Co-expression analysis

Gene ID At3g61470
Gene name LHCA2
Module size 40 genes
NF 0.85
%ile 96.5



Co-expression network

pink confeito: Transcription factor, green bicone: Binding protein, red cone: Enzyme protein, blue sphere: Other protein
large node: VF over 0.50, middle node: over 0.25, small node: 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
0.8894.01.00At3g61470825320LHCA2Encodes a component of the light harvesting antenna complex of photosystem I.O.I.H.G.S.X.
0.9697.30.97At1g30380839918PSAK (photosystem I subunit K)Encodes subunit K of photosystem I reaction center.O.I.H.G.S.X.
0.9597.00.96At5g66570836789PSBO1 (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.
0.9496.70.97At4g12800826892PSAL (photosystem I subunit L)Encodes subunit L of photosystem I reaction center.O.I.H.G.S.X.
0.9496.70.97At4g28750828996PSAE-1 (PSA E1 KNOCKOUT)mutant has Decreased effective quantum yield of photosystem II; Pale green plants; Reduced growth rate; Subunit E of Photosystem IO.I.H.G.S.X.
0.9496.70.97At5g01530830325chlorophyll 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;POMO.I.H.G.S.X.
0.9496.70.96At4g02770828183PSAD-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.
0.9396.40.97At3g54890824654LHCA1Encodes a component of the light harvesting complex associated with photosystem I.O.I.H.G.S.X.
0.9296.00.97At1g06680837178PSBP-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.
0.9296.00.97At1g31330840021PSAF (photosystem I subunit F)Encodes subunit F of photosystem I.O.I.H.G.S.X.
0.9195.60.98At1g55670842016PSAG (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.
0.9195.60.96At4g05180825866PSBQ-2Encodes the PsbQ subunit of the oxygen evolving complex of photosystem II.O.I.H.G.S.X.
0.9195.60.95At5g64040836525PSANEncodes 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.
0.9195.60.96At2g06520815210PSBX (photosystem II subunit X)Encodes a protein with sequence similarity to the spinach photosystem II subunit PsbX.O.I.H.G.S.X.
0.9195.60.97At3g47470823901LHCA4 (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.
0.9095.10.96At1g20340838622DRT112recombination 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.
0.9095.10.97At1g29910839869CAB3 (CHLOROPHYLL A/B BINDING PROTEIN 3)member of Chlorophyll a/b-binding protein familyO.I.H.G.S.X.
0.9095.10.96At5g54270835515LHCB3 (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.
0.8994.60.95At5g46110834652APE2 (ACCLIMATION OF PHOTOSYNTHESIS TO ENVIRONMENT 2)mutant has Altered acclimation responses; Chloroplast Triose Phosphate TranslocatorO.I.H.G.S.X.
0.8894.00.95At4g38970830052fructose-bisphosphate aldolase, putativeProtein is tyrosine-phosphorylated and its phosphorylation state is modulated in response to ABA in Arabidopsis thaliana seeds.O.I.H.G.S.X.
0.8793.50.98At1g79040844245PSBR (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.
0.8793.50.98At4g10340826626LHCB5 (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 apparatusO.I.H.G.S.X.
0.8592.40.94At1g52230841653PSAH2 (PHOTOSYSTEM I SUBUNIT H2)F:molecular_function unknown;P:photosynthesis;C:in 6 components;POO.I.H.G.S.X.
0.8592.40.95At3g16140820859PSAH-1 (photosystem I subunit H-1)Encodes subunit H of photosystem I reaction center subunit VI.O.I.H.G.S.X.
0.8491.90.96At2g39730818558RCA (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.
0.8290.90.94At1g15820838151LHCB6 (LIGHT HARVESTING COMPLEX PSII SUBUNIT 6)Lhcb6 protein (Lhcb6), light harvesting complex of photosystem II.O.I.H.G.S.X.
0.8190.40.94At1g67740843099PSBYPsbY 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.
0.7989.10.95At2g26500817191cytochrome b6f complex subunit (petM), putativeF:plastoquinol-plastocyanin reductase activity;P:unknown;C:chloroplast thylakoid membrane;PO.I.H.G.S.X.
0.7888.60.94At3g56940824861CRD1 (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.
0.7788.00.96At4g04640825797ATPC1One of two genes (with ATPC2) encoding the gamma subunit of Arabidopsis chloroplast ATP synthase.O.I.H.G.S.X.
0.7788.00.97At3g26650822277GAPA (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.
0.7788.00.96At4g03280827996PETC (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.
0.7788.00.94At3g21055821657PSBTN (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.
0.7687.40.94At4g32260829359ATP synthase familyF:hydrogen ion transmembrane transporter activity;P:defense response to bacterium;C:thylakoid, chloroplast thylakoid membrane, chloroplast, membrane, chloroplast envelope;BOPMAFVO.I.H.G.S.X.
