Co-expression analysis

Gene ID At3g26710
Gene name CCB1 (COFACTOR ASSEMBLY OF COMPLEX C)
Module size 40 genes
NF 0.44
%ile 62.2



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
1.00100.01.00At3g26710822283CCB1 (COFACTOR ASSEMBLY OF COMPLEX C)F:molecular_function unknown;P:cytochrome b6f complex assembly;C:chloroplast;OBPO.I.H.G.S.X.
0.6478.90.96At2g3541081810733 kDa ribonucleoprotein, chloroplast, putative / RNA-binding protein cp33, putativeF:RNA binding, nucleotide binding, nucleic acid binding;P:unknown;C:thylakoid, chloroplast stroma, chloroplast;MPFOBAO.I.H.G.S.X.
0.6378.10.95At1g6000084229429 kDa ribonucleoprotein, chloroplast, putative / RNA-binding protein cp29, putativeF:RNA binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:chloroplast;MPOFBAO.I.H.G.S.X.
0.6075.70.95At5g52970835375thylakoid lumen 15.0 kDa proteinF:molecular_function unknown;P:biological_process unknown;C:thylakoid, thylakoid lumen, chloroplast thylakoid lumen, chloroplast;OBPO.I.H.G.S.X.
0.6075.70.95At5g45680834607FK506-binding protein 1 (FKBP13)F:FK506 binding, peptidyl-prolyl cis-trans isomerase activity;P:protein folding;C:thylakoid lumen, chloroplast thylakoid lumen, chloroplast;BMOPFAO.I.H.G.S.X.
0.6075.70.95At4g14890827146ferredoxin family proteinF:electron carrier activity, iron-sulfur cluster binding, 2 iron, 2 sulfur cluster binding;P:electron transport chain;C:chloroplast;BOPAMFVO.I.H.G.S.X.
0.5974.70.94At4g24930828595thylakoid lumenal 17.9 kDa protein, chloroplastF:molecular_function unknown;P:biological_process unknown;C:thylakoid, thylakoid lumen, chloroplast thylakoid lumen, chloroplast;PO.I.H.G.S.X.
0.5873.80.95At5g062908305172-Cys Prx B (2-Cysteine peroxiredoxin B)Encodes a 2-Cys peroxiredoxin (2-Cys PrxB) that contains two catalytic Cys residues.O.I.H.G.S.X.
0.5773.80.95At4g17600827479LIL3:1Encodes Lil3:1 (light-harvesting-like) protein. 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. A generic LHC motif is present in Lil3:1.O.I.H.G.S.X.
0.5673.00.95At5g42765834286-F:unknown;P:biological_process unknown;C:thylakoid, chloroplast thylakoid membrane, chloroplast;PO.I.H.G.S.X.
0.5570.60.96At3g25805822172unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;BPOO.I.H.G.S.X.
0.5469.50.96At1g0108083946333 kDa ribonucleoprotein, chloroplast, putative / RNA-binding protein cp33, putativeF:RNA binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:chloroplast stroma, nucleus, chloroplast, chloroplast envelope;MPOFBAO.I.H.G.S.X.
0.5267.40.96At1g32990840194PRPL11 (PLASTID RIBOSOMAL PROTEIN L11)mutant has Decreased effective quantum yield of photosystem II; Pale green plants; Reduced growth rate; Plastid Ribosomal Protein L11O.I.H.G.S.X.
0.5267.40.95At1g32550840149ferredoxin family proteinF:electron carrier activity, iron-sulfur cluster binding, 2 iron, 2 sulfur cluster binding;P:electron transport chain;C:unknown;BOPAMVFO.I.H.G.S.X.
0.4862.50.96At5g13510831195ribosomal protein L10 family proteinF:structural constituent of ribosome;P:translation, ribosome biogenesis;C:cytosolic ribosome, ribosome, chloroplast, chloroplast stroma;BOAPMFO.I.H.G.S.X.
0.4862.50.96At3g55330824699PPL1 (PsbP-like protein 1)F:calcium ion binding;P:photosynthesis;C:in 6 components;POBO.I.H.G.S.X.
