Co-expression analysis

Gene ID At1g64720
Gene name CP5
Module size 55 genes
NF 0.29
%ile 34.2

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
1.00100.01.00At1g64720842780CP5membrane related protein CP5O.I.H.G.S.X.
0.5267.40.88At3g16520820900UDP-glucoronosyl/UDP-glucosyl transferase family proteinF:in 6 functions;P:metabolic process;C:cellular_component unknown;PMVBOFO.I.H.G.S.X.
0.4761.20.90At4g30993829225unknown proteinF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PO.I.H.G.S.X.
0.4355.30.89At3g07310819919unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;PBOO.I.H.G.S.X.
0.4050.80.89At2g22990816830SNG1 (SINAPOYLGLUCOSE 1)sinapoylglucose:malate sinapoyltransferase. Catalyzes the formation of sinapoylmalate from sinapoylglucose. Mutants accumulate excess sinapoylglucose.O.I.H.G.S.X.
0.3745.00.87At1g74880843827NDH-O (NAD(P)H:plastoquinone dehydrogenase complex subunit O)Encodes subunit NDH-O of NAD(P)H:plastoquinone dehydrogenase complex (Ndh complex) present in the thylakoid membrane of chloroplasts. This subunit is thought to be required for Ndh complex assembly.O.I.H.G.S.X.
0.3643.60.88At5g01920831741STN8Chloroplast thylakoid protein kinase STN8 is specific in phosphorylation of N-terminal threonine residues in D1, D2 and CP43 proteins, and Thr-4 in PsbH protein of photosystem II. Phosphorylation of Thr-4 in the wild type required both light and prior phosphorylation at Thr-2.O.I.H.G.S.X.
0.3541.60.90At1g65260842833PTAC4 (PLASTID TRANSCRIPTIONALLY ACTIVE4)F:unknown;P:biological_process unknown;C:in 8 components;BOMVFPAO.I.H.G.S.X.
0.3541.60.91At1g23310838940GGT1 (GLUTAMATE:GLYOXYLATE AMINOTRANSFERASE)Identified by cloning the gene that corresponded to a purified protein having glyoxylate aminotransferase activity. Localized to the peroxisome and thought to be involved in photorespiration/ metabolic salvage pathway.O.I.H.G.S.X.
0.3439.80.88At5g48790834937unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;PBOO.I.H.G.S.X.
0.3439.80.88At2g46220819229unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;BPMOO.I.H.G.S.X.
0.3439.80.87At5g35790833559G6PD1 (GLUCOSE-6-PHOSPHATE DEHYDROGENASE 1)Encodes a plastidic glucose-6-phosphate dehydrogenase that is sensitive to reduction by DTT and whose mRNA is more prevalent in developing organs but absent in the root.O.I.H.G.S.X.
0.3439.80.88At1g16720838243HCF173 (high chlorophyll fluorescence phenotype 173)Encodes HCF173, a protein with weak similarities to the superfamily of the short-chain dehydrogenases/reductases. HCF173 is involved in the initiation of translation of the psbA mRNA. Mutants shows a high chlorophyll fluorescence phenotype (hcf) and are severely affected in the accumulation of PSII subunits. The protein HCF173 is localized in the chloroplast, where it is mainly associated with the membrane system and is part of a higher molecular weight complex with psbA mRNA as a component of this complex.O.I.H.G.S.X.
0.3439.80.87At1g22850838890-F:unknown;P:biological_process unknown;C:chloroplast;BOMPFAO.I.H.G.S.X.
0.3338.10.88At4g08920826470CRY1 (CRYPTOCHROME 1)Encodes CRY1, a flavin-type blue-light photoreceptor with ATP binding and autophosphorylation activity. The photoreceptor may be involved in electron transport. Mutant phenotype displays a blue light-dependent inhibition of hypocotyl elongation. Photoreceptor activity requires light-induced homodimerisation of the N-terminal CNT1 domains of CRY1. Involved in blue-light induced stomatal opening. The C-terminal domain of the protein undergoes a light dependent conformational change. Also involved in response to circadian rhythm. Mutants exhibit long hypocotyl under blue light and are out of phase in their response to circadian rhythm. CRY1 is present in the nucleus and cytoplasm. Different subcellular pools of CRY1 have different functions during photomorphogenesis of Arabidopsis seedlings.O.I.H.G.S.X.
