CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At1g60590

Gene name polygalacturonase, putative / pectinase, putative

Module size 42 genes

NF 0.22

%ile 21.1

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 At1g60590 842353 polygalacturonase, putative / pectinase, putative F:polygalacturonase activity;P:carbohydrate metabolic process;C:unknown;FPBMOVA O.I. H.G. S.X.
0.47 61.2 0.78 At5g02830 831772 pentatricopeptide (PPR) repeat-containing protein F:unknown;P:biological_process unknown;C:chloroplast;POMFBA O.I. H.G. S.X.
0.41 52.4 0.78 At4g28080 828923 binding F:binding;P:unknown;C:unknown;MBFOPAV O.I. H.G. S.X.
0.39 48.4 0.77 At2g32640 817824 unknown protein F:unknown;P:unknown;C:chloroplast;BPO O.I. H.G. S.X.
0.38 46.7 0.76 At3g02830 821230 ZFN1 (ZINC FINGER PROTEIN 1) Encodes a zinc finger protein. O.I. H.G. S.X.
0.36 43.6 0.73 At3g03770 821164 leucine-rich repeat transmembrane protein kinase, putative F: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;PMOBFVA O.I. H.G. S.X.
0.34 39.8 0.77 At1g23205 838929 invertase/pectin methylesterase inhibitor family protein F:enzyme inhibitor activity, pectinesterase inhibitor activity, pectinesterase activity;P:biological_process unknown;C:endomembrane system;P O.I. H.G. S.X.
0.30 32.1 0.72 At5g21100 832234 L-ascorbate oxidase, putative F:oxidoreductase activity, copper ion binding, L-ascorbate oxidase activity;P:oxidation reduction;C:plant-type cell wall;BFPMOA O.I. H.G. S.X.
0.29 30.3 0.75 At1g15290 838097 binding F:binding;P:biological_process unknown;C:cellular_component unknown;MBOFPAV O.I. H.G. S.X.
0.29 30.3 0.74 At5g20220 832144 zinc knuckle (CCHC-type) family protein F:unfolded protein binding, heat shock protein binding, zinc ion binding, nucleic acid binding;P:protein folding;C:unknown;VMFOPB O.I. H.G. S.X.
0.28 30.3 0.74 At2g37450 818322 nodulin MtN21 family protein F:unknown;P:unknown;C:endomembrane system, membrane;PBOA O.I. H.G. S.X.
0.28 30.3 0.74 At5g64940 836618 ATATH13 Encodes a member of ATH subfamily of ATP-binding cassette (ABC) proteins. O.I. H.G. S.X.
0.27 26.2 0.73 At1g01790 837332 KEA1 (K EFFLUX ANTIPORTER 1) K efflux antiporter KEA1 O.I. H.G. S.X.
0.26 24.4 0.75 At3g22150 821779 pentatricopeptide (PPR) repeat-containing protein F:unknown;P:unknown;C:chloroplast;POMFBA O.I. H.G. S.X.
0.26 24.4 0.74 At1g62750 842573 SCO1 (SNOWY COTYLEDON 1) Nuclear encoded protein consists of the five domains conserved in EF-G proteins, with two GTP-binding sites in the first domain, and an additional transit peptide at the N-terminus. Localized in chloroplasts. Point mutation results in a delay in the onset of germination. At early developmental stage embryos still contain undifferentiated proplastids. The greening of cotyledons is severely impaired in light-grown mutant sco1 seedlings, whereas the following true leaves develop normally as in wild-type plants. O.I. H.G. S.X.
0.25 22.6 0.74 At4g29060 829027 emb2726 (embryo defective 2726) F:RNA binding, translation elongation factor activity;P:embryonic development ending in seed dormancy, translational elongation, response to cadmium ion;C:chloroplast stroma, chloroplast, chloroplast envelope;BOMFPAV O.I. H.G. S.X.
0.25 22.6 0.74 At1g49010 841324 myb family transcription factor F:transcription factor activity, DNA binding;P:in 6 processes;C:unknown;PMOFBV O.I. H.G. S.X.
0.24 20.7 0.74 At3g26570 822265 PHT2 low affinity phosphate transporter O.I. H.G. S.X.
0.23 19.3 0.73 At4g34610 829613 BLH6 (BELL1-LIKE HOMEODOMAIN 6) F:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent, regulation of transcription;C:nucleus;PMFOB O.I. H.G. S.X.
0.23 19.3 0.73 At1g01320 839293 tetratricopeptide repeat (TPR)-containing protein F:binding;P:unknown;C:cellular_component unknown;MBFOPAV O.I. H.G. S.X.
0.23 19.3 0.73 At1g07010 837211 calcineurin-like phosphoesterase family protein F:hydrolase activity, protein serine/threonine phosphatase activity;P:biological_process unknown;C:peroxisome;OBPFAV O.I. H.G. S.X.
