CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At1g59940

Gene name ARR3 (RESPONSE REGULATOR 3)

Module size 25 genes

NF 0.40

%ile 55.2

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
0.67 81.6 1.00 At1g59940 842288 ARR3 (RESPONSE REGULATOR 3) Type A response regulator highly similar to bacterial two-component response regulators. Rapidly induced by cytokinin. Involved in red-light signaling. Acts redundantly with ARR3 in the control of circadian period in a cytokinin-independent manner. O.I. H.G. S.X.
0.58 73.8 0.70 At4g37400 829894 CYP81F3 member of CYP81F O.I. H.G. S.X.
0.58 73.8 0.64 At5g57090 835813 EIR1 (ETHYLENE INSENSITIVE ROOT 1) Encodes an auxin efflux carrier that is similar to bacterial membrane transporters. Root-specific role in the transport of auxin. Acts downstream of CTR1 and ethylene biosynthesis, in the same pathway as EIN2 and AUX1, and independent from EIN3 and EIN5/AIN1 pathway. In the root, the protein localizes apically in epidermal and lateral root cap cells and predominantly basally in cortical cells. Functions may be regulated by phosphorylation status. EIR1 expression is induced by brassinolide treatment in the brassinosteroid-insensitive br1 mutant. Gravistimulation resulted in asymmetric PIN2 distribution, with more protein degraded at the upper side of the gravistimulated root. Protein turnover is affected by the proteasome and by endosomal cycling. Plasma membrane-localized PIN proteins mediate a saturable efflux of auxin. PINs mediate auxin efflux from mammalian and yeast cells without needing additional plant-specific factors. The action of PINs in auxin efflux is distinct from PGPs, rate-limiting, specific to auxins and sensitive to auxin transport inhibitors. Membrane sterol composition is essential for the acquisition of PIN2 polarity. O.I. H.G. S.X.
0.56 73.0 0.66 At5g10720 830938 AHK5 (ARABIDOPSIS HISTIDINE KINASE 5) member of Histidine Kinase O.I. H.G. S.X.
0.56 73.0 0.71 At2g24610 816997 ATCNGC14 member of Cyclic nucleotide gated channel family O.I. H.G. S.X.
0.54 69.5 0.68 At3g50640 824227 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;P O.I. H.G. S.X.
0.54 69.5 0.68 At1g53180 841752 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OPMF O.I. H.G. S.X.
0.54 69.5 0.64 At2g24300 816966 calmodulin-binding protein F:calmodulin binding;P:biological_process unknown;C:unknown;PB O.I. H.G. S.X.
0.49 63.5 0.68 At3g54770 824642 RNA recognition motif (RRM)-containing protein F:RNA binding, nucleotide binding, nucleic acid binding;P:unknown;C:cellular_component unknown;MPFOB O.I. H.G. S.X.
0.45 58.3 0.72 At3g01220 821232 ATHB20 (ARABIDOPSIS THALIANA HOMEOBOX PROTEIN 20) Encodes a homeodomain leucine zipper class I (HD-Zip I) protein, its expression is auxin-inducible and dependent on MP gene activity. O.I. H.G. S.X.
0.44 57.2 0.69 At2g45400 819146 BEN1 involved in the regulation of brassinosteroid metabolic pathway O.I. H.G. S.X.
0.44 57.2 0.64 At3g20130 821556 CYP705A22 member of CYP705A O.I. H.G. S.X.
0.42 53.9 0.63 At4g19030 827641 NLM1 an aquaporin whose expression level is reduced by ABA, NaCl, dark, and dessication. is expressed at relatively low levels under normal conditions. Also functions in arsenite transport and tolerance. O.I. H.G. S.X.
0.41 52.4 0.63 At1g73160 843647 glycosyl transferase family 1 protein F:transferase activity, transferring glycosyl groups;P:biosynthetic process;C:unknown;BOAFPM O.I. H.G. S.X.
0.40 50.8 0.63 At2g27000 817242 CYP705A8 member of CYP705A O.I. H.G. S.X.
0.37 45.0 0.69 At1g02810 838078 pectinesterase family protein F:enzyme inhibitor activity, pectinesterase activity;P:cell wall modification;C:endomembrane system, cell wall, plant-type cell wall;PBFMO O.I. H.G. S.X.
0.35 41.6 0.65 At4g28650 828983 leucine-rich repeat transmembrane protein kinase, putative F:protein binding, protein serine/threonine kinase activity, protein kinase activity, ATP binding;P:transmembrane receptor protein tyrosine kinase signaling pathway, protein amino acid phosphorylation;C:endomembrane system;MPOBFVA O.I. H.G. S.X.
0.32 35.7 0.74 At5g14020 831250 - F:unknown;P:N-terminal protein myristoylation;C:vacuole;P O.I. H.G. S.X.
0.30 32.1 0.66 At2g14100 815896 CYP705A13 a member of the cytochrome P450 family O.I. H.G. S.X.
0.29 30.3 0.67 At1g14080 837968 FUT6 (FUCOSYLTRANSFERASE 6) member of Xyloglucan fucosyltransferase family O.I. H.G. S.X.
0.29 30.3 0.66 At5g24100 832475 leucine-rich repeat transmembrane protein kinase, putative F:protein binding, protein serine/threonine kinase activity, protein tyrosine kinase activity, protein kinase activity, ATP binding;P:transmembrane receptor protein tyrosine kinase signaling pathway, protein amino acid phosphorylation;C:endomembrane system;PMOBFVA O.I. H.G. S.X.
0.29 30.3 0.73 At1g11670 837711 MATE efflux family protein F:antiporter activity, drug transporter activity, transporter activity;P:N-terminal protein myristoylation, multidrug transport;C:membrane;BOPFAM O.I. H.G. S.X.
0.27 26.2 0.64 At4g00080 828192 UNE11 (unfertilized embryo sac 11) F:enzyme inhibitor activity, pectinesterase inhibitor activity, pectinesterase activity;P:double fertilization forming a zygote and endosperm;C:endomembrane system;P O.I. H.G. S.X.
0.23 19.3 0.66 At1g15210 838087 PDR7 (PLEIOTROPIC DRUG RESISTANCE 7) F:ATPase activity, coupled to transmembrane movement of substances;P:multidrug transport;C:plasma membrane, chloroplast, membrane;BOMFAPV O.I. H.G. S.X.
0.22 17.5 0.65 At3g20960 821646 CYP705A33 member of CYP705A O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.67	81.6	1.00	At1g59940	842288	ARR3 (RESPONSE REGULATOR 3)	Type A response regulator highly similar to bacterial two-component response regulators. Rapidly induced by cytokinin. Involved in red-light signaling. Acts redundantly with ARR3 in the control of circadian period in a cytokinin-independent manner.	O.I.	H.G.	S.X.
0.58	73.8	0.70	At4g37400	829894	CYP81F3	member of CYP81F	O.I.	H.G.	S.X.
0.58	73.8	0.64	At5g57090	835813	EIR1 (ETHYLENE INSENSITIVE ROOT 1)	Encodes an auxin efflux carrier that is similar to bacterial membrane transporters. Root-specific role in the transport of auxin. Acts downstream of CTR1 and ethylene biosynthesis, in the same pathway as EIN2 and AUX1, and independent from EIN3 and EIN5/AIN1 pathway. In the root, the protein localizes apically in epidermal and lateral root cap cells and predominantly basally in cortical cells. Functions may be regulated by phosphorylation status. EIR1 expression is induced by brassinolide treatment in the brassinosteroid-insensitive br1 mutant. Gravistimulation resulted in asymmetric PIN2 distribution, with more protein degraded at the upper side of the gravistimulated root. Protein turnover is affected by the proteasome and by endosomal cycling. Plasma membrane-localized PIN proteins mediate a saturable efflux of auxin. PINs mediate auxin efflux from mammalian and yeast cells without needing additional plant-specific factors. The action of PINs in auxin efflux is distinct from PGPs, rate-limiting, specific to auxins and sensitive to auxin transport inhibitors. Membrane sterol composition is essential for the acquisition of PIN2 polarity.	O.I.	H.G.	S.X.
