CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At2g13560

Gene name malate oxidoreductase, putative

Module size 5 genes

NF 0.29

%ile 34.8

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
0.26 24.4 1.00 At2g13560 815842 malate oxidoreductase, putative F:oxidoreductase activity, acting on NADH or NADPH, NAD or NADP as acceptor, malic enzyme activity, ATP binding;P:response to salt stress, malate metabolic process;C:mitochondrion, chloroplast;BOMPFA O.I. H.G. S.X.
0.46 59.8 0.93 At4g23460 828445 beta-adaptin, putative F:protein transporter activity, protein binding, clathrin binding, binding;P:intracellular protein transport, vesicle-mediated transport, protein transport;C:plasma membrane;MFOPBA O.I. H.G. S.X.
0.29 30.3 0.93 At3g13870 820600 RHD3 (ROOT HAIR DEFECTIVE 3) required for regulated cell expansion and normal root hair development. Encodes an evolutionarily conserved protein with putative GTP-binding motifs that is implicated in the control of vesicle trafficking between the endoplasmic reticulum and the Golgi compartments. O.I. H.G. S.X.
0.27 26.2 0.93 At1g71820 843512 SEC6 F:molecular_function unknown;P:pollen germination, pollen tube growth;C:plasma membrane, exocyst;MFOPBA O.I. H.G. S.X.
0.24 20.7 0.94 At4g00570 828222 malate oxidoreductase, putative F:oxidoreductase activity, acting on NADH or NADPH, NAD or NADP as acceptor, malic enzyme activity, ATP binding;P:oxidation reduction, malate metabolic process, metabolic process;C:mitochondrion, chloroplast;BOMPFA O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.26	24.4	1.00	At2g13560	815842	malate oxidoreductase, putative	F:oxidoreductase activity, acting on NADH or NADPH, NAD or NADP as acceptor, malic enzyme activity, ATP binding;P:response to salt stress, malate metabolic process;C:mitochondrion, chloroplast;BOMPFA	O.I.	H.G.	S.X.
0.46	59.8	0.93	At4g23460	828445	beta-adaptin, putative	F:protein transporter activity, protein binding, clathrin binding, binding;P:intracellular protein transport, vesicle-mediated transport, protein transport;C:plasma membrane;MFOPBA	O.I.	H.G.	S.X.
0.29	30.3	0.93	At3g13870	820600	RHD3 (ROOT HAIR DEFECTIVE 3)	required for regulated cell expansion and normal root hair development. Encodes an evolutionarily conserved protein with putative GTP-binding motifs that is implicated in the control of vesicle trafficking between the endoplasmic reticulum and the Golgi compartments.	O.I.	H.G.	S.X.
0.27	26.2	0.93	At1g71820	843512	SEC6	F:molecular_function unknown;P:pollen germination, pollen tube growth;C:plasma membrane, exocyst;MFOPBA	O.I.	H.G.	S.X.
0.24	20.7	0.94	At4g00570	828222	malate oxidoreductase, putative	F:oxidoreductase activity, acting on NADH or NADPH, NAD or NADP as acceptor, malic enzyme activity, ATP binding;P:oxidation reduction, malate metabolic process, metabolic process;C:mitochondrion, chloroplast;BOMPFA	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
46.9 99.8 GSM106969 opr3_OPDA_22 hrs_Rep2 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
39.9 99.8 GSM106913 opr3_JA_8 hrs_Rep2 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
38.4 99.8 GSM131592 ATGE_36_B GSE5632 AtGenExpress: Developmental series (flowers and pollen)
37.0 99.7 GSM131593 ATGE_36_C GSE5632 AtGenExpress: Developmental series (flowers and pollen)
36.6 99.7 GSM106923 opr3_OPDA_2 hrs_Rep2 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
34.9 99.7 GSM106907 opr3_JA_0.5 hr_Rep2 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
32.0 99.7 GSM131591 ATGE_36_A GSE5632 AtGenExpress: Developmental series (flowers and pollen)
29.5 99.7 GSM106970 opr3_OPDA_22 hrs_Rep3 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
27.7 99.7 GSM106922 opr3_OPDA_2 hrs_Rep1 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
27.6 99.7 GSM106967 opr3_OPDA_22 hrs_Rep1 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
25.8 99.7 E-MEXP-1138-raw-cel-1432773258
25.3 99.6 GSM106916 opr3_JA_22 hrs_Rep2 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
23.5 99.6 GSM106973 ws_Rep1 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
23.3 99.6 GSM106920 opr3_OPDA_0.5 hr_Rep2 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
23.0 99.6 GSM106827 opr3_0 hr_Rep2 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
22.6 99.6 E-ATMX-35-raw-cel-1574334864
22.3 99.6 E-MEXP-1138-raw-cel-1432773290
22.2 99.6 GSM106910 opr3_JA_2 hrs_rep2 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
21.4 99.6 E-ATMX-35-raw-cel-1574334880
20.9 99.6 GSM106911 opr2_JA_2 hrs_Rep3 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
19.3 99.6 GSM106921 opr3_OPDA_0.5 hr_Rep3 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
19.3 99.6 GSM106917 opr3_JA_22 hrs_Rep3 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
19.2 99.6 GSM106966 opr3_OPDA_8 hrs_Rep3 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
19.0 99.5 GSM106912 opr3_JA 8hrs_Rep1 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
18.2 99.5 E-MEXP-1138-raw-cel-1432773322
18.1 99.5 GSM106825 opr3_0 hr_Rep1 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
17.5 99.5 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
17.2 99.5 GSM106934 opr3_OPDA_8 hrs_Rep1 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
16.8 99.5 GSM106828 opr3_0 hr_Rep3 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
16.8 99.5 GSM106914 opr3_JA_8 hrs_Rep3 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
16.2 99.5 GSM239254 CaMV::DME stamen GSE9408 Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
15.7 99.5 GSM106915 opr3_JA_22 hrs_Rep1 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
15.4 99.5 GSM106924 opr3_OPDA_2 hrs_Rep3 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
15.3 99.4 GSM106908 opr3_JA_0.5 hr_Rep3 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
14.9 99.4 E-ATMX-35-raw-cel-1574334848
14.1 99.4 GSM106909 opr3-JA_2 hrs_Rep1 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
14.0 99.4 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
13.9 99.4 GSM131636 ATGE_73_A GSE5632 AtGenExpress: Developmental series (flowers and pollen)
13.3 99.4 E-MEXP-1474-raw-cel-1593932577
12.0 99.3 GSM106919 opr3_OPDA_0.5 hr_Rep1 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
11.5 99.3 E-MEXP-1138-raw-cel-1432773066
10.8 99.2 GSM62695 Columbia flowers_stage 11-12 GSE2848 Auxin Response Factor mediated flower gene expression
9.9 99.1 GSM133773 Lindsey_1-25_torpedo-meristem_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.7 99.1 GSM62699 arf6/arf6 ARF8/arf8 flowers_stage 11-12 GSE2848 Auxin Response Factor mediated flower gene expression
9.7 99.1 E-MEXP-1474-raw-cel-1593932673
9.0 99.1 E-MEXP-1138-raw-cel-1432773034