0.22 17.5 0.73 At1g44000 841000 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;PBO O.I. H.G. S.X.
0.22 17.5 0.73 At1g12800 837836 S1 RNA-binding domain-containing protein F:RNA binding;P:unknown;C:chloroplast;BOMFPAV O.I. H.G. S.X.
0.21 15.8 0.72 At1g23740 838984 oxidoreductase, zinc-binding dehydrogenase family protein F:oxidoreductase activity, binding, catalytic activity, zinc ion binding;P:response to cold;C:in 6 components;BOFMPAV O.I. H.G. S.X.
0.21 15.8 0.72 At1g71810 843511 ABC1 family protein F:protein kinase activity, ATP binding;P:protein amino acid phosphorylation;C:chloroplast, plastoglobule;OBMPFAV O.I. H.G. S.X.
0.19 12.7 0.72 At1g17220 838293 FUG1 (fu-gaeri1) Encodes a chloroplast localized protein with similarity to translation initiation factor 2. Can complement loss of INFB in E.coli suggesting FUG1 does function as a translation initiation factor in vivo. Identified as a suppressor of the leaf variegation mutant var2-6. Suppression is only seen in hypomorphs as complete loss of function alleles are embryo lethal. O.I. H.G. S.X.
0.19 12.7 0.72 At1g31800 840067 CYP97A3 (CYTOCHROME P450-TYPE MONOOXYGENASE 97A3) Encodes a protein with β-ring carotenoid hydroxylase activity. O.I. H.G. S.X.
0.19 12.7 0.76 At3g10840 820253 hydrolase, alpha/beta fold family protein F:hydrolase activity, catalytic activity;P:unknown;C:chloroplast envelope;BOMPFAV O.I. H.G. S.X.
0.18 11.4 0.73 At3g47430 823897 PEX11B member of the peroxin11 (PEX11) gene family, located on the peroxisome membrane, controls peroxisome proliferation. O.I. H.G. S.X.
0.17 10.2 0.72 At5g13630 831207 GUN5 (GENOMES UNCOUPLED 5) Encodes magnesium chelatase involved in plastid-to-nucleus signal transduction. O.I. H.G. S.X.
0.17 10.2 0.72 At4g09350 826517 DNAJ heat shock N-terminal domain-containing protein F:heat shock protein binding;P:protein folding;C:chloroplast;BOMFPAV O.I. H.G. S.X.
0.17 10.2 0.72 At1g71720 843502 S1 RNA-binding domain-containing protein F:RNA binding;P:unknown;C:chloroplast;BOPMAF O.I. H.G. S.X.
0.16 8.8 0.73 At3g15520 820791 peptidyl-prolyl cis-trans isomerase TLP38, chloroplast / thylakoid lumen PPIase of 38 kDa / cyclophilin / rotamase F:peptidyl-prolyl cis-trans isomerase activity;P:unknown;C:thylakoid, thylakoid lumen, chloroplast thylakoid membrane, chloroplast thylakoid lumen, chloroplast;BOPA O.I. H.G. S.X.
0.16 8.8 0.72 At5g62140 836334 unknown protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast;PBO O.I. H.G. S.X.
0.15 7.8 0.72 At2g41680 818766 NTRC (NADPH-DEPENDENT THIOREDOXIN REDUCTASE C) Encodes a NADPH thioredoxin reductase involved in chloroplast protection against oxidative damage. O.I. H.G. S.X.
0.15 7.8 0.72 At4g26520 828758 fructose-bisphosphate aldolase, cytoplasmic F:fructose-bisphosphate aldolase activity;P:pentose-phosphate shunt, response to hypoxia;C:unknown;OMBPF O.I. H.G. S.X.
0.14 6.8 0.74 At5g17230 831587 phytoene synthase (PSY) / geranylgeranyl-diphosphate geranylgeranyl transferase Encodes phytoene synthase. O.I. H.G. S.X.
0.14 6.8 0.73 At5g62840 836405 phosphoglycerate/bisphosphoglycerate mutase family protein F:catalytic activity;P:metabolic process;C:chloroplast;PBOF O.I. H.G. S.X.
0.12 4.9 0.73 At5g16715 831533 EMB2247 (embryo defective 2247) F:valine-tRNA ligase activity, nucleotide binding, aminoacyl-tRNA ligase activity, ATP binding;P:embryonic development ending in seed dormancy, tRNA aminoacylation for protein translation;C:chloroplast stroma, chloroplast;OBMAFP O.I. H.G. S.X.
0.11 4.1 0.72 At1g32080 840100 membrane protein, putative F:unknown;P:unknown;C:chloroplast, chloroplast inner membrane, membrane, chloroplast envelope;BOFPA O.I. H.G. S.X.
0.09 2.8 0.73 At1g14345 837996 oxidoreductase F:oxidoreductase activity;P:oxidation reduction;C:chloroplast thylakoid membrane, chloroplast, membrane;OBP O.I. H.G. S.X.
