Co-expression analysis

Gene ID At4g22570
Module size 45 genes
NF 0.14
%ile 10.0

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
1.00100.01.00At4g22570828353APT3 (ADENINE PHOSPHORIBOSYL TRANSFERASE 3)Encodes an adenine phosphoribosyltransferase (APT; EC, which is a constitutively expressed enzyme involved in the one-step salvage of adenine to AMP. APT3 has higher affinity for zeatin, isopentenyladenine and benzyladenine than APT1 but lower Vmax than APT1.O.I.H.G.S.X.
0.2930.30.82At4g31310829258avirulence-responsive protein-related / avirulence induced gene (AIG) protein-relatedF:unknown;P:biological_process unknown;C:cellular_component unknown;OPFBAO.I.H.G.S.X.
0.2830.30.80At4g37550829910formamidase, putative / formamide amidohydrolase, putativeF:formamidase activity, hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides;P:metabolic process;C:vacuole;BOFAPO.I.H.G.S.X.
0.2319.30.80At2g17340816241pantothenate kinase-relatedF:molecular_function unknown;P:unknown;C:cellular_component unknown;MPABOO.I.H.G.S.X.
0.2217.50.79At5g63060836426transporterF:transporter activity;P:transport;C:chloroplast;MPFOO.I.H.G.S.X.
0.2115.80.81At2g01760814707ARR14 (ARABIDOPSIS RESPONSE REGULATOR 14)member of Response Regulator: B- TypeO.I.H.G.S.X.
0.2115.80.81At5g64460836567-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;FOPBMO.I.H.G.S.X.
0.2115.80.81At5g49970835061ATPPOX (A. THALIANA PYRIDOXIN (PYRODOXAMINE) 5'-PHOSPHATE OXIDASE)encodes the bifunctional pyridoxine (pyridoxamine) 5-phosphate oxidase (PPOX)(EC that is involved in the formation of pyridoxal 5'-phosphate (member of the vitamin B6 group)O.I.H.G.S.X.
0.1912.70.78At5g22830832346ATMGT10 (MAGNESIUM (MG) TRANSPORTER 10)putative Mg(2+) transport proteinO.I.H.G.S.X.
0.1912.70.79At5g52030835278TraB protein-relatedF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BMOAPO.I.H.G.S.X.
0.1912.70.82At4g26860828793pyridoxal phosphate bindingF:pyridoxal phosphate binding;P:biological_process unknown;C:unknown;OBMFPAO.I.H.G.S.X.
0.1912.70.79At5g57030835806LUT2 (LUTEIN DEFICIENT 2)Lutein-deficient 2 (LUT2) required for lutein biosynthesis, member of the xanthophyll class of carotenoids. Encodes lycopene epsilon cyclaseO.I.H.G.S.X.
0.1710.20.79At4g00430827956PIP1a member of the plasma membrane intrinsic protein subfamily PIP1.O.I.H.G.S.X.
0.1710.20.78At2g24270816962ALDH11A3Encodes a protein with non-phosphorylating NADP-dependent glyceraldehyde-3-phosphate dehydrogenase activity. The activity of the enzyme was determined from leaf extracts; the enzyme has not been purified to confirm activity.O.I.H.G.S.X.
0.1710.20.78At3g06510819829SFR2 (SENSITIVE TO FREEZING 2)Encodes a protein with beta-glucosidase activity, mutants show increased sensitivity to freezingO.I.H.G.S.X.
0.1710.20.80At5g55210835614unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;PO.I.H.G.S.X. (1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE)1-Deoxy-d-xylulose 5-phosphate reductoisomerase (DXR) catalyzes the first committed step of the 2-C-methyl-d-erythritol 4-phosphate pathway for isoprenoid biosynthesis. In Arabidopsis, DXR is encoded by a single-copy gene. Arabidopsis DXR is targeted to plastids and localizes into chloroplasts of leaf cells. DXR knockout or strongly silenced lines have a seedling lethal, albino phenotype. Transgenic, partially silenced lines expressing 35S:DXR have a variegated phenotype.O.I.H.G.S.X. (PLASTID DIVISION2)An integral outer envelope membrane protein (its homolog in A thaliana PDV1), component of the plastid division machinery. Similar to ARC6, PDV2 localizes to a continuous ring at the division site in wild-type plants. PDV1 and PDV2 are required for localization of ARC5 at the chloroplast division site.O.I.H.G.S.X. amino terminal protease family proteinF:molecular_function unknown;P:proteolysis;C:membrane;BOPAO.I.H.G.S.X. hydrolase/ phosphoglycolate phosphataseF:hydrolase activity, catalytic activity, phosphoglycolate phosphatase activity;P:metabolic process;C:chloroplast;BOAFPMO.I.H.G.S.X. protein-relatedF:molecular_function unknown;P:biological_process unknown;C:chloroplast stroma, chloroplast;BPOO.I.H.G.S.X. unknown;P:biological_process unknown;C:chloroplast;AOBPO.I.H.G.S.X. domain-containing protein / polygalacturonase, putativeF:polygalacturonase activity;P:biological_process unknown;C:endomembrane system;OBMPFAVO.I.H.G.S.X. synthase (PSY) / geranylgeranyl-diphosphate geranylgeranyl transferaseEncodes phytoene synthase.O.I.H.G.S.X.;P:unknown;C:chloroplast;POMFBO.I.H.G.S.X. family proteinF:unknown;P:cell redox homeostasis;C:chloroplast stroma, chloroplast;MPOFBAVO.I.H.G.S.X. (abscisic acid (ABA)-deficient 4)Involved in the photoprotection of PSII. aba4-1 mutant completely lacks neoxanthin,a component of the chromophore of the peripheral antenna system in PSII. Expresses neoxanthin synthase activity involved in the neoxanthin biosynthesis, an intermediary in the abscisic acid biosynthesis.O.I.H.G.S.X. (Adenosine monophosphate kinase)F:nucleobase, nucleoside, nucleotide kinase activity, nucleotide kinase activity, ATP binding, adenylate kinase activity, phosphotransferase activity, phosphate group as acceptor;P:nucleobase, nucleoside, nucleotide and nucleic acid metabolic process, anaerobic respiration, nucleotide metabolic process;C:chloroplast, chloroplast stroma;BOMFPAO.I.H.G.S.X. (GLUTATHIONE S-TRANSFERASE TAU 18)Encodes glutathione transferase belonging to the tau class of GSTs. Naming convention according to Wagner et al. (2002).O.I.H.G.S.X. dehydratase, putativeF:imidazoleglycerol-phosphate dehydratase activity;P:histidine biosynthetic process;C:chloroplast;BOFAPMO.I.H.G.S.X. (IAA8) gene is auxin inducible.O.I.H.G.S.X. (guanine-N7-)-methyltransferaseF:tRNA (guanine-N7-)-methyltransferase activity;P:tRNA modification;C:chloroplast;BOMPFO.I.H.G.S.X. family proteinF:hydrolase activity, acting on ester bonds, acyl-CoA thioesterase activity;P:biological_process unknown;C:unknown;BOPAO.I.H.G.S.X. dehydrogenase (NADP), chloroplast, putativeF:oxidoreductase activity, binding, malate dehydrogenase activity, catalytic activity, malate dehydrogenase (NADP+) activity;P:malate metabolic process, carbohydrate metabolic process, metabolic process;C:in 6 components;BOMPFAO.I.H.G.S.X. proteinF:unknown;P:biological_process unknown;C:chloroplast;PBOO.I.H.G.S.X. N-acetyltransferase (GNAT) family proteinF:N-acetyltransferase activity;P:metabolic process;C:chloroplast;BOPAO.I.H.G.S.X. (CONSTANS-LIKE 3)Positive regulator of photomorphogenesis that acts downstream of COP1 but can promote lateral root development independently of COP1 and also function as a daylength-sensitive regulator of shoot branching.O.I.H.G.S.X. a chloroplast form of ATP sulfurylaseO.I.H.G.S.X. migration inhibitory factor family protein / MIF family proteinF:molecular_function unknown;P:inflammatory response, response to other organism;C:chloroplast;MOBPFO.I.H.G.S.X. proteinF:molecular_function unknown;P:biological_process unknown;C:Golgi apparatus;PBOO.I.H.G.S.X. unknown;P:biological_process unknown;C:cellular_component unknown;MFPOBAO.I.H.G.S.X. (SPT4 HOMOLOG 2)F:positive transcription elongation factor activity, zinc ion binding;P:positive regulation of transcription, N-terminal protein myristoylation;C:nucleus;MFOPO.I.H.G.S.X. (D-CYSTEINE DESULFHYDRASE)Encodes an enzyme that decomposes D-cysteine into pyruvate, H2S, and NH3. Only D-cysteine but not L-cysteine was converted by D-CDes to pyruvate, H2S, and NH3. Unlike homologous bacterial enzymes, it does not have 1-aminocyclopropane-1-carboxylate deaminase activity.O.I.H.G.S.X. (HYPERSENSITIVE TO RED AND BLUE)Identified in a screen for mutations hypersensitive to red and blue light. Mutants have shorter hypocotyls. Encodes a nuclear localized protein with similarity to drought induced proteins. Contains a ZZ zinc finger domain which is thought to mediate protein-protein interactions.May be involved in red and blue light signal transduction.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
126.899.9GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
76.999.9GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
73.799.9GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
72.799.9GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
69.899.9GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
66.799.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
66.799.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
66.799.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
