0	GSM75521	slr-1 6h NAA replicate 2	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
8.6	99.0	GSM311289	Laser capture microdissected (LCM) cellularized endosperm at the linear-cotyledon stage, biological replicate 1	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.286 3 GO:0005983 The chemical reactions and pathways resulting in the breakdown of starch, the most important reserve polysaccharide in plants.
0.222 1 GO:0000025 The chemical reactions and pathways resulting in the breakdown of the disaccharide maltose (4-O-alpha-D-glucopyranosyl-D-glucopyranose).
0.222 1 GO:0005976 The chemical reactions and pathways involving polysaccharides, a polymer of more than 20 monosaccharide residues joined by glycosidic linkages.

SF	Genes	GO ID	Process Name
0.286	3	GO:0005983	The chemical reactions and pathways resulting in the breakdown of starch, the most important reserve polysaccharide in plants.
0.222	1	GO:0000025	The chemical reactions and pathways resulting in the breakdown of the disaccharide maltose (4-O-alpha-D-glucopyranosyl-D-glucopyranose).
0.222	1	GO:0005976	The chemical reactions and pathways involving polysaccharides, a polymer of more than 20 monosaccharide residues joined by glycosidic linkages.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.087 4 00500 Starch and sucrose metabolism
0.003 2 01100 Metabolic pathways

SF	Genes	KEGG ID	Pathway name	Link to KEGG
0.087	4	00500	Starch and sucrose metabolism
0.003	2	01100	Metabolic pathways

Inter-species module comparison

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

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Gene ID	At2g40840
Gene name	DPE2 (DISPROPORTIONATING ENZYME 2)
Module size	8 genes
NF	0.61
%ile	82.1

Co-expression analysis

Gene ID At2g40840 Gene name DPE2 (DISPROPORTIONATING ENZYME 2) Module size 8 genes NF 0.61 %ile 82.1

Co-expression network

: Transcription factor, : Binding protein, : Enzyme protein, : Other protein: VF over 0.50, : over 0.25, : below 0.25

Co-expressed genes

Click More genes

Link to AtGenExpress Visualization Tool

Specific experiments for the module

Biological processes inferred to relate to the module

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG0.087400500Starch and sucrose metabolism0.003201100Metabolic pathways

Inter-species module comparison

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

Gene ID At2g40840

Gene name DPE2 (DISPROPORTIONATING ENZYME 2)

Module size 8 genes

NF 0.61

%ile 82.1

: Transcription factor, : Binding protein, : Enzyme protein, : Other protein
: VF over 0.50, : over 0.25, : below 0.25

SF Genes KEGG ID Pathway name Link to KEGG
0.087 4 00500 Starch and sucrose metabolism
0.003 2 01100 Metabolic pathways

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