Co-expression analysis

Gene ID At1g73110
Gene name ribulose bisphosphate carboxylase/oxygenase activase, putative / RuBisCO activase, putative
Module size 22 genes
NF 0.56
%ile 77.8



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
0.5267.41.00At1g73110843642ribulose 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.
0.8391.40.93At1g55480841995binding / protein bindingF:protein binding, binding;P:unknown;C:chloroplast thylakoid membrane, chloroplast stroma, chloroplast, chloroplast envelope;PBOMFO.I.H.G.S.X.
0.7788.00.93At5g19220832042APL1 (ADP GLUCOSE PYROPHOSPHORYLASE LARGE SUBUNIT 1)Encodes the large subunit of ADP-glucose pyrophosphorylase which catalyzes the first, rate limiting step in starch biosynthesis. The large subunit plays a regulatory role whereas the small subunit (ApS) is the catalytic isoform. Four isoforms (ApL1-4) have been identified. ApL1 is the major large subunit isoform present in leaves. Mutational analysis of APS1 suggests that APL1 and APL2 can compensate for loss of APS1 catalytic activity,suggesting both have catalytic as well as regulatory functions.O.I.H.G.S.X.
0.7586.90.92At1g15980838168NDF1 (NDH-DEPENDENT CYCLIC ELECTRON FLOW 1)encodes a novel subunit of the chloroplast NAD(P)H dehydrogenase complex, involved in cyclic electron flow around photosystem I to produce ATP.O.I.H.G.S.X.
0.7385.50.93At1g32080840100membrane protein, putativeF:unknown;P:unknown;C:chloroplast, chloroplast inner membrane, membrane, chloroplast envelope;BOFPAO.I.H.G.S.X.
0.7184.20.93At5g36700833635PGLP1 (2-PHOSPHOGLYCOLATE PHOSPHATASE 1)F:phosphoglycolate phosphatase activity;P:metabolic process;C:chloroplast stroma, chloroplast;BOMFAPO.I.H.G.S.X.
0.7083.50.94At1g09340837455CRB (CHLOROPLAST RNA BINDING)Encodes CHLOROPLAST RNA BINDING (CRB), a putative RNA-binding protein. CRB is important for the proper functioning of the chloroplast. Mutations in CRB also affects the circadian system, altering the expression of both oscillator and output genes.O.I.H.G.S.X.
0.6882.20.92At3g48420824000haloacid dehalogenase-like hydrolase family proteinF:hydrolase activity, catalytic activity;P:metabolic process;C:chloroplast, chloroplast stroma, chloroplast envelope;BOPMFAVO.I.H.G.S.X.
0.6781.60.92At3g63140825489CSP41A (CHLOROPLAST STEM-LOOP BINDING PROTEIN OF 41 KDA)Encodes a protein with ribonuclease activity that is involved in plastid rRNA maturation.O.I.H.G.S.X.
0.6579.60.93At3g54050824572fructose-1,6-bisphosphatase, putative / D-fructose-1,6-bisphosphate 1-phosphohydrolase, putative / FBPase, putativeF:fructose 1,6-bisphosphate 1-phosphatase activity, phosphoric ester hydrolase activity;P:response to cold, fructose metabolic process;C:apoplast, stromule, chloroplast stroma, chloroplast;BOMPFAO.I.H.G.S.X.
0.6378.10.94At1g56500842103haloacid dehalogenase-like hydrolase family proteinF:hydrolase activity, oxidoreductase activity, catalytic activity;P:metabolic process, cell redox homeostasis;C:chloroplast, chloroplast stroma;BOMPAFVO.I.H.G.S.X.
0.6378.10.94At5g08650830766GTP-binding protein LepA, putativeF:GTP binding, translation elongation factor activity, GTPase activity;P:unknown;C:chloroplast;BOMFPAO.I.H.G.S.X.
0.5974.70.93At4g35250829678vestitone reductase-relatedF:transcription repressor activity, binding, catalytic activity;P:regulation of nitrogen utilization, metabolic process;C:chloroplast;BOPFMAO.I.H.G.S.X.
0.5570.60.94At3g55800824746SBPASE (sedoheptulose-bisphosphatase)Encodes the chloroplast enzyme sedoheptulose-1,7-bisphosphatase (SBPase), involved in the carbon reduction of the Calvin cycle. Increase in SBPase activity in transgenic lines accumulate up to 50% more sucrose and starch than wild-type.O.I.H.G.S.X.
0.5368.60.95At1g11860837733aminomethyltransferase, putativeF:aminomethyltransferase activity;P:response to cadmium ion;C:in 6 components;OBMFAPO.I.H.G.S.X.
0.5065.30.92At5g58260835938-Encodes subunit NDH-N 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.
0.4558.30.93At1g32060840098PRK (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.
0.4253.90.92At3g61870825360unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast, chloroplast inner membrane, chloroplast envelope;BOPO.I.H.G.S.X.
0.4253.90.92At1g77090844043thylakoid lumenal 29.8 kDa proteinF:calcium ion binding;P:photosynthesis;C:thylakoid, thylakoid lumen, chloroplast thylakoid lumen, chloroplast stroma, chloroplast;POBO.I.H.G.S.X.