66.199.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
65.299.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
64.799.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
63.599.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
63.399.8GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
61.399.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
60.899.8GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
60.299.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
57.699.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
57.499.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
55.099.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
51.199.8GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
49.399.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
46.499.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
44.699.8GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
44.299.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
31.199.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
29.299.7GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
23.499.6GSM142737DH001_ATH1_A4-UNM2GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
22.399.6GSM142738DH001_ATH1_A5-BCP2GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
18.999.5GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
18.899.5GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
18.799.5GSM142735DH001_ATH1_A2-BCP1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
15.399.4GSM142734DH001_ATH1_A1-UNM1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
15.199.4GSM184483Lateral Root Cap root cells 2hr continuous KNO3 treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
14.399.4GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
13.099.4GSM184477Lateral Root Cap root cells 2hr KCl control treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
10.199.2GSM184478Lateral Root Cap root cells 2hr KCl control treated, biological rep3GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.999.1GSM311291Laser 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
9.399.1GSM184480Lateral Root Cap root cells 2hr transitory KNO3 treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
8.799.0GSM10454WT Post-Mature Green Seed 1GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
8.699.0GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0752GO:0010161The series of molecular signals initiated upon sensing of red light by a photoreceptor molecule. Red light is electromagnetic radiation of wavelength of 580-700nm. An example of this response is seen at the beginning of many plant species developmental stages. These include germination, and the point when cotyledon expansion is triggered. In certain species these processes take place in response to absorption of red light by the pigment molecule phytochrome, but the signal can be reversed by exposure to far red light. During the initial phase the phytochrome molecule is only present in the red light absorbing form, but on absorption of red light it changes to a far red light absorbing form, triggering progress through development. An immediate short period of exposure to far red light entirely returns the pigment to its initial state and prevents triggering of the developmental process. A thirty minute break between red and subsequent far red light exposure renders the red light effect irreversible, and development then occurs regardless of whether far red light exposure subsequently occurs.Link to AmiGO
0.0692GO:0016117The chemical reactions and pathways resulting in the formation of carotenoids, tetraterpenoid compounds in which two units of 4 isoprenoid residues joined head-to-tail are themselves joined tail-to-tail.Link to AmiGO
0.0431GO:0032928Any process that modulates the frequency, rate or extent of enzymatic generation of superoxide by a cell.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.060200906Carotenoid biosynthesisLink to KEGG PATHWAY
0.052200630Glyoxylate and dicarboxylate metabolismLink to KEGG PATHWAY
0.034401062Biosynthesis of terpenoids and steroidsLink to KEGG PATHWAY

Inter-species module comparison

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

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