CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At1g79040

Gene name PSBR (photosystem II subunit R)

Module size 40 genes

NF 0.85

%ile 96.8

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
0.87 93.5 1.00 At1g79040 844245 PSBR (photosystem II subunit R) Encodes for the 10 kDa PsbR subunit of photosystem II (PSII). This subunit appears to be involved in the stable assembly of PSII, particularly that of the oxygen-evolving complex subunit PsbP. Mutants defective in this gene have reduced amounts of subunits PsbP and PsbQ in PSII. In turn, assembly of PsbR is dependent on the presence of PsbJ. O.I. H.G. S.X.
0.96 97.3 0.98 At1g30380 839918 PSAK (photosystem I subunit K) Encodes subunit K of photosystem I reaction center. O.I. H.G. S.X.
0.95 97.0 0.96 At5g66570 836789 PSBO1 (PS II OXYGEN-EVOLVING COMPLEX 1) Encodes a protein which is an extrinsic subunit of photosystem II and which has been proposed to play a central role in stabilization of the catalytic manganese cluster. In Arabidopsis thaliana the PsbO proteins are encoded by two genes: psbO1 and psbO2. PsbO1 is the major isoform in the wild-type. O.I. H.G. S.X.
0.94 96.7 0.97 At4g12800 826892 PSAL (photosystem I subunit L) Encodes subunit L of photosystem I reaction center. O.I. H.G. S.X.
0.94 96.7 0.97 At4g28750 828996 PSAE-1 (PSA E1 KNOCKOUT) mutant has Decreased effective quantum yield of photosystem II; Pale green plants; Reduced growth rate; Subunit E of Photosystem I O.I. H.G. S.X.
0.94 96.7 0.96 At5g01530 830325 chlorophyll A-B binding protein CP29 (LHCB4) F:chlorophyll binding;P:response to blue light, response to red light, response to far red light, photosynthesis;C:in 6 components;POM O.I. H.G. S.X.
0.94 96.7 0.94 At4g02770 828183 PSAD-1 (photosystem I subunit D-1) Encodes a protein predicted by sequence similarity with spinach PsaD to be photosystem I reaction center subunit II (PsaD1) O.I. H.G. S.X.
0.93 96.4 0.97 At3g54890 824654 LHCA1 Encodes a component of the light harvesting complex associated with photosystem I. O.I. H.G. S.X.
0.92 96.0 0.97 At1g06680 837178 PSBP-1 (PHOTOSYSTEM II SUBUNIT P-1) Encodes a 23 kD extrinsic protein that is part of photosystem II and participates in the regulation of oxygen evolution. O.I. H.G. S.X.
0.92 96.0 0.96 At1g31330 840021 PSAF (photosystem I subunit F) Encodes subunit F of photosystem I. O.I. H.G. S.X.
0.92 96.0 0.96 At5g46110 834652 APE2 (ACCLIMATION OF PHOTOSYNTHESIS TO ENVIRONMENT 2) mutant has Altered acclimation responses; Chloroplast Triose Phosphate Translocator O.I. H.G. S.X.
0.91 95.6 0.97 At1g61520 842446 LHCA3 PSI type III chlorophyll a/b-binding protein (Lhca31) O.I. H.G. S.X.
0.91* 95.6 0.97 At1g55670 842016 PSAG (PHOTOSYSTEM I SUBUNIT G) Encodes subunit G of photosystem I, an 11-kDa membrane protein that plays an important role in electron transport between plastocyanin and PSI and is involved in the stability of the PSI complex. PSI-G subunit is bound to PSI-B and is in contact with Lhca1. The protein inserts into thylakoids by a direct or "spontaneous" pathway that does not involve the activities of any known chloroplast protein-targeting machinery. PSI-G appears to be directly or indirectly involved in the interaction between Photosystem I and plastocyanin. O.I. H.G. S.X.
0.91 95.6 0.96 At5g64040 836525 PSAN Encodes the only subunit of photosystem I located entirely in the thylakoid lumen. May be involved in the interaction between plastocyanin and the photosystem I complex. O.I. H.G. S.X.
0.91 95.6 0.96 At4g05180 825866 PSBQ-2 Encodes the PsbQ subunit of the oxygen evolving complex of photosystem II. O.I. H.G. S.X.
0.91 95.6 0.97 At2g06520 815210 PSBX (photosystem II subunit X) Encodes a protein with sequence similarity to the spinach photosystem II subunit PsbX. O.I. H.G. S.X.
0.91 95.6 0.96 At3g47470 823901 LHCA4 (LIGHT-HARVESTING CHLOROPHYLL-PROTEIN COMPLEX I SUBUNIT A4) Encodes a chlorophyll a/b-binding protein that is more similar to the PSI Cab proteins than the PSII cab proteins. The predicted protein is about 20 amino acids shorter than most known Cab proteins. O.I. H.G. S.X.
0.90 95.1 0.96 At1g20340 838622 DRT112 recombination and DNA-damage resistance protein (DRT112) One of two Arabidopsis plastocyanin genes. Predominant form, expressed 10x higher than PETE1. PETE2 is thought to be post-transcriptionally regulated via copper accumulation and is involved in copper homeostasis. O.I. H.G. S.X.