0.09 2.8 0.72 At1g60000 842294 29 kDa ribonucleoprotein, chloroplast, putative / RNA-binding protein cp29, putative F:RNA binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:chloroplast;MPOFBA 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	At1g60590	842353	polygalacturonase, putative / pectinase, putative	F:polygalacturonase activity;P:carbohydrate metabolic process;C:unknown;FPBMOVA	O.I.	H.G.	S.X.
0.47	61.2	0.78	At5g02830	831772	pentatricopeptide (PPR) repeat-containing protein	F:unknown;P:biological_process unknown;C:chloroplast;POMFBA	O.I.	H.G.	S.X.
0.41	52.4	0.78	At4g28080	828923	binding	F:binding;P:unknown;C:unknown;MBFOPAV	O.I.	H.G.	S.X.
0.39	48.4	0.77	At2g32640	817824	unknown protein	F:unknown;P:unknown;C:chloroplast;BPO	O.I.	H.G.	S.X.
0.38	46.7	0.76	At3g02830	821230	ZFN1 (ZINC FINGER PROTEIN 1)	Encodes a zinc finger protein.	O.I.	H.G.	S.X.
0.36	43.6	0.73	At3g03770	821164	leucine-rich repeat transmembrane protein kinase, putative	F: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;PMOBFVA	O.I.	H.G.	S.X.
0.34	39.8	0.77	At1g23205	838929	invertase/pectin methylesterase inhibitor family protein	F:enzyme inhibitor activity, pectinesterase inhibitor activity, pectinesterase activity;P:biological_process unknown;C:endomembrane system;P	O.I.	H.G.	S.X.
0.30	32.1	0.72	At5g21100	832234	L-ascorbate oxidase, putative	F:oxidoreductase activity, copper ion binding, L-ascorbate oxidase activity;P:oxidation reduction;C:plant-type cell wall;BFPMOA	O.I.	H.G.	S.X.
0.29	30.3	0.75	At1g15290	838097	binding	F:binding;P:biological_process unknown;C:cellular_component unknown;MBOFPAV	O.I.	H.G.	S.X.
0.29	30.3	0.74	At5g20220	832144	zinc knuckle (CCHC-type) family protein	F:unfolded protein binding, heat shock protein binding, zinc ion binding, nucleic acid binding;P:protein folding;C:unknown;VMFOPB	O.I.	H.G.	S.X.
0.28	30.3	0.74	At2g37450	818322	nodulin MtN21 family protein	F:unknown;P:unknown;C:endomembrane system, membrane;PBOA	O.I.	H.G.	S.X.
0.28	30.3	0.74	At5g64940	836618	ATATH13	Encodes a member of ATH subfamily of ATP-binding cassette (ABC) proteins.	O.I.	H.G.	S.X.
0.27	26.2	0.73	At1g01790	837332	KEA1 (K EFFLUX ANTIPORTER 1)	K efflux antiporter KEA1	O.I.	H.G.	S.X.
0.26	24.4	0.75	At3g22150	821779	pentatricopeptide (PPR) repeat-containing protein	F:unknown;P:unknown;C:chloroplast;POMFBA	O.I.	H.G.	S.X.
0.26	24.4	0.74	At1g62750	842573	SCO1 (SNOWY COTYLEDON 1)	Nuclear encoded protein consists of the five domains conserved in EF-G proteins, with two GTP-binding sites in the first domain, and an additional transit peptide at the N-terminus. Localized in chloroplasts. Point mutation results in a delay in the onset of germination. At early developmental stage embryos still contain undifferentiated proplastids. The greening of cotyledons is severely impaired in light-grown mutant sco1 seedlings, whereas the following true leaves develop normally as in wild-type plants.	O.I.	H.G.	S.X.
0.25	22.6	0.74	At4g29060	829027	emb2726 (embryo defective 2726)	F:RNA binding, translation elongation factor activity;P:embryonic development ending in seed dormancy, translational elongation, response to cadmium ion;C:chloroplast stroma, chloroplast, chloroplast envelope;BOMFPAV	O.I.	H.G.	S.X.
0.25	22.6	0.74	At1g49010	841324	myb family transcription factor	F:transcription factor activity, DNA binding;P:in 6 processes;C:unknown;PMOFBV	O.I.	H.G.	S.X.
0.24	20.7	0.74	At3g26570	822265	PHT2	low affinity phosphate transporter	O.I.	H.G.	S.X.
0.23	19.3	0.73	At4g34610	829613	BLH6 (BELL1-LIKE HOMEODOMAIN 6)	F:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent, regulation of transcription;C:nucleus;PMFOB	O.I.	H.G.	S.X.
0.23	19.3	0.73	At1g01320	839293	tetratricopeptide repeat (TPR)-containing protein	F:binding;P:unknown;C:cellular_component unknown;MBFOPAV	O.I.	H.G.	S.X.
0.23	19.3	0.73	At1g07010	837211	calcineurin-like phosphoesterase family protein	F:hydrolase activity, protein serine/threonine phosphatase activity;P:biological_process unknown;C:peroxisome;OBPFAV	O.I.	H.G.	S.X.
0.22	17.5	0.73	At1g44000	841000	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;PBO	O.I.	H.G.	S.X.