0.56	73.0	0.66	At5g10720	830938	AHK5 (ARABIDOPSIS HISTIDINE KINASE 5)	member of Histidine Kinase	O.I.	H.G.	S.X.
0.56	73.0	0.71	At2g24610	816997	ATCNGC14	member of Cyclic nucleotide gated channel family	O.I.	H.G.	S.X.
0.54	69.5	0.68	At3g50640	824227	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;P	O.I.	H.G.	S.X.
0.54	69.5	0.68	At1g53180	841752	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OPMF	O.I.	H.G.	S.X.
0.54	69.5	0.64	At2g24300	816966	calmodulin-binding protein	F:calmodulin binding;P:biological_process unknown;C:unknown;PB	O.I.	H.G.	S.X.
0.49	63.5	0.68	At3g54770	824642	RNA recognition motif (RRM)-containing protein	F:RNA binding, nucleotide binding, nucleic acid binding;P:unknown;C:cellular_component unknown;MPFOB	O.I.	H.G.	S.X.
0.45	58.3	0.72	At3g01220	821232	ATHB20 (ARABIDOPSIS THALIANA HOMEOBOX PROTEIN 20)	Encodes a homeodomain leucine zipper class I (HD-Zip I) protein, its expression is auxin-inducible and dependent on MP gene activity.	O.I.	H.G.	S.X.
0.44	57.2	0.69	At2g45400	819146	BEN1	involved in the regulation of brassinosteroid metabolic pathway	O.I.	H.G.	S.X.
0.44	57.2	0.64	At3g20130	821556	CYP705A22	member of CYP705A	O.I.	H.G.	S.X.
0.42	53.9	0.63	At4g19030	827641	NLM1	an aquaporin whose expression level is reduced by ABA, NaCl, dark, and dessication. is expressed at relatively low levels under normal conditions. Also functions in arsenite transport and tolerance.	O.I.	H.G.	S.X.
0.41	52.4	0.63	At1g73160	843647	glycosyl transferase family 1 protein	F:transferase activity, transferring glycosyl groups;P:biosynthetic process;C:unknown;BOAFPM	O.I.	H.G.	S.X.
0.40	50.8	0.63	At2g27000	817242	CYP705A8	member of CYP705A	O.I.	H.G.	S.X.
0.37	45.0	0.69	At1g02810	838078	pectinesterase family protein	F:enzyme inhibitor activity, pectinesterase activity;P:cell wall modification;C:endomembrane system, cell wall, plant-type cell wall;PBFMO	O.I.	H.G.	S.X.
0.35	41.6	0.65	At4g28650	828983	leucine-rich repeat transmembrane protein kinase, putative	F:protein binding, protein serine/threonine kinase activity, protein kinase activity, ATP binding;P:transmembrane receptor protein tyrosine kinase signaling pathway, protein amino acid phosphorylation;C:endomembrane system;MPOBFVA	O.I.	H.G.	S.X.
0.32	35.7	0.74	At5g14020	831250	-	F:unknown;P:N-terminal protein myristoylation;C:vacuole;P	O.I.	H.G.	S.X.
0.30	32.1	0.66	At2g14100	815896	CYP705A13	a member of the cytochrome P450 family	O.I.	H.G.	S.X.
0.29	30.3	0.67	At1g14080	837968	FUT6 (FUCOSYLTRANSFERASE 6)	member of Xyloglucan fucosyltransferase family	O.I.	H.G.	S.X.
0.29	30.3	0.66	At5g24100	832475	leucine-rich repeat transmembrane protein kinase, putative	F:protein binding, protein serine/threonine kinase activity, protein tyrosine kinase activity, protein kinase activity, ATP binding;P:transmembrane receptor protein tyrosine kinase signaling pathway, protein amino acid phosphorylation;C:endomembrane system;PMOBFVA	O.I.	H.G.	S.X.
0.29	30.3	0.73	At1g11670	837711	MATE efflux family protein	F:antiporter activity, drug transporter activity, transporter activity;P:N-terminal protein myristoylation, multidrug transport;C:membrane;BOPFAM	O.I.	H.G.	S.X.
0.27	26.2	0.64	At4g00080	828192	UNE11 (unfertilized embryo sac 11)	F:enzyme inhibitor activity, pectinesterase inhibitor activity, pectinesterase activity;P:double fertilization forming a zygote and endosperm;C:endomembrane system;P	O.I.	H.G.	S.X.
0.23	19.3	0.66	At1g15210	838087	PDR7 (PLEIOTROPIC DRUG RESISTANCE 7)	F:ATPase activity, coupled to transmembrane movement of substances;P:multidrug transport;C:plasma membrane, chloroplast, membrane;BOMFAPV	O.I.	H.G.	S.X.
0.22	17.5	0.65	At3g20960	821646	CYP705A33	member of CYP705A	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
109.5 99.9 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
78.9 99.9 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
67.1 99.8 GSM311292 Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 2 GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
63.9 99.8 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
62.3 99.8 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
59.1 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
57.0 99.8 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
56.1 99.8 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
55.9 99.8 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
54.9 99.8 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.6 99.8 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
51.2 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
50.9 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
45.6 99.8 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
45.2 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.5 99.8 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
41.0 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.1 99.7 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
35.8 99.7 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
34.8 99.7 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
29.3 99.7 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
28.4 99.7 GSM133757 Lindsey_1-8_heart-stage-cotyledon_Rep2_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
24.4 99.6 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
23.4 99.6 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
20.9 99.6 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.5 99.5 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
17.3 99.5 E-MEXP-509-raw-cel-829148561
17.0 99.5 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.5 99.5 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.2 99.5 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.8 99.4 GSM265423 Arabidopsis, root, longitudinal zone 3, standard conditions, rep 2 GSE10497 Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
14.3 99.4 E-MEXP-509-raw-cel-829148348
11.7 99.3 GSM134301 Penfield_1-3_endosperm-control_Rep3_ATH1 GSE5751 The early post-germinative embryo and endosperm transcriptomes in Arabidopsis
11.7 99.3 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
11.4 99.3 E-MEXP-509-raw-cel-829148420
11.3 99.3 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
11.3 99.3 E-MEXP-509-raw-cel-829148456
10.2 99.2 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.8 99.1 GSM134300 Penfield_1-2_endosperm-control_Rep2_ATH1 GSE5751 The early post-germinative embryo and endosperm transcriptomes in Arabidopsis
9.6 99.1 GSM290756 root - 01% oxygen - 30min - D GSE11558 transcript profiling of the adaptive response to decreases in oxygen concentration in the roots of Arabidopsis plants
8.8 99.0 GSM290755 root - 01% oxygen - 2h - F GSE11558 transcript profiling of the adaptive response to decreases in oxygen concentration in the roots of Arabidopsis plants
8.8 99.0 E-MEXP-509-raw-cel-829148525