0.90 95.1 0.97 At1g29910 839869 CAB3 (CHLOROPHYLL A/B BINDING PROTEIN 3) member of Chlorophyll a/b-binding protein family O.I. H.G. S.X.
0.90 95.1 0.96 At5g54270 835515 LHCB3 (LIGHT-HARVESTING CHLOROPHYLL B-BINDING PROTEIN 3) Lhcb3 protein is a component of the main light harvesting chlorophyll a/b-protein complex of Photosystem II (LHC II). O.I. H.G. S.X.
0.88 94.0 0.95 At1g52230 841653 PSAH2 (PHOTOSYSTEM I SUBUNIT H2) F:molecular_function unknown;P:photosynthesis;C:in 6 components;PO O.I. H.G. S.X.
0.88 94.0 0.95 At4g38970 830052 fructose-bisphosphate aldolase, putative Protein is tyrosine-phosphorylated and its phosphorylation state is modulated in response to ABA in Arabidopsis thaliana seeds. O.I. H.G. S.X.
0.87 93.5 0.96 At3g16140 820859 PSAH-1 (photosystem I subunit H-1) Encodes subunit H of photosystem I reaction center subunit VI. O.I. H.G. S.X.
0.87 93.5 0.98 At4g10340 826626 LHCB5 (LIGHT HARVESTING COMPLEX OF PHOTOSYSTEM II 5) photosystem II encoding the light-harvesting chlorophyll a/b binding protein CP26 of the antenna system of the photosynthetic apparatus O.I. H.G. S.X.
0.85 92.4 0.94 At1g15820 838151 LHCB6 (LIGHT HARVESTING COMPLEX PSII SUBUNIT 6) Lhcb6 protein (Lhcb6), light harvesting complex of photosystem II. O.I. H.G. S.X.
0.84 91.9 0.96 At2g39730 818558 RCA (RUBISCO ACTIVASE) Rubisco activase, a nuclear-encoded chloroplast protein that consists of two isoforms arising from alternative splicing in most plants. Required for the light activation of rubisco. O.I. H.G. S.X.
0.82 90.9 0.95 At1g67740 843099 PSBY PsbY precursor (psbY) mRNA. This single nuclear gene is imported into the chloroplasts where it is processed into two integral membrane proteins with identical topology (PsbY-1 and PsbY-2). The protein appears to bind manganese but its role is not well understood. O.I. H.G. S.X.
0.79 89.1 0.96 At4g03280 827996 PETC (PHOTOSYNTHETIC ELECTRON TRANSFER C) Encodes the Rieske FeS center of cytochrome b6f complex. Gene is expressed in shoot but not in root. Mutant has reduced electron transport at saturating light intensities and Q-cycle activity is hypersensitive to acidification of the thylakoid lumen. O.I. H.G. S.X.
0.79 89.1 0.96 At4g04640 825797 ATPC1 One of two genes (with ATPC2) encoding the gamma subunit of Arabidopsis chloroplast ATP synthase. O.I. H.G. S.X.
0.79 89.1 0.97 At2g26500 817191 cytochrome b6f complex subunit (petM), putative F:plastoquinol-plastocyanin reductase activity;P:unknown;C:chloroplast thylakoid membrane;P O.I. H.G. S.X.
0.78 88.6 0.94 At3g56940 824861 CRD1 (COPPER RESPONSE DEFECT 1) Encodes a putative ZIP protein with varying mRNA accumulation in leaves, stems and roots. Has a consensus carboxylate-bridged di-iron binding site. O.I. H.G. S.X.
0.78 88.6 0.95 At3g21055 821657 PSBTN (photosystem II subunit T) Encodes photosystem II 5 kD protein subunit PSII-T. This is a nuclear-encoded gene (PsbTn) which also has a plastid-encoded paralog (PsbTc). O.I. H.G. S.X.
0.77 88.0 0.97 At3g26650 822277 GAPA (GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE A SUBUNIT) Encodes one of the two subunits forming the photosynthetic glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and as such a constituent of the supramolecular complex with phosphoribulokinase (PRK) thought to be linked by a small peptide encoded by CP12-2. GapA-1 is coordinately expressed by light with PRK and CP12-2. The enzyme activity, tested in leaf protein extracts dropped significantly after external sucrose treatment for the photosynthetic GAPDH (NADPH-dependent) but not for the cytosolic GAPDH (NADH-dependent). O.I. H.G. S.X.
0.76 87.4 0.95 At4g32260 829359 ATP synthase family F:hydrogen ion transmembrane transporter activity;P:defense response to bacterium;C:thylakoid, chloroplast thylakoid membrane, chloroplast, membrane, chloroplast envelope;BOPMAFV O.I. H.G. S.X.
0.74 86.1 0.95 At1g12900 837848 GAPA-2 (GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE A SUBUNIT 2) F:NAD or NADH binding, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) activity, binding, glyceraldehyde-3-phosphate dehydrogenase activity, catalytic activity;P:glycolysis, glucose metabolic process, metabolic process;C:apoplast, chloroplast stroma, chloroplast, membrane, chloroplast envelope;BOPFMA O.I. H.G. S.X.