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
46.9	99.8	GSM106969	opr3_OPDA_22 hrs_Rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
39.9	99.8	GSM106913	opr3_JA_8 hrs_Rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
38.4	99.8	GSM131592	ATGE_36_B	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
37.0	99.7	GSM131593	ATGE_36_C	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
36.6	99.7	GSM106923	opr3_OPDA_2 hrs_Rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
34.9	99.7	GSM106907	opr3_JA_0.5 hr_Rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
32.0	99.7	GSM131591	ATGE_36_A	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
29.5	99.7	GSM106970	opr3_OPDA_22 hrs_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
27.7	99.7	GSM106922	opr3_OPDA_2 hrs_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
27.6	99.7	GSM106967	opr3_OPDA_22 hrs_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
25.8	99.7	E-MEXP-1138-raw-cel-1432773258
25.3	99.6	GSM106916	opr3_JA_22 hrs_Rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
23.5	99.6	GSM106973	ws_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
23.3	99.6	GSM106920	opr3_OPDA_0.5 hr_Rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
23.0	99.6	GSM106827	opr3_0 hr_Rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
22.6	99.6	E-ATMX-35-raw-cel-1574334864
22.3	99.6	E-MEXP-1138-raw-cel-1432773290
22.2	99.6	GSM106910	opr3_JA_2 hrs_rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
21.4	99.6	E-ATMX-35-raw-cel-1574334880
20.9	99.6	GSM106911	opr2_JA_2 hrs_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
19.3	99.6	GSM106921	opr3_OPDA_0.5 hr_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
19.3	99.6	GSM106917	opr3_JA_22 hrs_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
19.2	99.6	GSM106966	opr3_OPDA_8 hrs_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
19.0	99.5	GSM106912	opr3_JA 8hrs_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
18.2	99.5	E-MEXP-1138-raw-cel-1432773322
18.1	99.5	GSM106825	opr3_0 hr_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
17.5	99.5	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
17.2	99.5	GSM106934	opr3_OPDA_8 hrs_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
16.8	99.5	GSM106828	opr3_0 hr_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
16.8	99.5	GSM106914	opr3_JA_8 hrs_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
16.2	99.5	GSM239254	CaMV::DME stamen	GSE9408	Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
15.7	99.5	GSM106915	opr3_JA_22 hrs_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
15.4	99.5	GSM106924	opr3_OPDA_2 hrs_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
15.3	99.4	GSM106908	opr3_JA_0.5 hr_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
14.9	99.4	E-ATMX-35-raw-cel-1574334848
14.1	99.4	GSM106909	opr3-JA_2 hrs_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
14.0	99.4	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
13.9	99.4	GSM131636	ATGE_73_A	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
13.3	99.4	E-MEXP-1474-raw-cel-1593932577
12.0	99.3	GSM106919	opr3_OPDA_0.5 hr_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
11.5	99.3	E-MEXP-1138-raw-cel-1432773066
10.8	99.2	GSM62695	Columbia flowers_stage 11-12	GSE2848	Auxin Response Factor mediated flower gene expression
9.9	99.1	GSM133773	Lindsey_1-25_torpedo-meristem_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.7	99.1	GSM62699	arf6/arf6 ARF8/arf8 flowers_stage 11-12	GSE2848	Auxin Response Factor mediated flower gene expression
9.7	99.1	E-MEXP-1474-raw-cel-1593932673
9.0	99.1	E-MEXP-1138-raw-cel-1432773034

