Co-expression analysis

Gene ID At2g05070
Gene name LHCB2.2
Module size 41 genes
NF 0.85
%ile 96.8



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
0.8793.51.00At2g05070815055LHCB2.2Encodes Lhcb2.2. Belongs to the Lhc super-gene family encodes the light-harvesting chlorophyll a/b-binding (LHC) proteins that constitute the antenna system of the photosynthetic apparatus.O.I.H.G.S.X.
0.9597.00.96At1g08380837358PSAO (photosystem I subunit O)Encodes subunit O of photosystem I.O.I.H.G.S.X.
0.9597.00.95At1g30380839918PSAK (photosystem I subunit K)Encodes subunit K of photosystem I reaction center.O.I.H.G.S.X.
0.9496.70.93At5g66570836789PSBO1 (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.
0.9396.40.95At4g12800826892PSAL (photosystem I subunit L)Encodes subunit L of photosystem I reaction center.O.I.H.G.S.X.
0.9396.40.94At4g28750828996PSAE-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.
0.9396.40.95At5g01530830325chlorophyll 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.
0.9396.40.96At1g61520842446LHCA3PSI type III chlorophyll a/b-binding protein (Lhca3*1)O.I.H.G.S.X.
0.9396.40.94At4g02770828183PSAD-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.
0.9296.00.93At1g20340838622DRT112recombination 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.
0.9296.00.95At1g29910839869CAB3 (CHLOROPHYLL A/B BINDING PROTEIN 3)member of Chlorophyll a/b-binding protein familyO.I.H.G.S.X.
0.9195.60.95At1g06680837178PSBP-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.
0.9195.60.98At5g54270835515LHCB3 (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.
0.9195.60.94At1g31330840021PSAF (photosystem I subunit F)Encodes subunit F of photosystem I.O.I.H.G.S.X.
0.9095.10.93At2g06520815210PSBX (photosystem II subunit X)Encodes a protein with sequence similarity to the spinach photosystem II subunit PsbX.O.I.H.G.S.X.
0.9095.10.94At1g55670842016PSAG (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.
0.9095.10.96At3g61470825320LHCA2Encodes a component of the light harvesting antenna complex of photosystem I.O.I.H.G.S.X.
0.9095.10.94At4g05180825866PSBQ-2Encodes the PsbQ subunit of the oxygen evolving complex of photosystem II.O.I.H.G.S.X.
0.9095.10.94At5g64040836525PSANEncodes 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.
0.8994.60.94At1g79040844245PSBR (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.
0.8894.00.96At4g10340826626LHCB5 (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.
0.8894.00.93At5g46110834652APE2 (ACCLIMATION OF PHOTOSYNTHESIS TO ENVIRONMENT 2)mutant has Altered acclimation responses; Chloroplast Triose Phosphate TranslocatorO.I.H.G.S.X.
0.8793.50.93At4g38970830052fructose-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.
0.8693.10.92At3g16140820859PSAH-1 (photosystem I subunit H-1)Encodes subunit H of photosystem I reaction center subunit VI.O.I.H.G.S.X.
0.8491.90.94At1g52230841653PSAH2 (PHOTOSYSTEM I SUBUNIT H2)F:molecular_function unknown;P:photosynthesis;C:in 6 components;POO.I.H.G.S.X.
0.8491.90.95At1g15820838151LHCB6 (LIGHT HARVESTING COMPLEX PSII SUBUNIT 6)Lhcb6 protein (Lhcb6), light harvesting complex of photosystem II.O.I.H.G.S.X.
0.8391.40.93At2g39730818558RCA (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.
0.8391.40.93At1g67740843099PSBYPsbY 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.
0.8290.90.91At2g26500817191cytochrome b6f complex subunit (petM), putativeF:plastoquinol-plastocyanin reductase activity;P:unknown;C:chloroplast thylakoid membrane;PO.I.H.G.S.X.
0.8190.40.92At4g03280827996PETC (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.
0.8190.40.93At3g26650822277GAPA (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.
0.8089.80.92At4g04640825797ATPC1One of two genes (with ATPC2) encoding the gamma subunit of Arabidopsis chloroplast ATP synthase.O.I.H.G.S.X.
0.8089.80.91At3g21055821657PSBTN (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.
0.7687.40.90At4g32260829359ATP 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.
0.7687.40.93At1g12900837848GAPA-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.
0.7586.90.92At1g54780841919thylakoid 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.
0.7586.90.93At1g60950842386FED Aencodes a major leaf ferredoxinO.I.H.G.S.X.
0.7586.90.93At3g56940824861CRD1 (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.
0.7184.20.91At4g01150828181unknown proteinF:molecular_function unknown;P:biological_process unknown;C:thylakoid, chloroplast thylakoid membrane, chloroplast, plastoglobule, chloroplast envelope;PBOO.I.H.G.S.X.
0.7083.50.91At2g46820819295PSI-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.
0.6781.60.91At3g50820824246PSBO2 (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
35.899.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.399.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.199.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
29.899.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
27.999.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
27.699.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
26.599.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
25.899.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
25.799.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
25.699.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
25.599.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
24.999.6GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
24.999.6GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
24.999.6GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
24.099.6GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
23.899.6E-MEXP-1474-raw-cel-1593932865
23.399.6GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
23.199.6GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
22.699.6GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
22.599.6GSM62704arf6 arf8 flowers_stage 13-14GSE2848Auxin Response Factor mediated flower gene expressionLink to GEO
22.499.6E-MEXP-1474-raw-cel-1593932801
21.799.6GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
18.999.5GSM311291Laser 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
18.799.5GSM311292Laser 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
16.499.5GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
15.899.5GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
15.099.4GSM133762Lindsey_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
12.299.3GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
12.099.3GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
11.499.3GSM131699ATGE_81_CGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
11.399.3GSM131698ATGE_81_BGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
11.099.2E-MEXP-1474-raw-cel-1593932833
9.799.1GSM106833opr3_JA_0.5 hr_Rep1GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
9.799.1GSM311274Laser 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
9.799.1GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
9.699.1E-MEXP-1474-raw-cel-1593932929
9.599.1GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
9.199.1GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
9.099.1E-ATMX-1-raw-cel-1112746154
8.799.0GSM142625MC002_ATH1_A1.3-dubos-wtxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
8.799.0GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.33919GO: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
0.1604GO:0009765Absorption and transfer of the energy absorbed from light photons between photosystem reaction centers.Link to AmiGO
0.1404GO: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

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.3512000195PhotosynthesisLink to KEGG PATHWAY
0.233700196Photosynthesis - antenna proteinsLink to KEGG PATHWAY
0.052300710Carbon fixation in photosynthetic organismsLink to KEGG PATHWAY
0.0432701100Metabolic 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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