0.74 86.1 0.97 At1g60950 842386 FED A encodes a major leaf ferredoxin O.I. H.G. S.X.
0.73 85.5 0.94 At1g54780 841919 thylakoid lumen 18.3 kDa protein F:molecular_function unknown;P:biological_process unknown;C:thylakoid, thylakoid lumen, chloroplast thylakoid membrane, chloroplast thylakoid lumen, chloroplast;BPOM O.I. H.G. S.X.
0.69 82.9 0.96 At4g01150 828181 unknown protein F:molecular_function unknown;P:biological_process unknown;C:thylakoid, chloroplast thylakoid membrane, chloroplast, plastoglobule, chloroplast envelope;PBO O.I. H.G. S.X.
0.68 82.2 0.94 At2g46820 819295 PSI-P (PHOTOSYSTEM I P SUBUNIT) Encodes the P subunit of Photosystem I. About 25% of the TMP14 pool appeared to be phosphorylated, and this ratio is not affected by light. Contains seven phosphorylation sites on threonine residue and chloroplast targeting signal. Located in the proximity of PSI-L, -H and -O subunits. O.I. H.G. S.X.
0.66 80.1 0.93 At3g50820 824246 PSBO2 (PHOTOSYSTEM II SUBUNIT O-2) Encodes a protein which is an extrinsic subunit of photosystem II and which has been proposed to play a central role in stabilization of the catalytic manganese cluster. In Arabidopsis thaliana the PsbO proteins are encoded by two genes: psbO1 and psbO2. PsbO2 is the minor isoform in the wild-type. Mutants defective in this gene have been shown to be affected in the dephosphorylation of the D1 protein of PSII. O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.87	93.5	1.00	At1g79040	844245	PSBR (photosystem II subunit R)	Encodes for the 10 kDa PsbR subunit of photosystem II (PSII). This subunit appears to be involved in the stable assembly of PSII, particularly that of the oxygen-evolving complex subunit PsbP. Mutants defective in this gene have reduced amounts of subunits PsbP and PsbQ in PSII. In turn, assembly of PsbR is dependent on the presence of PsbJ.	O.I.	H.G.	S.X.
0.96	97.3	0.98	At1g30380	839918	PSAK (photosystem I subunit K)	Encodes subunit K of photosystem I reaction center.	O.I.	H.G.	S.X.
0.95	97.0	0.96	At5g66570	836789	PSBO1 (PS II OXYGEN-EVOLVING COMPLEX 1)	Encodes a protein which is an extrinsic subunit of photosystem II and which has been proposed to play a central role in stabilization of the catalytic manganese cluster. In Arabidopsis thaliana the PsbO proteins are encoded by two genes: psbO1 and psbO2. PsbO1 is the major isoform in the wild-type.	O.I.	H.G.	S.X.
0.94	96.7	0.97	At4g12800	826892	PSAL (photosystem I subunit L)	Encodes subunit L of photosystem I reaction center.	O.I.	H.G.	S.X.
0.94	96.7	0.97	At4g28750	828996	PSAE-1 (PSA E1 KNOCKOUT)	mutant has Decreased effective quantum yield of photosystem II; Pale green plants; Reduced growth rate; Subunit E of Photosystem I	O.I.	H.G.	S.X.
0.94	96.7	0.96	At5g01530	830325	chlorophyll A-B binding protein CP29 (LHCB4)	F:chlorophyll binding;P:response to blue light, response to red light, response to far red light, photosynthesis;C:in 6 components;POM	O.I.	H.G.	S.X.
0.94	96.7	0.94	At4g02770	828183	PSAD-1 (photosystem I subunit D-1)	Encodes a protein predicted by sequence similarity with spinach PsaD to be photosystem I reaction center subunit II (PsaD1)	O.I.	H.G.	S.X.
0.93	96.4	0.97	At3g54890	824654	LHCA1	Encodes a component of the light harvesting complex associated with photosystem I.	O.I.	H.G.	S.X.
0.92	96.0	0.97	At1g06680	837178	PSBP-1 (PHOTOSYSTEM II SUBUNIT P-1)	Encodes a 23 kD extrinsic protein that is part of photosystem II and participates in the regulation of oxygen evolution.	O.I.	H.G.	S.X.
0.92	96.0	0.96	At1g31330	840021	PSAF (photosystem I subunit F)	Encodes subunit F of photosystem I.	O.I.	H.G.	S.X.
0.92	96.0	0.96	At5g46110	834652	APE2 (ACCLIMATION OF PHOTOSYNTHESIS TO ENVIRONMENT 2)	mutant has Altered acclimation responses; Chloroplast Triose Phosphate Translocator	O.I.	H.G.	S.X.
0.91	95.6	0.97	At1g61520	842446	LHCA3	PSI type III chlorophyll a/b-binding protein (Lhca3*1)	O.I.	H.G.	S.X.
0.91	95.6	0.97	At1g55670	842016	PSAG (PHOTOSYSTEM I SUBUNIT G)	Encodes subunit G of photosystem I, an 11-kDa membrane protein that plays an important role in electron transport between plastocyanin and PSI and is involved in the stability of the PSI complex. PSI-G subunit is bound to PSI-B and is in contact with Lhca1. The protein inserts into thylakoids by a direct or "spontaneous" pathway that does not involve the activities of any known chloroplast protein-targeting machinery. PSI-G appears to be directly or indirectly involved in the interaction between Photosystem I and plastocyanin.	O.I.	H.G.	S.X.