0.4152.40.95At3g01480821137CYP38 (cyclophilin 38)Encodes a chloroplast cyclophilin functioning in the assembly and maintenance of photosystem II (PSII) supercomplexes.O.I.H.G.S.X.
0.4152.40.94At5g23120832376HCF136encodes a stability and/or assembly factor of photosystem IIO.I.H.G.S.X.
0.3643.60.93At1g76450843978oxygen-evolving complex-relatedF:unknown;P:unknown;C:thylakoid, thylakoid lumen, chloroplast thylakoid membrane, chloroplast thylakoid lumen, chloroplast;POO.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
133.799.9GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
111.499.9GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
107.399.9GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
90.999.9GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
78.499.9GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
70.799.9GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
68.399.9GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
66.599.8GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
64.199.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
64.099.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
63.999.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
61.699.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
61.599.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
60.699.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
59.899.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
57.699.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
56.399.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
56.099.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
53.899.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
52.999.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
51.799.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
51.599.8GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
50.399.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
45.799.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
38.299.8GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
37.599.7GSM284394Arabidopsis GCE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
31.299.7E-MEXP-509-raw-cel-829148666
30.399.7GSM284392Arabidopsis GCE1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
25.399.6GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
22.399.6GSM284393Arabidopsis GCE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
20.399.6GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
17.199.5GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
15.799.5GSM311280Laser capture microdissected (LCM) chalazal endosperm at the pre-globular stage, biological replicate 2GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
15.199.4GSM154505Arabidopsis hydrated pollen grains rep1GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
14.899.4GSM131604ATGE_41_BGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
13.599.4GSM154503Arabidopsis desiccated mature pollen grains rep1GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
13.499.4GSM131603ATGE_41_AGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
12.099.3GSM131605ATGE_41_CGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
11.799.3GSM133819Yang_1-4_old-pod_Rep2_ATH1GSE5736To identify changes in gene expression during silique senescence in Arabidopsis thalianaLink to GEO
10.499.2GSM133765Lindsey_1-17_torpedo-cotyledon_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
9.299.1GSM131608ATGE_42_DGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
9.099.1E-ATMX-35-raw-cel-1574334880

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0801GO:0006000The chemical reactions and pathways involving fructose, the ketohexose arabino-2-hexulose. Fructose exists in a open chain form or as a ring compound. D-fructose is the sweetest of the sugars and is found free in a large number of fruits and honey.Link to AmiGO
0.0801GO:0010258The aggregation, arrangement and bonding together of a set of components to form NADH:plastoquinone dehydrogenase complex, which is involved in the non-photochemical reduction of plastoquinones, as well as the cyclic electron transport around photosystem I.Link to AmiGO
0.0742GO:0006364Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.062300710Carbon fixation in photosynthetic organismsLink to KEGG PATHWAY
0.051100670One carbon pool by folateLink to KEGG PATHWAY
0.030100260Glycine, serine and threonine 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



Back to the CoP portal site

Back to the KAGIANA project homepage