0.7486.10.95At1g12900837848GAPA-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;BOPFMAO.I.H.G.S.X.
0.7486.10.96At1g60950842386FED Aencodes a major leaf ferredoxinO.I.H.G.S.X.
0.7385.50.94At1g54780841919thylakoid lumen 18.3 kDa proteinF:molecular_function unknown;P:biological_process unknown;C:thylakoid, thylakoid lumen, chloroplast thylakoid membrane, chloroplast thylakoid lumen, chloroplast;BPOMO.I.H.G.S.X.
0.6982.90.96At4g01150828181unknown proteinF:molecular_function unknown;P:biological_process unknown;C:thylakoid, chloroplast thylakoid membrane, chloroplast, plastoglobule, chloroplast envelope;PBOO.I.H.G.S.X.
0.6882.20.94At2g46820819295PSI-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.
0.6680.10.93At3g50820824246PSBO2 (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
36.299.7E-MEXP-1443-raw-cel-1581869515
36.099.7GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
34.799.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.699.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.799.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.999.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
29.399.7GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
29.399.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
28.699.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
28.399.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
27.699.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
27.599.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
27.299.7GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
26.599.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
26.299.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
26.299.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
26.199.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
25.399.6GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
24.699.6GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
24.599.6GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
24.499.6E-MEXP-1474-raw-cel-1593932865
23.299.6GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
23.199.6GSM62704arf6 arf8 flowers_stage 13-14GSE2848Auxin Response Factor mediated flower gene expressionLink to GEO
23.099.6GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
22.999.6E-MEXP-1474-raw-cel-1593932801
22.799.6GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
19.399.6GSM311291Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 1GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
19.199.6GSM311292Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 2GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
18.099.5GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
16.199.5GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
14.499.4GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
14.199.4GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
11.299.2E-MEXP-1474-raw-cel-1593932833
11.199.2GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
10.599.2E-MEXP-1443-raw-cel-1581869573
10.399.2GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
10.099.2GSM106833opr3_JA_0.5 hr_Rep1GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
9.999.1GSM311274Laser capture microdissected (LCM) embryo proper at the pre-globular stage, biological replicate 2GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
9.999.1GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
9.899.1E-MEXP-1474-raw-cel-1593932929
8.999.0GSM142625MC002_ATH1_A1.3-dubos-wtxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.34219GO:0015979The 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.Link to AmiGO
0.1434GO:0019684The 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.Link to AmiGO
0.1363GO:0010196The process to maintain the balance between dissipation and utilization of light energy to minimize generation of oxidizing molecules, thereby protecting the plant against photo-oxidative damage.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.3542000195PhotosynthesisLink to KEGG PATHWAY
0.237700196Photosynthesis - antenna proteinsLink to KEGG PATHWAY
0.052300710Carbon fixation in photosynthetic organismsLink to KEGG PATHWAY
0.0412601100Metabolic pathwaysLink to KEGG PATHWAY

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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