0.91	95.6	0.96	At5g64040	836525	PSAN	Encodes the only subunit of photosystem I located entirely in the thylakoid lumen. May be involved in the interaction between plastocyanin and the photosystem I complex.	O.I.	H.G.	S.X.
0.91	95.6	0.96	At4g05180	825866	PSBQ-2	Encodes the PsbQ subunit of the oxygen evolving complex of photosystem II.	O.I.	H.G.	S.X.
0.91	95.6	0.97	At2g06520	815210	PSBX (photosystem II subunit X)	Encodes a protein with sequence similarity to the spinach photosystem II subunit PsbX.	O.I.	H.G.	S.X.
0.91	95.6	0.96	At3g47470	823901	LHCA4 (LIGHT-HARVESTING CHLOROPHYLL-PROTEIN COMPLEX I SUBUNIT A4)	Encodes a chlorophyll a/b-binding protein that is more similar to the PSI Cab proteins than the PSII cab proteins. The predicted protein is about 20 amino acids shorter than most known Cab proteins.	O.I.	H.G.	S.X.
0.90	95.1	0.96	At1g20340	838622	DRT112	recombination and DNA-damage resistance protein (DRT112) One of two Arabidopsis plastocyanin genes. Predominant form, expressed 10x higher than PETE1. PETE2 is thought to be post-transcriptionally regulated via copper accumulation and is involved in copper homeostasis.	O.I.	H.G.	S.X.
0.90	95.1	0.97	At1g29910	839869	CAB3 (CHLOROPHYLL A/B BINDING PROTEIN 3)	member of Chlorophyll a/b-binding protein family	O.I.	H.G.	S.X.
0.90	95.1	0.96	At5g54270	835515	LHCB3 (LIGHT-HARVESTING CHLOROPHYLL B-BINDING PROTEIN 3)	Lhcb3 protein is a component of the main light harvesting chlorophyll a/b-protein complex of Photosystem II (LHC II).	O.I.	H.G.	S.X.
0.88	94.0	0.95	At1g52230	841653	PSAH2 (PHOTOSYSTEM I SUBUNIT H2)	F:molecular_function unknown;P:photosynthesis;C:in 6 components;PO	O.I.	H.G.	S.X.
0.88	94.0	0.95	At4g38970	830052	fructose-bisphosphate aldolase, putative	Protein is tyrosine-phosphorylated and its phosphorylation state is modulated in response to ABA in Arabidopsis thaliana seeds.	O.I.	H.G.	S.X.
0.87	93.5	0.96	At3g16140	820859	PSAH-1 (photosystem I subunit H-1)	Encodes subunit H of photosystem I reaction center subunit VI.	O.I.	H.G.	S.X.
0.87	93.5	0.98	At4g10340	826626	LHCB5 (LIGHT HARVESTING COMPLEX OF PHOTOSYSTEM II 5)	photosystem II encoding the light-harvesting chlorophyll a/b binding protein CP26 of the antenna system of the photosynthetic apparatus	O.I.	H.G.	S.X.
0.85	92.4	0.94	At1g15820	838151	LHCB6 (LIGHT HARVESTING COMPLEX PSII SUBUNIT 6)	Lhcb6 protein (Lhcb6), light harvesting complex of photosystem II.	O.I.	H.G.	S.X.
0.84	91.9	0.96	At2g39730	818558	RCA (RUBISCO ACTIVASE)	Rubisco activase, a nuclear-encoded chloroplast protein that consists of two isoforms arising from alternative splicing in most plants. Required for the light activation of rubisco.	O.I.	H.G.	S.X.
0.82	90.9	0.95	At1g67740	843099	PSBY	PsbY precursor (psbY) mRNA. This single nuclear gene is imported into the chloroplasts where it is processed into two integral membrane proteins with identical topology (PsbY-1 and PsbY-2). The protein appears to bind manganese but its role is not well understood.	O.I.	H.G.	S.X.
0.79	89.1	0.96	At4g03280	827996	PETC (PHOTOSYNTHETIC ELECTRON TRANSFER C)	Encodes the Rieske FeS center of cytochrome b6f complex. Gene is expressed in shoot but not in root. Mutant has reduced electron transport at saturating light intensities and Q-cycle activity is hypersensitive to acidification of the thylakoid lumen.	O.I.	H.G.	S.X.
0.79	89.1	0.96	At4g04640	825797	ATPC1	One of two genes (with ATPC2) encoding the gamma subunit of Arabidopsis chloroplast ATP synthase.	O.I.	H.G.	S.X.
0.79	89.1	0.97	At2g26500	817191	cytochrome b6f complex subunit (petM), putative	F:plastoquinol-plastocyanin reductase activity;P:unknown;C:chloroplast thylakoid membrane;P	O.I.	H.G.	S.X.
0.78	88.6	0.94	At3g56940	824861	CRD1 (COPPER RESPONSE DEFECT 1)	Encodes a putative ZIP protein with varying mRNA accumulation in leaves, stems and roots. Has a consensus carboxylate-bridged di-iron binding site.	O.I.	H.G.	S.X.
0.78	88.6	0.95	At3g21055	821657	PSBTN (photosystem II subunit T)	Encodes photosystem II 5 kD protein subunit PSII-T. This is a nuclear-encoded gene (PsbTn) which also has a plastid-encoded paralog (PsbTc).	O.I.	H.G.	S.X.
