Co-expression analysis

Gene ID At2g23130
Module size 49 genes
NF 0.27
%ile 31.5

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
1.00100.01.00At2g23130816845AGP17 (ARABINOGALACTAN PROTEIN 17)AGP17 is a lysine-rich arabinogalactan-protein (AGP) and part of a multi-gene family of glycoproteins with approx. 50 members. It falls into one subclass with AGP18 and AGP19, other lysine-rich AGPs. 84% of its proline residues are hydroxylated to hydroproline and its heavy glycosylation accounts for appr. 69% of the molecular weight. The main glycosyl residues are arabinose (30.1%) and galactose (55.1%). Glycosyl linkages are consistent with type II arabinogalactans. AGP17 is predicted to have a glycosylphosphatidylinositol (GPI)anchor and is localized to the plasma membrane and Hechtian strands. It is expressed in young/old leaves, shoots, suspension cultures and flowers.O.I.H.G.S.X.
0.4659.80.81At4g16980827406arabinogalactan-protein familyF:unknown;P:biological_process unknown;C:endomembrane system;MPBOFVAO.I.H.G.S.X.
0.3846.70.80At2g34510818014-F:molecular_function unknown;P:biological_process unknown;C:anchored to membrane;PBO.I.H.G.S.X.
0.3541.60.80At4g16410827335unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;OBPO.I.H.G.S.X.
0.3338.10.80At3g54900824655CXIP1 (CAX INTERACTING PROTEIN 1)A.thaliana PICOT protein.It activates CAX1 gene Calcium transport activity.In other organisms, PICOT proteins appear to play a negative regulatory role in cellular stress responses.O.I.H.G.S.X.
0.3338.10.80At4g34190829567SEP1 (STRESS ENHANCED PROTEIN 1)Encodes a stress enhanced protein that localizes to the thylakoid membrane and whose mRNA is upregulated in response to high light intensity. It may be involved in chlorophyll binding.O.I.H.G.S.X.
0.3338.10.79At3g06750819860hydroxyproline-rich glycoprotein family proteinF:molecular_function unknown;P:biological_process unknown;C:anchored to membrane;MPFOBVO.I.H.G.S.X.
0.3235.70.80At1g74970843836RPS9 (RIBOSOMAL PROTEIN S9)ribosomal protein S9, nuclear encoded component of the chloroplast ribosomeO.I.H.G.S.X.
0.3235.70.80At1g50900841512-F:molecular_function unknown;P:biological_process unknown;C:chloroplast, chloroplast stroma;POO.I.H.G.S.X.
0.3235.70.80At1g03600839449photosystem II family proteinF:molecular_function unknown;P:biological_process unknown;C:thylakoid, chloroplast thylakoid membrane, chloroplast photosystem II, chloroplast thylakoid lumen, chloroplast;BOPO.I.H.G.S.X.
0.3235.70.81At5g511108351854-alpha-hydroxytetrahydrobiopterin dehydrataseF:4-alpha-hydroxytetrahydrobiopterin dehydratase activity;P:tetrahydrobiopterin biosynthetic process;C:chloroplast;OBPAFO.I.H.G.S.X.
0.3133.80.80At2g44920819101thylakoid 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.
0.3133.80.80At4g09650826551ATPD (ATP SYNTHASE DELTA-SUBUNIT GENE)Encodes the chloroplast ATPase delta-subunit.O.I.H.G.S.X.
0.3133.80.80At1g34000840297OHP2 (ONE-HELIX PROTEIN 2)Encodes a novel member of the Lhc family from Arabidopsis with one predicted transmembrane alpha-helix closely related to helix I of Lhc protein from PSI (Lhca4). Gene expression is triggered by light stress and both transcript and protein accumulate in a light intensity-dependent manner. Ohp2 is associated with PSI under low- or high-light conditions.O.I.H.G.S.X.
0.3133.80.79At3g59400825109GUN4GUN, genomes uncoupled, is necessary for coupling the expression of some nuclear genes to the functional state of the chloroplast. Binds to the magnesium chelatase complex and promotes formation of the substrate,a tetrapyrrole signaling molecule. Porphyrin-binding protein that enhances the activity of Mg-chelatase. Although required for chlorophyll accumulation under normal growth conditions, GUN4 is not essential for chlorophyll synthesis.O.I.H.G.S.X.
0.3032.10.79At4g25050828608ACP4 (acyl carrier protein 4)encodes an acyl carrier protein predominantly expressed in leaves. Gene expression is upregulated by light.O.I.H.G.S.X.
0.3032.10.80At2g48070819419RPH1 (RESISTANCE TO PHYTOPHTHORA 1)Encodes a chloroplast protein RPH1 (resistance to Phytophthora 1). Involved in immune response to Phytophthora brassicae. rph1 mutant plants (in Ws background) are susceptible to P. brassicae.O.I.H.G.S.X.