0.22	17.5	0.73	At1g12800	837836	S1 RNA-binding domain-containing protein	F:RNA binding;P:unknown;C:chloroplast;BOMFPAV	O.I.	H.G.	S.X.
0.21	15.8	0.72	At1g23740	838984	oxidoreductase, zinc-binding dehydrogenase family protein	F:oxidoreductase activity, binding, catalytic activity, zinc ion binding;P:response to cold;C:in 6 components;BOFMPAV	O.I.	H.G.	S.X.
0.21	15.8	0.72	At1g71810	843511	ABC1 family protein	F:protein kinase activity, ATP binding;P:protein amino acid phosphorylation;C:chloroplast, plastoglobule;OBMPFAV	O.I.	H.G.	S.X.
0.19	12.7	0.72	At1g17220	838293	FUG1 (fu-gaeri1)	Encodes a chloroplast localized protein with similarity to translation initiation factor 2. Can complement loss of INFB in E.coli suggesting FUG1 does function as a translation initiation factor in vivo. Identified as a suppressor of the leaf variegation mutant var2-6. Suppression is only seen in hypomorphs as complete loss of function alleles are embryo lethal.	O.I.	H.G.	S.X.
0.19	12.7	0.72	At1g31800	840067	CYP97A3 (CYTOCHROME P450-TYPE MONOOXYGENASE 97A3)	Encodes a protein with β-ring carotenoid hydroxylase activity.	O.I.	H.G.	S.X.
0.19	12.7	0.76	At3g10840	820253	hydrolase, alpha/beta fold family protein	F:hydrolase activity, catalytic activity;P:unknown;C:chloroplast envelope;BOMPFAV	O.I.	H.G.	S.X.
0.18	11.4	0.73	At3g47430	823897	PEX11B	member of the peroxin11 (PEX11) gene family, located on the peroxisome membrane, controls peroxisome proliferation.	O.I.	H.G.	S.X.
0.17	10.2	0.72	At5g13630	831207	GUN5 (GENOMES UNCOUPLED 5)	Encodes magnesium chelatase involved in plastid-to-nucleus signal transduction.	O.I.	H.G.	S.X.
0.17	10.2	0.72	At4g09350	826517	DNAJ heat shock N-terminal domain-containing protein	F:heat shock protein binding;P:protein folding;C:chloroplast;BOMFPAV	O.I.	H.G.	S.X.
0.17	10.2	0.72	At1g71720	843502	S1 RNA-binding domain-containing protein	F:RNA binding;P:unknown;C:chloroplast;BOPMAF	O.I.	H.G.	S.X.
0.16	8.8	0.73	At3g15520	820791	peptidyl-prolyl cis-trans isomerase TLP38, chloroplast / thylakoid lumen PPIase of 38 kDa / cyclophilin / rotamase	F:peptidyl-prolyl cis-trans isomerase activity;P:unknown;C:thylakoid, thylakoid lumen, chloroplast thylakoid membrane, chloroplast thylakoid lumen, chloroplast;BOPA	O.I.	H.G.	S.X.
0.16	8.8	0.72	At5g62140	836334	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;PBO	O.I.	H.G.	S.X.
0.15	7.8	0.72	At2g41680	818766	NTRC (NADPH-DEPENDENT THIOREDOXIN REDUCTASE C)	Encodes a NADPH thioredoxin reductase involved in chloroplast protection against oxidative damage.	O.I.	H.G.	S.X.
0.15	7.8	0.72	At4g26520	828758	fructose-bisphosphate aldolase, cytoplasmic	F:fructose-bisphosphate aldolase activity;P:pentose-phosphate shunt, response to hypoxia;C:unknown;OMBPF	O.I.	H.G.	S.X.
0.14	6.8	0.74	At5g17230	831587	phytoene synthase (PSY) / geranylgeranyl-diphosphate geranylgeranyl transferase	Encodes phytoene synthase.	O.I.	H.G.	S.X.
0.14	6.8	0.73	At5g62840	836405	phosphoglycerate/bisphosphoglycerate mutase family protein	F:catalytic activity;P:metabolic process;C:chloroplast;PBOF	O.I.	H.G.	S.X.
0.12	4.9	0.73	At5g16715	831533	EMB2247 (embryo defective 2247)	F:valine-tRNA ligase activity, nucleotide binding, aminoacyl-tRNA ligase activity, ATP binding;P:embryonic development ending in seed dormancy, tRNA aminoacylation for protein translation;C:chloroplast stroma, chloroplast;OBMAFP	O.I.	H.G.	S.X.
0.11	4.1	0.72	At1g32080	840100	membrane protein, putative	F:unknown;P:unknown;C:chloroplast, chloroplast inner membrane, membrane, chloroplast envelope;BOFPA	O.I.	H.G.	S.X.
0.09	2.8	0.73	At1g14345	837996	oxidoreductase	F:oxidoreductase activity;P:oxidation reduction;C:chloroplast thylakoid membrane, chloroplast, membrane;OBP	O.I.	H.G.	S.X.
0.09	2.8	0.72	At1g60000	842294	29 kDa ribonucleoprotein, chloroplast, putative / RNA-binding protein cp29, putative	F:RNA binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:chloroplast;MPOFBA	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
47.4 99.8 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