0.77	88.0	0.97	At3g26650	822277	GAPA (GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE A SUBUNIT)	Encodes one of the two subunits forming the photosynthetic glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and as such a constituent of the supramolecular complex with phosphoribulokinase (PRK) thought to be linked by a small peptide encoded by CP12-2. GapA-1 is coordinately expressed by light with PRK and CP12-2. The enzyme activity, tested in leaf protein extracts dropped significantly after external sucrose treatment for the photosynthetic GAPDH (NADPH-dependent) but not for the cytosolic GAPDH (NADH-dependent).	O.I.	H.G.	S.X.
0.76	87.4	0.95	At4g32260	829359	ATP synthase family	F:hydrogen ion transmembrane transporter activity;P:defense response to bacterium;C:thylakoid, chloroplast thylakoid membrane, chloroplast, membrane, chloroplast envelope;BOPMAFV	O.I.	H.G.	S.X.
0.74	86.1	0.95	At1g12900	837848	GAPA-2 (GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE A SUBUNIT 2)	F:NAD or NADH binding, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) activity, binding, glyceraldehyde-3-phosphate dehydrogenase activity, catalytic activity;P:glycolysis, glucose metabolic process, metabolic process;C:apoplast, chloroplast stroma, chloroplast, membrane, chloroplast envelope;BOPFMA	O.I.	H.G.	S.X.
0.74	86.1	0.97	At1g60950	842386	FED A	encodes a major leaf ferredoxin	O.I.	H.G.	S.X.
0.73	85.5	0.94	At1g54780	841919	thylakoid lumen 18.3 kDa protein	F:molecular_function unknown;P:biological_process unknown;C:thylakoid, thylakoid lumen, chloroplast thylakoid membrane, chloroplast thylakoid lumen, chloroplast;BPOM	O.I.	H.G.	S.X.
0.69	82.9	0.96	At4g01150	828181	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:thylakoid, chloroplast thylakoid membrane, chloroplast, plastoglobule, chloroplast envelope;PBO	O.I.	H.G.	S.X.
0.68	82.2	0.94	At2g46820	819295	PSI-P (PHOTOSYSTEM I P SUBUNIT)	Encodes the P subunit of Photosystem I. About 25% of the TMP14 pool appeared to be phosphorylated, and this ratio is not affected by light. Contains seven phosphorylation sites on threonine residue and chloroplast targeting signal. Located in the proximity of PSI-L, -H and -O subunits.	O.I.	H.G.	S.X.
0.66	80.1	0.93	At3g50820	824246	PSBO2 (PHOTOSYSTEM II SUBUNIT O-2)	Encodes a protein which is an extrinsic subunit of photosystem II and which has been proposed to play a central role in stabilization of the catalytic manganese cluster. In Arabidopsis thaliana the PsbO proteins are encoded by two genes: psbO1 and psbO2. PsbO2 is the minor isoform in the wild-type. Mutants defective in this gene have been shown to be affected in the dephosphorylation of the D1 protein of PSII.	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
36.3 99.7 E-MEXP-1443-raw-cel-1581869515
36.0 99.7 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
34.7 99.7 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.5 99.7 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
32.7 99.7 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
30.9 99.7 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
29.3 99.7 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
29.2 99.7 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
28.5 99.7 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
28.2 99.7 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
27.6 99.7 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.5 99.7 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.2 99.7 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
26.5 99.7 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
26.2 99.7 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
26.1 99.7 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
26.1 99.7 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
25.2 99.6 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
24.6 99.6 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
24.4 99.6 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
24.4 99.6 E-MEXP-1474-raw-cel-1593932865
23.2 99.6 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
23.0 99.6 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
23.0 99.6 GSM62704 arf6 arf8 flowers_stage 13-14 GSE2848 Auxin Response Factor mediated flower gene expression
22.9 99.6 E-MEXP-1474-raw-cel-1593932801
22.7 99.6 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
19.3 99.6 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