0.2930.30.79At1g72610843593GER1 (GERMIN-LIKE PROTEIN 1)germin-like protein (GLP1)O.I.H.G.S.X.
0.2930.30.80At3g116308203352-cys peroxiredoxin, chloroplast (BAS1)Encodes a 2-Cys peroxiredoxin (2-Cys PrxA) that contains two catalytic Cys residues.O.I.H.G.S.X.
0.2930.30.80At4g20360827784ATRABE1B (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.
0.2830.30.79At3g15190820750chloroplast 30S ribosomal protein S20, putativeF:structural constituent of ribosome, RNA binding;P:translation, ribosome biogenesis;C:ribosome, chloroplast stroma, chloroplast, membrane;BOPMO.I.H.G.S.X.
0.2830.30.81At4g32260829359ATP 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.
0.2830.30.79At3g16140820859PSAH-1 (photosystem I subunit H-1)Encodes subunit H of photosystem I reaction center subunit VI.O.I.H.G.S.X.
0.2830.30.80At1g64510842759ribosomal protein S6 family proteinF:structural constituent of ribosome;P:translation, ribosome biogenesis;C:thylakoid, chloroplast thylakoid membrane, ribosome, chloroplast;BOPO.I.H.G.S.X.
0.2830.30.79At3g54210824588ribosomal protein L17 family proteinF:structural constituent of ribosome;P:translation;C:ribosome, chloroplast;BOMFPO.I.H.G.S.X.
0.2726.20.80At1g67740843099PSBYPsbY precursor (psbY) mRNA. This single nuclear gene is imported into the chloroplasts where it is processed into two integral membrane proteins with identical topology (PsbY-1 and PsbY-2). The protein appears to bind manganese but its role is not well understood.O.I.H.G.S.X.
0.2726.20.79At4g02130827438GATL6Encodes a protein with putative galacturonosyltransferase activity.O.I.H.G.S.X.
0.2726.20.80At2g20890816623PSB29Chloroplast-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.
0.2726.20.79At2g47400819353CP12-1CP12-1 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. The annotation of this gene is based on article 32494.O.I.H.G.S.X.
0.2726.20.80At5g46110834652APE2 (ACCLIMATION OF PHOTOSYNTHESIS TO ENVIRONMENT 2)mutant has Altered acclimation responses; Chloroplast Triose Phosphate TranslocatorO.I.H.G.S.X.
0.2726.20.80At1g76100843942PETE1 (PLASTOCYANIN 1)One of two Arabidopsis plastocyanin genes. Expressed at 1/10th level of PETE2. Does not respond to increased copper levels and is thought to be the isoform that participates in electron transport under copper-limiting conditions.O.I.H.G.S.X.
0.2624.40.79At3g56940824861CRD1 (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.
0.2624.40.79At2g17230816228EXL5 (EXORDIUM LIKE 5)F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PBO.I.H.G.S.X.
0.2624.40.79At1g29070839781ribosomal protein L34 family proteinF:structural constituent of ribosome;P:translation, ribosome biogenesis;C:ribosome, intracellular, chloroplast;BPOFO.I.H.G.S.X.
0.2420.70.80At5g35100833461peptidyl-prolyl cis-trans isomeraseF:peptidyl-prolyl cis-trans isomerase activity;P:protein folding, peptidyl-cysteine S-nitrosylation;C:thylakoid lumen, chloroplast;MFPOBAO.I.H.G.S.X.
0.2420.70.81At4g24930828595thylakoid 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.
0.2420.70.79At4g03280827996PETC (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.
0.2420.70.79At4g22830828382unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;BOPO.I.H.G.S.X.
0.2319.30.79At1g50320841454ATHXencodes a prokaryotic thioredoxinO.I.H.G.S.X.
0.1912.70.81At3g07470819935unknown proteinF:unknown;P:biological_process unknown;C:vacuole;POO.I.H.G.S.X.
0.1912.70.79At3g52500824415aspartyl protease family proteinF:aspartic-type endopeptidase activity;P:proteolysis;C:cell wall, membrane, plant-type cell wall;PMFOO.I.H.G.S.X.
0.1811.40.80At2g21170816652TIM (TRIOSEPHOSPHATE ISOMERASE)Encodes triosephosphate isomerase.O.I.H.G.S.X.
0.1811.40.79At3g05410819705unknown proteinF:unknown;P:unknown;C:unknown;POO.I.H.G.S.X.