45.8 99.8 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
43.4 99.8 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
41.6 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
39.4 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.5 99.8 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
38.2 99.8 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.2 99.8 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
37.0 99.7 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
36.4 99.7 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
36.0 99.7 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.3 99.7 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.3 99.7 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.8 99.7 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
32.5 99.7 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
32.5 99.7 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
31.2 99.7 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
30.7 99.7 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
29.2 99.7 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
28.6 99.7 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
26.5 99.7 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
26.4 99.7 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
24.4 99.6 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
23.9 99.6 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
18.6 99.5 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
15.0 99.4 E-ATMX-33-raw-cel-1562596241
13.2 99.4 GSM176876 AWP_AL_Txed_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
10.8 99.2 E-ATMX-31-raw-cel-1516947916
10.5 99.2 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
47.4	99.8	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
45.8	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
43.4	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
41.6	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
39.4	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.5	99.8	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
38.2	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.2	99.8	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
37.0	99.7	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
36.4	99.7	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
36.0	99.7	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.3	99.7	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.3	99.7	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.8	99.7	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
32.5	99.7	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
32.5	99.7	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
31.2	99.7	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
30.7	99.7	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
29.2	99.7	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
28.6	99.7	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
26.5	99.7	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
26.4	99.7	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
24.4	99.6	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
23.9	99.6	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
18.6	99.5	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
15.0	99.4	E-ATMX-33-raw-cel-1562596241
13.2	99.4	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
10.8	99.2	E-ATMX-31-raw-cel-1516947916
10.5	99.2	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.073 2 GO:0016117 The chemical reactions and pathways resulting in the formation of carotenoids, tetraterpenoid compounds in which two units of 4 isoprenoid residues joined head-to-tail are themselves joined tail-to-tail.
0.043 1 GO:0042744 The chemical reactions and pathways resulting in the breakdown of hydrogen peroxide (H2O2).
0.042 1 GO:0016123 The chemical reactions and pathways resulting in the formation of xanthophylls, oxygen-containing carotenoids.