0.3338.10.88At4g15545827228unknown proteinF:unknown;P:unknown;C:unknown;MOBPFVO.I.H.G.S.X.
0.3235.70.88At5g16400831501ATF2Encodes an f-type thioredoxin (Trx-f2) localized in chloroplast stroma.O.I.H.G.S.X.
0.3235.70.87At5g35170833471adenylate kinase family proteinF:nucleobase, nucleoside, nucleotide kinase activity, nucleotide kinase activity, phosphotransferase activity, phosphate group as acceptor, adenylate kinase activity, ATP binding;P:nucleobase, nucleoside, nucleotide and nucleic acid metabolic process, anaerobic respiration, nucleotide metabolic process;C:chloroplast thylakoid membrane, chloroplast, chloroplast envelope;BOMFPAO.I.H.G.S.X.
0.3133.80.92At2g14910815980unknown proteinF:unknown;P:unknown;C:chloroplast;BOPMO.I.H.G.S.X.
0.3133.80.88At2g25080817046ATGPX1 (GLUTATHIONE PEROXIDASE 1)Encodes glutathione peroxidase.O.I.H.G.S.X.
0.3032.10.88At3g08940820043LHCB4.2 (light harvesting complex PSII)Lhcb4.2 protein (Lhcb4.2, protein involved in the light harvesting complex of photosystem IIO.I.H.G.S.X.
0.3032.10.89At4g15560827230CLA1 (CLOROPLASTOS ALTERADOS 1)Encodes a protein with 1-deoxyxylulose 5-phosphate synthase activity involved in the MEP pathway. It is essential for chloroplast development in ArabidopsisO.I.H.G.S.X.
0.2930.30.87At5g59750836096riboflavin biosynthesis protein, putativeF:3,4-dihydroxy-2-butanone-4-phosphate synthase activity, GTP cyclohydrolase II activity;P:riboflavin biosynthetic process;C:chloroplast;BOFAPO.I.H.G.S.X.
0.2930.30.88At1g35420840434dienelactone hydrolase family proteinF:hydrolase activity;P:biological_process unknown;C:chloroplast, chloroplast stroma;BFOPMAO.I.H.G.S.X.
0.2930.30.88At2g13360815822AGT (ALANINE:GLYOXYLATE AMINOTRANSFERASE)Encodes a peroxisomal photorespiratory enzyme that catalyzes transamination reactions with multiple substrates. It is involved in photorespiration.O.I.H.G.S.X.
0.2930.30.89At2g28800817429ALB3 (ALBINO 3)member of Chloroplast membrane protein ALBINO3 familyO.I.H.G.S.X.
0.2930.30.88At1g51400841564photosystem II 5 kD proteinF:molecular_function unknown;P:response to UV-B, response to wounding, response to ozone;C:chloroplast thylakoid membrane, chloroplast photosystem II, chloroplast thylakoid lumen;PO.I.H.G.S.X.
0.2830.30.88At3g23700821951S1 RNA-binding domain-containing proteinF:RNA binding;P:response to cold;C:chloroplast stroma, nucleus, chloroplast;BOPMFAO.I.H.G.S.X.
0.2726.20.88At1g68010843129HPREncodes hydroxypyruvate reductase.O.I.H.G.S.X.
0.2726.20.88At5g19940832116plastid-lipid associated protein PAP-related / fibrillin-relatedF:structural molecule activity;P:biological_process unknown;C:chloroplast, chloroplast envelope;PBOO.I.H.G.S.X.
0.2726.20.88At1g71500843491Rieske (2Fe-2S) domain-containing proteinF:electron carrier activity, oxidoreductase activity, 2 iron, 2 sulfur cluster binding;P:oxidation reduction;C:chloroplast thylakoid membrane, chloroplast, chloroplast envelope;BPOO.I.H.G.S.X.