0.4862.50.95At3g52380824403CP33chloroplast RNA-binding proteinO.I.H.G.S.X.
0.4761.20.95At3g56010824767unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast thylakoid membrane;PO.I.H.G.S.X.
0.4761.20.94At3g56650824832thylakoid lumenal 20 kDa proteinF:unknown;P:unknown;C:thylakoid, thylakoid lumen, chloroplast thylakoid lumen, chloroplast stroma, chloroplast;PBOO.I.H.G.S.X.
0.4659.80.95At2g34860818051EDA3 (embryo sac development arrest 3)F:unfolded protein binding, heat shock protein binding;P:megagametogenesis;C:chloroplast thylakoid membrane, chloroplast;BOPAMFO.I.H.G.S.X.
0.4457.20.95At1g29070839781ribosomal protein L34 family proteinF:structural constituent of ribosome;P:translation, ribosome biogenesis;C:ribosome, intracellular, chloroplast;BPOFO.I.H.G.S.X.
0.4253.90.95At2g20890816623PSB29Chloroplast-localized Thylakoid formation1 gene product involved in vesicle-mediated formation of thylakoid membranes. Thf1 antisense lines contain abnormal chloroplasts early in leaf development (chloroplasts have loosely stacked thylakoid membranes). Expression was induced in the light and decreased under dark conditions. G-alpha interaction partner that functions downstream of the plasma membrane–delimited heterotrimeric G-protein (GPA1) in a D-glucose signaling pathway. Localized to both the outer plastid membrane and the stroma. Probably involved in the metabolic pathway that controls the assembly of the PS II complex.O.I.H.G.S.X.
0.4253.90.95At4g18370827564DEG5 (DEGP PROTEASE 5)Encodes DEG5. Forms a hexamer with DEG8 in the thylakoid lumen. Involved in the cleavage of photodamaged D2 protein of photosystem II (PSII).O.I.H.G.S.X.
0.4152.40.94At2g24090816943ribosomal protein L35 family proteinF:structural constituent of ribosome;P:translation;C:ribosome, chloroplast;BOPMFO.I.H.G.S.X.
0.4152.40.94At1g20810838672immunophilin / FKBP-type peptidyl-prolyl cis-trans isomerase family proteinF:FK506 binding, peptidyl-prolyl cis-trans isomerase activity;P:protein folding;C:thylakoid lumen, chloroplast thylakoid lumen, chloroplast;BOPMFO.I.H.G.S.X.
0.4050.80.95At1g05190839273emb2394 (embryo defective 2394)F:structural constituent of ribosome;P:embryonic development ending in seed dormancy, translation;C:chloroplast stroma, chloroplast, large ribosomal subunit, membrane, chloroplast envelope;BOAFPMO.I.H.G.S.X.
0.4050.80.95At5g1432083128230S ribosomal protein S13, chloroplast (CS13)F:structural constituent of ribosome, RNA binding, nucleic acid binding;P:translation;C:small ribosomal subunit, chloroplast, chloroplast envelope;BOPMFAO.I.H.G.S.X.
0.3948.40.96At3g08740820021elongation factor P (EF-P) family proteinF:translation elongation factor activity;P:translational elongation;C:chloroplast, chloroplast stroma;BOPAO.I.H.G.S.X.
0.3846.70.94At4g18480827580CHLI1Encodes the CHLI subunit of magnesium chelatase which is required for chlorophyll biosynthesis. All four cysteine residues of the protein form two disulfide bonds (Cys102-Cys193 and Cys354-Cys396) under oxidized conditions but are fully reduced by reduction. It was suggested that the redox state of CHLI is regulated in vivo by the change of the redox environment in the chloroplasts probably via the Trx system.O.I.H.G.S.X.
0.3846.70.96At5g511108351854-alpha-hydroxytetrahydrobiopterin dehydrataseF:4-alpha-hydroxytetrahydrobiopterin dehydratase activity;P:tetrahydrobiopterin biosynthetic process;C:chloroplast;OBPAFO.I.H.G.S.X.