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
109.5	99.9	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
78.9	99.9	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
67.1	99.8	GSM311292	Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 2	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
63.9	99.8	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
62.3	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
59.1	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
57.0	99.8	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
56.1	99.8	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
55.9	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
54.9	99.8	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.6	99.8	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
51.2	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
50.9	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
45.6	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
45.2	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.5	99.8	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
41.0	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.1	99.7	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
35.8	99.7	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
34.8	99.7	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
29.3	99.7	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
28.4	99.7	GSM133757	Lindsey_1-8_heart-stage-cotyledon_Rep2_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
24.4	99.6	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
23.4	99.6	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
20.9	99.6	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.5	99.5	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
17.3	99.5	E-MEXP-509-raw-cel-829148561
17.0	99.5	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.5	99.5	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.2	99.5	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.8	99.4	GSM265423	Arabidopsis, root, longitudinal zone 3, standard conditions, rep 2	GSE10497	Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
14.3	99.4	E-MEXP-509-raw-cel-829148348
11.7	99.3	GSM134301	Penfield_1-3_endosperm-control_Rep3_ATH1	GSE5751	The early post-germinative embryo and endosperm transcriptomes in Arabidopsis
11.7	99.3	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
11.4	99.3	E-MEXP-509-raw-cel-829148420
11.3	99.3	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
11.3	99.3	E-MEXP-509-raw-cel-829148456
10.2	99.2	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.8	99.1	GSM134300	Penfield_1-2_endosperm-control_Rep2_ATH1	GSE5751	The early post-germinative embryo and endosperm transcriptomes in Arabidopsis
9.6	99.1	GSM290756	root - 01% oxygen - 30min - D	GSE11558	transcript profiling of the adaptive response to decreases in oxygen concentration in the roots of Arabidopsis plants
8.8	99.0	GSM290755	root - 01% oxygen - 2h - F	GSE11558	transcript profiling of the adaptive response to decreases in oxygen concentration in the roots of Arabidopsis plants
8.8	99.0	E-MEXP-509-raw-cel-829148525