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.267 2 GO:0006108 The chemical reactions and pathways involving malate, the anion of hydroxybutanedioic acid, a chiral hydroxydicarboxylic acid. The (+) enantiomer is an important intermediate in metabolism as a component of both the TCA cycle and the glyoxylate cycle.
0.143 1 GO:0009932 Growth that occurs specifically at the tip of a cell.
0.118 1 GO:0010053 The process whereby a relatively unspecialized cell in the root epidermis acquires the specialized features of a trichoblast or atrichoblast.

SF	Genes	GO ID	Process Name
0.267	2	GO:0006108	The chemical reactions and pathways involving malate, the anion of hydroxybutanedioic acid, a chiral hydroxydicarboxylic acid. The (+) enantiomer is an important intermediate in metabolism as a component of both the TCA cycle and the glyoxylate cycle.
0.143	1	GO:0009932	Growth that occurs specifically at the tip of a cell.
0.118	1	GO:0010053	The process whereby a relatively unspecialized cell in the root epidermis acquires the specialized features of a trichoblast or atrichoblast.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.029 1 00620 Pyruvate metabolism
0.025 1 00710 Carbon fixation in photosynthetic organisms
0.013 1 01066 Biosynthesis of alkaloids derived from terpenoid and polyketide

SF	Genes	KEGG ID	Pathway name
0.029	1	00620	Pyruvate metabolism
0.025	1	00710	Carbon fixation in photosynthetic organisms
0.013	1	01066	Biosynthesis of alkaloids derived from terpenoid and polyketide

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

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Gene ID	At2g13560
Gene name	malate oxidoreductase, putative
Module size	5 genes
NF	0.29
%ile	34.8

Co-expression analysis

Gene ID At2g13560 Gene name malate oxidoreductase, putative Module size 5 genes NF 0.29 %ile 34.8

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 KEGG0.029100620Pyruvate metabolism0.025100710Carbon fixation in photosynthetic organisms0.013101066Biosynthesis of alkaloids derived from terpenoid and polyketide

Inter-species module comparison

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

Gene ID At2g13560

Gene name malate oxidoreductase, putative

Module size 5 genes

NF 0.29

%ile 34.8

: 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
0.029 1 00620 Pyruvate metabolism
0.025 1 00710 Carbon fixation in photosynthetic organisms
0.013 1 01066 Biosynthesis of alkaloids derived from terpenoid and polyketide

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