19.1 99.6 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
18.0 99.5 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
16.1 99.5 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
14.4 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
14.1 99.4 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
11.2 99.2 E-MEXP-1474-raw-cel-1593932833
11.1 99.2 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
10.6 99.2 E-MEXP-1443-raw-cel-1581869573
10.3 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
10.0 99.2 GSM106833 opr3_JA_0.5 hr_Rep1 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
10.0 99.2 GSM311274 Laser capture microdissected (LCM) embryo proper at the pre-globular stage, biological replicate 2 GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
9.8 99.1 E-MEXP-1474-raw-cel-1593932929
8.9 99.0 GSM142625 MC002_ATH1_A1.3-dubos-wtx GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
36.3	99.7	E-MEXP-1443-raw-cel-1581869515
36.0	99.7	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
34.7	99.7	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.5	99.7	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
32.7	99.7	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
30.9	99.7	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
29.3	99.7	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
29.2	99.7	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
28.5	99.7	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
28.2	99.7	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
27.6	99.7	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.5	99.7	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.2	99.7	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
26.5	99.7	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
26.2	99.7	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
26.1	99.7	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
26.1	99.7	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
25.2	99.6	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
24.6	99.6	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
24.4	99.6	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
24.4	99.6	E-MEXP-1474-raw-cel-1593932865
23.2	99.6	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
23.0	99.6	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
23.0	99.6	GSM62704	arf6 arf8 flowers_stage 13-14	GSE2848	Auxin Response Factor mediated flower gene expression
22.9	99.6	E-MEXP-1474-raw-cel-1593932801
22.7	99.6	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
19.3	99.6	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
19.1	99.6	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
18.0	99.5	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
16.1	99.5	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
14.4	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
14.1	99.4	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
11.2	99.2	E-MEXP-1474-raw-cel-1593932833
11.1	99.2	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
10.6	99.2	E-MEXP-1443-raw-cel-1581869573
10.3	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
10.0	99.2	GSM106833	opr3_JA_0.5 hr_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
10.0	99.2	GSM311274	Laser capture microdissected (LCM) embryo proper at the pre-globular stage, biological replicate 2	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
9.8	99.1	E-MEXP-1474-raw-cel-1593932929
8.9	99.0	GSM142625	MC002_ATH1_A1.3-dubos-wtx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.342 19 GO:0015979 The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
0.163 4 GO:0009765 Absorption and transfer of the energy absorbed from light photons between photosystem reaction centers.
0.143 4 GO:0019684 The light reactions of photosynthesis, which take place in photosystems II and I. Light energy is harvested and used to power the transfer of electrons among a series of electron donors and acceptors. The final electron acceptor is NADP+, which is reduced to NADPH. NADPH generated from light reactions is used in sugar synthesis in dark reactions. Light reactions also generate a proton motive force across the thylakoid membrane, and the proton gradient is used to synthesize ATP. There are two chemical reactions involved in the light reactions: water oxidation in photosystem II, and NADP reduction in photosystem I.