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.077 1 GO:0010422 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of brassinosteroids.
0.071 1 GO:0015700 The directed movement of arsenite into, out of, within or between cells.
0.065 1 GO:0016131 The chemical reactions and pathways involving brassinosteroids, any of a group of steroid derivatives that occur at very low concentrations in plant tissues and may have hormone-like effects.

SF	Genes	GO ID	Process Name
0.077	1	GO:0010422	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of brassinosteroids.
0.071	1	GO:0015700	The directed movement of arsenite into, out of, within or between cells.
0.065	1	GO:0016131	The chemical reactions and pathways involving brassinosteroids, any of a group of steroid derivatives that occur at very low concentrations in plant tissues and may have hormone-like effects.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.022 1 00945 Stilbenoid, diarylheptanoid and gingerol biosynthesis
0.021 1 00903 Limonene and pinene degradation

SF	Genes	KEGG ID	Pathway name	Link to KEGG
0.022	1	00945	Stilbenoid, diarylheptanoid and gingerol biosynthesis
0.021	1	00903	Limonene and pinene degradation

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	At1g59940
Gene name	ARR3 (RESPONSE REGULATOR 3)
Module size	25 genes
NF	0.40
%ile	55.2

Co-expression analysis

Gene ID At1g59940 Gene name ARR3 (RESPONSE REGULATOR 3) Module size 25 genes NF 0.40 %ile 55.2

Co-expression network

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

Co-expressed genes

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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 KEGG0.022100945Stilbenoid, diarylheptanoid and gingerol biosynthesis0.021100903Limonene and pinene degradation

Inter-species module comparison

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

Gene ID At1g59940

Gene name ARR3 (RESPONSE REGULATOR 3)

Module size 25 genes

NF 0.40

%ile 55.2

: 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
0.022 1 00945 Stilbenoid, diarylheptanoid and gingerol biosynthesis
0.021 1 00903 Limonene and pinene degradation

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