CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At5g20250

Gene name DIN10 (DARK INDUCIBLE 10)

Module size 7 genes

NF 0.64

%ile 85.2

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
0.92 96.0 1.00 At5g20250 832147 DIN10 (DARK INDUCIBLE 10) encodes a member of glycosyl hydrolase family 36. Expression is induced within 3 hours of dark treatment, in senescing leaves and treatment with exogenous photosynthesis inhibitor. Induction of gene expression was suppressed in excised leaves supplied with sugar. The authors suggest that the gene's expression pattern is responding to the level of sugar in the cell. O.I. H.G. S.X.
0.71 84.2 0.90 At5g22920 832356 zinc finger (C3HC4-type RING finger) family protein F:protein binding, zinc ion binding;P:unknown;C:unknown;MPOFBA O.I. H.G. S.X.
0.67 81.6 0.85 At1g11260 837667 STP1 (SUGAR TRANSPORTER 1) Encodes a H+/hexose cotransporter. O.I. H.G. S.X.
0.67 81.6 0.85 At2g30600 817610 BTB/POZ domain-containing protein F:protein binding;P:cell adhesion;C:cellular_component unknown;MPOVF O.I. H.G. S.X.
0.55 70.6 0.86 At5g19120 832032 aspartic-type endopeptidase F:aspartic-type endopeptidase activity;P:proteolysis;C:endomembrane system;PF O.I. H.G. S.X.
0.50 65.3 0.85 At5g49360 834996 BXL1 (BETA-XYLOSIDASE 1) Encodes a bifunctional {beta}-D-xylosidase/{alpha}-L-arabinofuranosidase required for pectic arabinan modification. Located in the extracellular matrix. Gene is expressed specifically in tissues undergoing secondary wall thickening. This is a member of glycosyl hydrolase family 3 and has six other closely related members. O.I. H.G. S.X.
0.47 61.2 0.86 At5g21170 832243 5'-AMP-activated protein kinase beta-2 subunit, putative F:AMP-activated protein kinase activity;P:N-terminal protein myristoylation;C:chloroplast;MFPOB O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.92	96.0	1.00	At5g20250	832147	DIN10 (DARK INDUCIBLE 10)	encodes a member of glycosyl hydrolase family 36. Expression is induced within 3 hours of dark treatment, in senescing leaves and treatment with exogenous photosynthesis inhibitor. Induction of gene expression was suppressed in excised leaves supplied with sugar. The authors suggest that the gene's expression pattern is responding to the level of sugar in the cell.	O.I.	H.G.	S.X.
0.71	84.2	0.90	At5g22920	832356	zinc finger (C3HC4-type RING finger) family protein	F:protein binding, zinc ion binding;P:unknown;C:unknown;MPOFBA	O.I.	H.G.	S.X.
0.67	81.6	0.85	At1g11260	837667	STP1 (SUGAR TRANSPORTER 1)	Encodes a H+/hexose cotransporter.	O.I.	H.G.	S.X.
0.67	81.6	0.85	At2g30600	817610	BTB/POZ domain-containing protein	F:protein binding;P:cell adhesion;C:cellular_component unknown;MPOVF	O.I.	H.G.	S.X.
0.55	70.6	0.86	At5g19120	832032	aspartic-type endopeptidase	F:aspartic-type endopeptidase activity;P:proteolysis;C:endomembrane system;PF	O.I.	H.G.	S.X.
0.50	65.3	0.85	At5g49360	834996	BXL1 (BETA-XYLOSIDASE 1)	Encodes a bifunctional {beta}-D-xylosidase/{alpha}-L-arabinofuranosidase required for pectic arabinan modification. Located in the extracellular matrix. Gene is expressed specifically in tissues undergoing secondary wall thickening. This is a member of glycosyl hydrolase family 3 and has six other closely related members.	O.I.	H.G.	S.X.
0.47	61.2	0.86	At5g21170	832243	5'-AMP-activated protein kinase beta-2 subunit, putative	F:AMP-activated protein kinase activity;P:N-terminal protein myristoylation;C:chloroplast;MFPOB	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
101.1 99.9 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
88.6 99.9 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
76.6 99.9 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
71.7 99.9 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
56.9 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
54.7 99.8 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
49.8 99.8 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
45.4 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
38.0 99.8 E-MEXP-849-raw-cel-1181980982
36.3 99.7 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.5 99.7 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
32.9 99.7 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
30.8 99.7 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
30.8 99.7 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
26.7 99.7 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
26.7 99.7 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
22.9 99.6 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
21.9 99.6 E-MEXP-449-raw-cel-676423253
21.0 99.6 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
20.5 99.6 GSM339546 Environmental regulation of leaf colour in red 35S:PAP1 Arabidopsis -8 GSE13469 Environmental regulation of leaf colour in red 35S:PAP1 Arabidopsis
20.4 99.6 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
19.2 99.6 E-MEXP-285-raw-cel-440783213
18.8 99.5 GSM147963 WT Globular Stage Seed 1 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle
18.7 99.5 E-MEXP-285-raw-cel-440783152
17.6 99.5 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
16.3 99.5 GSM147964 WT Globular Stage Seed 2 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle
16.1 99.5 GSM147965 lec1-1 Globular Stage Seed 1 GSE1051 Seed development in LEAFY COTYLEDON1 mutants
14.7 99.4 GSM184551 Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
13.4 99.4 GSM284398 Arabidopsis GGSc2 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
12.7 99.3 GSM184497 Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
12.0 99.3 GSM133820 Yang_1-5_young-pod_Rep3_ATH1 GSE5736 To identify changes in gene expression during silique senescence in Arabidopsis thaliana
