Co-expression analysis

Gene ID At3g62410
Gene name CP12-2
Module size 6 genes
NF 0.58
%ile 79.4



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
1.00100.01.00At3g62410825414CP12-2CP12-2 encodes a small peptide found in the chloroplast stroma. It belongs to the CP12 gene family thought to be involved in the formation of a supramolecular complex with glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK) embedded in the Calvin cycle. CP12-2 is coordinately regulated by light with the photosynthetic GAPDH and PRK. The annotation of this gene is based on article 32494.O.I.H.G.S.X.
0.5773.80.95At1g14150837974oxygen evolving enhancer 3 (PsbQ) family proteinF:calcium ion binding;P:photosynthesis;C:chloroplast thylakoid membrane, chloroplast photosystem II, chloroplast thylakoid lumen, chloroplast;PO.I.H.G.S.X.
0.5773.80.92At5g20935832218unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;BPOO.I.H.G.S.X.
0.4457.20.93At1g70760843413CRR23 ((chlororespiratory reduction 23)a subunit of the chloroplast NAD(P)H dehydrogenase complex, involved in PSI cyclic electron transport. Located on the thylakoid membrane. Mutant has impaired NAD(P)H dehydrogenase activity.O.I.H.G.S.X.
0.3338.10.93At3g19800821517unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.3338.10.93At5g58260835938-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.

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Link to AtGenExpress Visualization Tool



Specific experiments for the module

Std2 GX %ile GSM ID Assay name GSE ID Experiment title Link to GEO
235.0100.0GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
114.999.9GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
114.499.9GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
107.599.9GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
97.399.9GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
91.799.9GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
89.799.9GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
89.299.9GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
89.099.9GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
84.599.9GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
83.799.9GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
81.399.9GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
81.399.9GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
81.299.9GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
81.099.9GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
80.299.9GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
80.099.9GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
79.899.9GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
75.199.9GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
72.799.9GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
58.499.8GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
55.199.8GSM154505Arabidopsis hydrated pollen grains rep1GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
53.199.8GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
49.499.8GSM154503Arabidopsis desiccated mature pollen grains rep1GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
32.899.7E-ATMX-35-raw-cel-1574334880
30.699.7GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
29.899.7E-ATMX-35-raw-cel-1574334864
27.499.7GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
26.799.7GSM266668Arabidopsis, root cells, columella root cap, -Fe, replicate 3GSE10501Expression analysis of root cell-types after iron deficiency (-Fe) treatmentLink to GEO
25.099.6E-MEXP-1138-raw-cel-1432772746
24.599.6E-MEXP-1138-raw-cel-1432772874
24.299.6GSM239251Columbia glabrous (C24) wild type pollenGSE9408Identification of putative Arabidopsis DEMETER target genes by GeneChip AnalysisLink to GEO
24.099.6GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
23.899.6GSM239253CaMV::DME pollenGSE9408Identification of putative Arabidopsis DEMETER target genes by GeneChip AnalysisLink to GEO
23.199.6GSM311282Laser capture microdissected (LCM) chalazal seed coat at the pre-globular stage, biological replicate 2GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
22.899.6E-MEXP-1138-raw-cel-1432772842
22.899.6E-MEXP-1138-raw-cel-1432772714
22.399.6GSM154506Arabidopsis hydrated pollen grains rep2GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
22.399.6GSM154507Arabidopsis growing pollen tubes rep1GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
21.499.6GSM266667Arabidopsis, root cells, columella root cap, -Fe, replicate 2GSE10501Expression analysis of root cell-types after iron deficiency (-Fe) treatmentLink to GEO
21.199.6GSM131638ATGE_73_CGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
18.799.5GSM131637ATGE_73_BGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
18.699.5GSM142740DH001_ATH1_A7-MPG1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
18.499.5GSM131636ATGE_73_AGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
17.399.5E-MEXP-1138-raw-cel-1432773002
17.299.5GSM239252Columbia glabrous (C24) wild type stamenGSE9408Identification of putative Arabidopsis DEMETER target genes by GeneChip AnalysisLink to GEO
16.899.5E-MEXP-1138-raw-cel-1432772586
16.899.5E-MEXP-1138-raw-cel-1432773098
16.699.5E-MEXP-1138-raw-cel-1432772554
16.599.5GSM266666Arabidopsis, root cells, columella root cap, -Fe, replicate 1GSE10501Expression analysis of root cell-types after iron deficiency (-Fe) treatmentLink to GEO
16.499.5GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
16.499.5E-MEXP-1138-raw-cel-1432772810
16.499.5GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
15.499.5E-MEXP-1138-raw-cel-1432773162
15.399.4E-MEXP-1138-raw-cel-1432773130
15.299.4E-MEXP-1138-raw-cel-1432772906
15.299.4E-MEXP-1138-raw-cel-1432772650
15.299.4E-MEXP-1138-raw-cel-1432772778
15.099.4E-MEXP-1138-raw-cel-1432772522
15.099.4GSM311281Laser capture microdissected (LCM) chalazal seed coat at the pre-globular stage, biological replicate 1GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
14.899.4GSM184893Arabidopsis, root cells, columella root cap, standard conditions, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
14.899.4E-MEXP-1138-raw-cel-1432773226
14.199.4GSM154504Arabidopsis desiccated mature pollen grains rep2GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
13.499.4E-MEXP-285-raw-cel-440782725
13.299.4E-MEXP-1138-raw-cel-1432772938
13.199.4GSM184923Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
12.999.3E-MEXP-1138-raw-cel-1432773354
12.999.3E-MEXP-1138-raw-cel-1432772970
12.699.3E-MEXP-1138-raw-cel-1432772682
12.599.3GSM184894Arabidopsis, root cells, columella root cap, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
12.499.3E-MEXP-1138-raw-cel-1432772618
12.299.3GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
12.099.3E-ATMX-35-raw-cel-1574334848
12.099.3E-MEXP-1138-raw-cel-1432773194
11.299.2E-MEXP-285-raw-cel-440782791
11.099.2GSM154508Arabidopsis growing pollen tubes rep2GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
10.299.2GSM142736DH001_ATH1_A3-TCP1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
9.899.1GSM184906Arabidopsis, root cells, protophloem, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
9.799.1GSM184912Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
9.499.1E-MEXP-1138-raw-cel-1432773386
9.499.1GSM142739DH001_ATH1_A6-TCP2GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
8.699.0GSM184892Arabidopsis, root cells, columella root cap, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.2861GO:0018316The oxidation of two peptidyl-cysteine residues to form a peptidyl-L-cystine (dicysteine) in which segments of peptide chain are linked by a disulfide bond; the cross-link may be between different or the same peptide chain.Link to AmiGO
0.2221GO: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
0.1671GO:0019253The fixation of carbon dioxide (CO2) as glucose in the chloroplasts of C3 plants; uses ATP and NADPH formed in the light reactions of photosynthesis; carbon dioxide reacts with ribulose 1,5-bisphosphate (catalyzed by the function of ribulose-bisphosphate carboxylase) to yield two molecules of 3-phosphoglycerate; these are then phosphorylated by ATP to 1,3-bisphosphateglyceraldehyde which, in turn, is then reduced by NADPH to glyceraldehyde 3-phosphate. The glyceraldehyde 3-phosphate is converted to fructose 5-phosphate and ribulose 5-phosphate by aldolase and other enzymes; the ribulose 5-phosphate is phosphorylated by ATP to ribulose 1,5-bisphosphate.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.025100195PhotosynthesisLink to KEGG PATHWAY
0.002101100Metabolic 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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