0.2726.20.88At4g28030828918GCN5-related N-acetyltransferase (GNAT) family proteinF:N-acetyltransferase activity;P:metabolic process;C:chloroplast;BPOAO.I.H.G.S.X.
0.2726.20.88At5g14260831276SET domain-containing proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;PMFOO.I.H.G.S.X.
0.2726.20.88At2g30950817646VAR2 (VARIEGATED 2)Metalloprotease that functions in thylakoid membrane biogenesis. Involved in the repair of PSII following damaged incurred during photoinhibition. Forms a complex with VAR1. Mutants show a variegated phenotype, which decreases during development. Transcript and protein levels increase with light intensity.O.I.H.G.S.X.
0.2726.20.87At3g61080825280fructosamine kinase family proteinF:kinase activity;P:biological_process unknown;C:mitochondrion, chloroplast;BOMFPAO.I.H.G.S.X.
0.2726.20.87At1g32060840098PRK (PHOSPHORIBULOKINASE)F:protein binding, phosphoribulokinase activity, ATP binding;P:response to cold, defense response to bacterium, peptidyl-cysteine S-nitrosylation, biosynthetic process;C:in 8 components;BPOMFAVO.I.H.G.S.X.
0.2624.40.88At5g01530830325chlorophyll 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.
0.2624.40.87At5g09660830825PMDH2 (peroxisomal NAD-malate dehydrogenase 2)encodes a microbody NAD-dependent malate dehydrogenase encodes an peroxisomal NAD-malate dehydrogenase that is involved in fatty acid beta-oxidation through providing NAD to the process of converting fatty acyl CoA to acetyl CoA.O.I.H.G.S.X.
0.2624.40.87At4g22890828388PGR5-LIKE AEncodes PGRL1A, a transmembrane protein present in thylakoids. PGRL1A has a highly homologous isoform PGRL1B encoded by At4g11960. Plants lacking PGRL1 show perturbation of cyclic electron flow, similar to PGR5-deficient plants. PGRL1 and PGR5 interact physically and associate with PSI (photosystem I).O.I.H.G.S.X.
0.2624.40.88At3g17650821032YSL5 (YELLOW STRIPE LIKE 5)Arabidopsis thaliana metal-nicotianamine transporter YSL5O.I.H.G.S.X.
0.2624.40.88At3g10230820185LYC (LYCOPENE CYCLASE)Encodes a protein with lycopene β-cyclase activity. This enzyme uses the linear, symmetrical lycopene as substrate. However, unlike the ε-cyclase which adds only one ring, the β-cyclase introduces a ring at both ends of lycopene to form the bicyclic β-carotene.O.I.H.G.S.X.
0.2420.70.88At1g74470843788geranylgeranyl reductaseEncodes for a multifunctional protein with geranylgeranyl reductase activity shown to catalyze the reduction of prenylated geranylgeranyl-chlorophyll a to phytyl-chlorophyll a (chlorophyll a) and free geranylgeranyl pyrophosphate to phytyl pyrophosphate.O.I.H.G.S.X.
0.2319.30.87At1g35340840423ATP-dependent protease La (LON) domain-containing proteinF:ATP-dependent peptidase activity;P:ATP-dependent proteolysis;C:chloroplast;BOPFMO.I.H.G.S.X.
0.2319.30.87At1g23400838948CAF2Promotes the splicing of chloroplast group II introns.O.I.H.G.S.X.
0.2319.30.87At1g54780841919thylakoid 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.
0.2319.30.88At3g56940824861CRD1 (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.
0.2217.50.88At4g01800827922preprotein translocase secA subunit, putativeF:protein binding, ATP binding;P:intracellular protein transport, protein targeting, protein import;C:chloroplast stroma, chloroplast, chloroplast envelope;OBPMAO.I.H.G.S.X.
0.2217.50.88At1g67700843095unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast, chloroplast envelope;POO.I.H.G.S.X.
0.2115.80.87At1g19000838481myb family transcription factorF:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:unknown;POO.I.H.G.S.X.