SF	Genes	GO ID	Process Name
0.342	19	GO:0015979	The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
0.163	4	GO:0009765	Absorption and transfer of the energy absorbed from light photons between photosystem reaction centers.
0.143	4	GO:0019684	The light reactions of photosynthesis, which take place in photosystems II and I. Light energy is harvested and used to power the transfer of electrons among a series of electron donors and acceptors. The final electron acceptor is NADP+, which is reduced to NADPH. NADPH generated from light reactions is used in sugar synthesis in dark reactions. Light reactions also generate a proton motive force across the thylakoid membrane, and the proton gradient is used to synthesize ATP. There are two chemical reactions involved in the light reactions: water oxidation in photosystem II, and NADP reduction in photosystem I.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.354 20 00195 Photosynthesis
0.237 7 00196 Photosynthesis - antenna proteins
0.052 3 00710 Carbon fixation in photosynthetic organisms
0.041 26 01100 Metabolic pathways

SF	Genes	KEGG ID	Pathway name
0.354	20	00195	Photosynthesis
0.237	7	00196	Photosynthesis - antenna proteins
0.052	3	00710	Carbon fixation in photosynthetic organisms
0.041	26	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	At1g79040
Gene name	PSBR (photosystem II subunit R)
Module size	40 genes
NF	0.85
%ile	96.8

Co-expression analysis

Gene ID At1g79040 Gene name PSBR (photosystem II subunit R) Module size 40 genes NF 0.85 %ile 96.8

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 KEGG0.3542000195Photosynthesis0.237700196Photosynthesis - antenna proteins0.052300710Carbon fixation in photosynthetic organisms0.0412601100Metabolic 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 At1g79040

Gene name PSBR (photosystem II subunit R)

Module size 40 genes

NF 0.85

%ile 96.8

: 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
0.354 20 00195 Photosynthesis
0.237 7 00196 Photosynthesis - antenna proteins
0.052 3 00710 Carbon fixation in photosynthetic organisms
0.041 26 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