11.8 99.3 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
11.4 99.3 GSM147966 lec1-1 Globular Stage Seed 2 GSE1051 Seed development in LEAFY COTYLEDON1 mutants
10.4 99.2 GSM311291 Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 1 GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
10.1 99.2 GSM131688 ATGE_77_D GSE5634 AtGenExpress: Developmental series (siliques and seeds)
10.0 99.2 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.8 99.1 GSM131689 ATGE_77_E GSE5634 AtGenExpress: Developmental series (siliques and seeds)
9.7 99.1 GSM239251 Columbia glabrous (C24) wild type pollen GSE9408 Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
9.5 99.1 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
9.0 99.1 GSM142904 WW002_ATH1_A1-willa-CON-REP2 GSE6181 Assembly of the cell wall pectic matrix.
8.8 99.0 GSM239253 CaMV::DME pollen GSE9408 Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
101.1	99.9	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
88.6	99.9	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
76.6	99.9	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
71.7	99.9	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
56.9	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
54.7	99.8	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
49.8	99.8	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
45.4	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
38.0	99.8	E-MEXP-849-raw-cel-1181980982
36.3	99.7	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.5	99.7	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
32.9	99.7	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
30.8	99.7	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
30.8	99.7	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
26.7	99.7	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
26.7	99.7	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
22.9	99.6	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
21.9	99.6	E-MEXP-449-raw-cel-676423253
21.0	99.6	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
20.5	99.6	GSM339546	Environmental regulation of leaf colour in red 35S:PAP1 Arabidopsis -8	GSE13469	Environmental regulation of leaf colour in red 35S:PAP1 Arabidopsis
20.4	99.6	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
19.2	99.6	E-MEXP-285-raw-cel-440783213
18.8	99.5	GSM147963	WT Globular Stage Seed 1	GSE680	Transcript Profiling of Arabidopsis Plant Life Cycle
18.7	99.5	E-MEXP-285-raw-cel-440783152
17.6	99.5	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
16.3	99.5	GSM147964	WT Globular Stage Seed 2	GSE680	Transcript Profiling of Arabidopsis Plant Life Cycle
16.1	99.5	GSM147965	lec1-1 Globular Stage Seed 1	GSE1051	Seed development in LEAFY COTYLEDON1 mutants
14.7	99.4	GSM184551	Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
13.4	99.4	GSM284398	Arabidopsis GGSc2	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
12.7	99.3	GSM184497	Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
12.0	99.3	GSM133820	Yang_1-5_young-pod_Rep3_ATH1	GSE5736	To identify changes in gene expression during silique senescence in Arabidopsis thaliana
11.8	99.3	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
11.4	99.3	GSM147966	lec1-1 Globular Stage Seed 2	GSE1051	Seed development in LEAFY COTYLEDON1 mutants
10.4	99.2	GSM311291	Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 1	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
10.1	99.2	GSM131688	ATGE_77_D	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
10.0	99.2	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.8	99.1	GSM131689	ATGE_77_E	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
9.7	99.1	GSM239251	Columbia glabrous (C24) wild type pollen	GSE9408	Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
9.5	99.1	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
9.0	99.1	GSM142904	WW002_ATH1_A1-willa-CON-REP2	GSE6181	Assembly of the cell wall pectic matrix.
8.8	99.0	GSM239253	CaMV::DME pollen	GSE9408	Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.167 1 GO:0043562 A change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of inorganic nitrogen.
0.133 1 GO:0010214 The process whose specific outcome is the progression of the seed coat over time, from its formation to the mature structure.
0.118 1 GO:0007155 The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.

SF	Genes	GO ID	Process Name
0.167	1	GO:0043562	A change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of inorganic nitrogen.
0.133	1	GO:0010214	The process whose specific outcome is the progression of the seed coat over time, from its formation to the mature structure.
0.118	1	GO:0007155	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.019 1 04120 Ubiquitin mediated proteolysis

SF	Genes	KEGG ID	Pathway name	Link to KEGG
0.019	1	04120	Ubiquitin mediated proteolysis

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

Back to the CoP portal site

Back to the KAGIANA project homepage

Gene ID	At5g20250
Gene name	DIN10 (DARK INDUCIBLE 10)
Module size	7 genes
NF	0.64
%ile	85.2

Co-expression analysis

Gene ID At5g20250 Gene name DIN10 (DARK INDUCIBLE 10) Module size 7 genes NF 0.64 %ile 85.2

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 KEGG0.019104120Ubiquitin mediated proteolysis

Inter-species module comparison

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

Gene ID At5g20250

Gene name DIN10 (DARK INDUCIBLE 10)

Module size 7 genes

NF 0.64

%ile 85.2

: 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
0.019 1 04120 Ubiquitin mediated proteolysis

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