SF	Genes	GO ID	Process Name
0.073	2	GO:0016117	The chemical reactions and pathways resulting in the formation of carotenoids, tetraterpenoid compounds in which two units of 4 isoprenoid residues joined head-to-tail are themselves joined tail-to-tail.
0.043	1	GO:0042744	The chemical reactions and pathways resulting in the breakdown of hydrogen peroxide (H2O2).
0.042	1	GO:0016123	The chemical reactions and pathways resulting in the formation of xanthophylls, oxygen-containing carotenoids.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.031 1 00906 Carotenoid biosynthesis
0.029 1 00860 Porphyrin and chlorophyll metabolism
0.027 1 00290 Valine, leucine and isoleucine biosynthesis

SF	Genes	KEGG ID	Pathway name
0.031	1	00906	Carotenoid biosynthesis
0.029	1	00860	Porphyrin and chlorophyll metabolism
0.027	1	00290	Valine, leucine and isoleucine biosynthesis

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	At1g60590
Gene name	polygalacturonase, putative / pectinase, putative
Module size	42 genes
NF	0.22
%ile	21.1

Co-expression analysis

Gene ID At1g60590 Gene name polygalacturonase, putative / pectinase, putative Module size 42 genes NF 0.22 %ile 21.1

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 KEGG0.031100906Carotenoid biosynthesis0.029100860Porphyrin and chlorophyll metabolism0.027100290Valine, leucine and isoleucine biosynthesis

Inter-species module comparison

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

Gene ID At1g60590

Gene name polygalacturonase, putative / pectinase, putative

Module size 42 genes

NF 0.22

%ile 21.1

: 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
0.031 1 00906 Carotenoid biosynthesis
0.029 1 00860 Porphyrin and chlorophyll metabolism
0.027 1 00290 Valine, leucine and isoleucine biosynthesis

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