Co-expression analysis

Gene ID At3g16140
Gene name PSAH-1 (photosystem I subunit H-1)
Module size 38 genes
NF 0.86
%ile 97.1

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
0.8491.91.00At3g16140820859PSAH-1 (photosystem I subunit H-1)Encodes subunit H of photosystem I reaction center subunit VI.O.I.H.G.S.X.
0.9697.30.98At1g08380837358PSAO (photosystem I subunit O)Encodes subunit O of photosystem I.O.I.H.G.S.X.
0.9697.30.98At1g30380839918PSAK (photosystem I subunit K)Encodes subunit K of photosystem I reaction center.O.I.H.G.S.X.
0.9597.00.97At1g06680837178PSBP-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.
0.9597.00.97At4g28750828996PSAE-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.
0.9496.70.97At1g31330840021PSAF (photosystem I subunit F)Encodes subunit F of photosystem I.O.I.H.G.S.X.
0.9496.70.98At4g12800826892PSAL (photosystem I subunit L)Encodes subunit L of photosystem I reaction center.O.I.H.G.S.X.
0.9496.70.96At1g61520842446LHCA3PSI type III chlorophyll a/b-binding protein (Lhca3*1)O.I.H.G.S.X.
0.9496.70.98At5g01530830325chlorophyll 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.
0.9396.40.96At3g54890824654LHCA1Encodes a component of the light harvesting complex associated with photosystem I.O.I.H.G.S.X.
0.9296.00.97At5g66570836789PSBO1 (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.
0.9296.00.97At1g20340838622DRT112recombination 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.
0.9296.00.98At1g55670842016PSAG (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.
0.9195.60.96At4g02770828183PSAD-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.
0.9195.60.96At4g10340826626LHCB5 (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.
0.9095.10.95At5g54270835515LHCB3 (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.
0.9095.10.98At2g06520815210PSBX (photosystem II subunit X)Encodes a protein with sequence similarity to the spinach photosystem II subunit PsbX.O.I.H.G.S.X.
0.9095.10.96At3g47470823901LHCA4 (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.
0.9095.10.95At3g61470825320LHCA2Encodes a component of the light harvesting antenna complex of photosystem I.O.I.H.G.S.X.
0.9095.10.98At4g05180825866PSBQ-2Encodes the PsbQ subunit of the oxygen evolving complex of photosystem II.O.I.H.G.S.X.
0.8994.60.96At1g79040844245PSBR (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.
0.8994.60.97At5g46110834652APE2 (ACCLIMATION OF PHOTOSYNTHESIS TO ENVIRONMENT 2)mutant has Altered acclimation responses; Chloroplast Triose Phosphate TranslocatorO.I.H.G.S.X.
0.8894.00.97At5g64040836525PSANEncodes 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.
0.8894.00.95At4g38970830052fructose-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.
0.8592.40.97At1g52230841653PSAH2 (PHOTOSYSTEM I SUBUNIT H2)F:molecular_function unknown;P:photosynthesis;C:in 6 components;POO.I.H.G.S.X.
0.8391.40.96At2g39730818558RCA (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.
0.8290.90.97At1g15820838151LHCB6 (LIGHT HARVESTING COMPLEX PSII SUBUNIT 6)Lhcb6 protein (Lhcb6), light harvesting complex of photosystem II.O.I.H.G.S.X.
0.8190.40.97At4g03280827996PETC (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.
0.8190.40.96At3g26650822277GAPA (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.
0.8190.40.96At2g26500817191cytochrome b6f complex subunit (petM), putativeF:plastoquinol-plastocyanin reductase activity;P:unknown;C:chloroplast thylakoid membrane;PO.I.H.G.S.X.
0.7687.40.97At1g60950842386FED Aencodes a major leaf ferredoxinO.I.H.G.S.X.
0.7687.40.98At4g04640825797ATPC1One of two genes (with ATPC2) encoding the gamma subunit of Arabidopsis chloroplast ATP synthase.O.I.H.G.S.X.
0.7586.90.98At3g21055821657PSBTN (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.
0.7586.90.96At3g56940824861CRD1 (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.
0.7184.20.97At1g12900837848GAPA-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.
0.7184.20.98At4g32260829359ATP 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.
0.7083.50.97At1g54780841919thylakoid 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.
0.6680.10.97At4g01150828181unknown proteinF:molecular_function unknown;P:biological_process unknown;C:thylakoid, chloroplast thylakoid membrane, chloroplast, plastoglobule, chloroplast envelope;PBOO.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
37.999.8GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
35.099.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.999.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
33.199.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.499.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.799.7GSM205364met1-3_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
28.799.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
28.699.7GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
28.599.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
27.899.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
27.799.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
26.699.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
26.499.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
26.399.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
26.299.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
24.799.6GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
24.699.6GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
24.599.6GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
24.199.6GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
23.599.6GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
22.699.6GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
19.499.6GSM311292Laser 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
19.199.6GSM311291Laser 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
18.999.5GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
15.899.5GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
15.199.4GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
14.799.4GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
10.899.2GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
10.799.2GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
10.599.2GSM106833opr3_JA_0.5 hr_Rep1GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
10.599.2GSM311274Laser 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
10.399.2GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
9.299.1GSM142625MC002_ATH1_A1.3-dubos-wtxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
8.899.0GSM142624MC002_ATH1_A1.2-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
0.33018GO: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
0.1433GO: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
0.1403GO:0009768After a photon of light is absorbed by one of the many chlorophyll molecules, in one of the light-harvesting complexes of an antenna on photosystem I, some of the absorbed energy is transferred to the pair of chlorophyll molecules in the reaction center.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.3241800195PhotosynthesisLink to KEGG PATHWAY
0.281800196Photosynthesis - antenna proteinsLink to KEGG PATHWAY
0.053300710Carbon fixation in photosynthetic organismsLink to KEGG PATHWAY
0.0382401100Metabolic pathwaysLink to KEGG PATHWAY

Inter-species module comparison

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

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