0.1710.20.79At5g15410831393DND1 (DEFENSE NO DEATH 1)'defense, no death' gene (DND1) encodes a mutated cyclic nucleotide-gated cation channel; Same as CNGC2 (article ID 229): Cyclic nucleotide gated channel, activated by cAMP, conducts K+ and other monovalent cations but excludes Na+, does not contain the GYG amino acid sequence found in other channels with this conductivity profile. Conducts Ca2+ into cells which is linked to the generation of NO and the NO signaling pathway involved in the innate immune response to pathogens.O.I.H.G.S.X. (FASCICLIN-LIKE ARABINOGALACTAN PROTEIN 18 PRECURSOR)F:molecular_function unknown;P:response to cyclopentenone, cell adhesion;C:vacuole;BPOMO.I.H.G.S.X. heat shock N-terminal domain-containing proteinF:binding, heat shock protein binding;P:protein folding;C:cellular_component unknown;PMFOBO.I.H.G.S.X. (IQ-domain 2)F:calmodulin binding;P:biological_process unknown;C:plasma membrane;PMOFO.I.H.G.S.X. proteinF:molecular_function unknown;P:biological_process unknown;C:plasma membrane;PBO.I.H.G.S.X. (COBRA)Encodes a glycosylphosphatidylinositol-anchored protein localized primarily in the plasma membrane of the longitudinal sides of root cells. Necessary for oriented cell expansion in Arabidopsis. Cob mutants have abnormal roots that expand radially rather than longitudinally under certain growth conditions.O.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
45.799.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.399.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
41.699.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
39.399.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
39.199.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.499.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.499.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.399.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.499.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.199.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.099.7GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
35.899.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.599.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.099.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.899.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
27.199.7GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
26.799.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
26.599.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
25.999.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
25.899.7GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
24.699.6GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
21.899.6GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
20.999.6GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
19.499.6GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
19.199.6GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
18.199.5GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
18.099.5GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
17.699.5GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
13.699.4GSM184477Lateral Root Cap root cells 2hr KCl control treated, biological rep2GSE7631Cell-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
9.999.1GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
9.299.1GSM184480Lateral Root Cap root cells 2hr transitory KNO3 treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.299.1GSM157306Gan_1-3_wildtype-nitrate-minus(WNM)_Rep2_ATH1GSE6824Identification of genes involved in nutritional regulation of root architectureLink to GEO
8.799.0GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
8.699.0GSM133963Fukuda_1-8_6B_Rep2_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
8.699.0GSM184917Arabidopsis, root cells, endodermis and quiescent center, 140 mM NaCl, 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
0.0835GO: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
0.0692GO:0043085Any process that activates or increases the activity of an enzyme.Link to AmiGO
0.0532GO: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

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.115700195PhotosynthesisLink to KEGG PATHWAY
0.027100860Porphyrin and chlorophyll metabolismLink to KEGG PATHWAY
0.023100562Inositol phosphate metabolismLink to KEGG PATHWAY

Inter-species module comparison

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

Back to the CoP portal site

Back to the KAGIANA project homepage