0.3745.00.94At5g47190834765ribosomal protein L19 family proteinF:structural constituent of ribosome;P:translation, ribosome biogenesis;C:ribosome, chloroplast stroma, chloroplast, membrane, chloroplast envelope;BOPMFO.I.H.G.S.X.
0.3643.60.95At5g14910831343heavy-metal-associated domain-containing proteinF:metal ion binding;P:metal ion transport;C:thylakoid, chloroplast thylakoid membrane, chloroplast stroma, chloroplast;PO.I.H.G.S.X.
0.3541.60.95At3g1312082050030S ribosomal protein S10, chloroplast, putativeF:structural constituent of ribosome, RNA binding;P:translation;C:small ribosomal subunit, chloroplast;BOMAPFO.I.H.G.S.X.
0.3541.60.95At3g26900822306shikimate kinase family proteinF:shikimate kinase activity, ATP binding;P:aromatic amino acid family biosynthetic process;C:chloroplast stroma, chloroplast;BOPMAFO.I.H.G.S.X.
0.3439.80.94At3g54210824588ribosomal protein L17 family proteinF:structural constituent of ribosome;P:translation;C:ribosome, chloroplast;BOMFPO.I.H.G.S.X.
0.3338.10.95At1g73110843642ribulose bisphosphate carboxylase/oxygenase activase, putative / RuBisCO activase, putativeF:ATPase activity, ATP binding;P:unknown;C:chloroplast thylakoid membrane, chloroplast;PBFOAMO.I.H.G.S.X.
0.3235.70.95At1g11860837733aminomethyltransferase, putativeF:aminomethyltransferase activity;P:response to cadmium ion;C:in 6 components;OBMFAPO.I.H.G.S.X.
0.3032.10.95At5g53580835440aldo/keto reductase family proteinF:oxidoreductase activity, aldo-keto reductase activity;P:oxidation reduction;C:chloroplast;BOMFPAO.I.H.G.S.X.
0.3032.10.95At4g36390829791radical SAM domain-containing protein / TRAM domain-containing proteinF:iron-sulfur cluster binding, catalytic activity;P:biological_process unknown;C:chloroplast;OBMAPO.I.H.G.S.X.
0.2726.20.95At5g23120832376HCF136encodes a stability and/or assembly factor of photosystem IIO.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
89.599.9GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
77.999.9GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
75.899.9GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
74.599.9GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
73.699.9GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
73.399.9GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
69.299.9GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
69.099.9GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
63.099.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
61.799.8GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
60.999.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
56.899.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
55.999.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
55.499.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
49.199.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
47.799.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
47.199.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
46.499.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
45.099.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.899.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
40.799.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.399.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.399.7GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
34.299.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
33.999.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
31.399.7GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
30.499.7GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
30.299.7GSM284393Arabidopsis GCE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
28.099.7E-MEXP-807-raw-cel-1173273252
23.099.6E-MEXP-807-raw-cel-1173273144
22.499.6GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
21.899.6GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
21.199.6GSM184923Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
19.499.6GSM284394Arabidopsis GCE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
19.099.5GSM133759Lindsey_1-9_heart-stage-cotyledon_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
17.899.5GSM284392Arabidopsis GCE1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
13.599.4GSM184906Arabidopsis, root cells, protophloem, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
12.499.3GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
11.099.2GSM184905Arabidopsis, root cells, protophloem, standard conditions, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0852GO:0022900A process whereby a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.Link to AmiGO
0.0544GO:0042254The process of the formation of the constituents of the ribosome subunits, their assembly, and their transport to the sites of protein synthesis.Link to AmiGO
0.0481GO:0006729The chemical reactions and pathways resulting in the formation of tetrahydrobiopterin, the reduced form of biopterin (2-amino-4-hydroxy-6-(1,2-dihydroxypropyl)-pteridine). It functions as a hydroxylation coenzyme, e.g. in the conversion of phenylalanine to tyrosine.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.053300195PhotosynthesisLink to KEGG PATHWAY
0.035100670One carbon pool by folateLink to KEGG PATHWAY
0.030100860Porphyrin and chlorophyll metabolismLink 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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