0.2014.40.89At4g25080828611CHLM (magnesium-protoporphyrin IX methyltransferase)Encodes a protein with methyltransferase activity responsible for the methylation of magnesium protoporphyrin IX. Mutants defective in this gene are affected in chlorophyll biosynthesis and show a reduction in the accumulation of a number of major thylakoid-associated proteins including components of PSI (LHCI), PSII (LHCII, D1, CP43) and the cytochrome b6f complex (Cytf). By contrast, no significant changes were detected for the proteins of the stroma and the chloroplast envelope.O.I.H.G.S.X.
0.1912.70.89At3g26900822306shikimate 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.
0.1912.70.88At2g44920819101thylakoid lumenal 15 kDa protein, chloroplastF:molecular_function unknown;P:unknown;C:thylakoid, thylakoid lumen, chloroplast thylakoid membrane, chloroplast thylakoid lumen, chloroplast;BOAMPVO.I.H.G.S.X. (ARABIDOPSIS RAB GTPASE HOMOLOG E1B)F:GTP binding, translation elongation factor activity, GTPase activity;P:peptidyl-cysteine S-nitrosylation;C:in 9 components;BOMFPAVO.I.H.G.S.X. binding / zinc ion bindingF:protein binding, zinc ion binding;P:unknown;C:unknown;MBOPAFVO.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
86.799.9GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
79.499.9GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
76.599.9GSM133760Lindsey_1-12_heart-stage-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
69.999.9GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
63.199.8GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
59.799.8GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
57.799.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
54.999.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
50.399.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
46.599.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
45.899.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
44.099.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
43.499.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
42.299.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.499.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.899.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.199.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
39.299.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
38.199.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.999.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.699.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.699.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.499.7GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
33.299.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.599.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
29.099.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
25.199.6GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
22.299.6GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
19.699.6GSM284389Arabidopsis GMPE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
18.799.5GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
17.099.5GSM265423Arabidopsis, root, longitudinal zone 3, standard conditions, rep 2GSE10497Expression analysis of root developmental zones after iron deficiency (-Fe) treatmentLink to GEO
16.999.5GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
12.599.3GSM265431Arabidopsis, root, longitudinal zone 3, -Fe conditions, rep 2GSE10497Expression analysis of root developmental zones after iron deficiency (-Fe) treatmentLink to GEO
11.299.2GSM311291Laser 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
10.999.2GSM311292Laser 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
10.999.2GSM142625MC002_ATH1_A1.3-dubos-wtxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
10.899.2GSM133766Lindsey_1-18_torpedo-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
10.499.2GSM311275Laser capture microdissected (LCM) micropylar endosperm at the pre-globular stage, biological replicate 1GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
10.499.2GSM142736DH001_ATH1_A3-TCP1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
10.099.2GSM265430Arabidopsis, root, longitudinal zone 3, -Fe conditions, rep 1GSE10497Expression analysis of root developmental zones after iron deficiency (-Fe) treatmentLink to GEO
8.799.0GSM142739DH001_ATH1_A6-TCP2GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0994GO:0015995The chemical reactions and pathways resulting in the formation of chlorophyll, any compound of magnesium complexed in a porphyrin (tetrapyrrole) ring and which functions as a photosynthetic pigment, from less complex precursors.Link to AmiGO
0.0823GO:0010027A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the thylakoid membrane.Link to AmiGO
0.0683GO:0009853A light-dependent catabolic process occurring concomitantly with photosynthesis in plants (especially C3 plants) whereby dioxygen (O2) is consumed and carbon dioxide (CO2) is evolved. The substrate is glycolate formed in large quantities in chloroplasts from 2-phosphoglycolate generated from ribulose 1,5-bisphosphate by the action of ribulose-bisphosphate carboxylase; the glycolate enters the peroxisomes where it is converted by glycolate oxidase to glyoxylate which undergoes transamination to glycine. This then passes into the mitochondria where it is decarboxylated forming one molecule of serine for every two molecules of glycine. This pathway also exists in photosynthetic bacteria.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.054200196Photosynthesis - antenna proteinsLink to KEGG PATHWAY
0.049203060Protein exportLink to KEGG PATHWAY
0.046300710Carbon fixation in photosynthetic organismsLink to KEGG PATHWAY

Inter-species module comparison

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

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