Co-expression analysis

Gene ID At4g00840
Gene name zinc ion binding
Module size 34 genes
NF 0.32
%ile 40.8



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
0.6579.61.00At4g00840826193zinc ion bindingF:zinc ion binding;P:biological_process unknown;C:endomembrane system;MOFPO.I.H.G.S.X.
0.5570.60.87At3g60720825243PDLP8 (PLASMODESMATA-LOCATED PROTEIN 8)Encodes a plasmodesmal protein that may be involved in the intercellular movement of molecules through the plasmodesmata. The protein has two DUF26 domains and a single transmembrane domain.O.I.H.G.S.X.
0.4862.50.87At5g51290835203ceramide kinase-relatedF:diacylglycerol kinase activity;P:activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway;C:cellular_component unknown;MOPBFO.I.H.G.S.X.
0.4659.80.92At3g18350821364unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.4659.80.89At4g00590827968asparaginase 2 family proteinF:hydrolase activity;P:unknown;C:unknown;BOMFPAO.I.H.G.S.X.
0.4558.30.87At3g55820824748-F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PBO.I.H.G.S.X.
0.4355.30.90At5g45370834573nodulin-related / integral membrane family proteinF:unknown;P:unknown;C:membrane;BOPAMFO.I.H.G.S.X.
0.4355.30.89At4g20310827778metalloendopeptidaseF:metalloendopeptidase activity;P:proteolysis;C:membrane;MAPOBFO.I.H.G.S.X.
0.4253.90.87At1g63730842677disease resistance protein (TIR-NBS-LRR class), putativeF:protein binding, transmembrane receptor activity, nucleoside-triphosphatase activity, nucleotide binding, ATP binding;P:defense response;C:intrinsic to membrane;PMBOAFO.I.H.G.S.X.
0.4152.40.88At4g16320--O.I.H.G.S.X.
0.3846.70.88At5g40820834082ATRAD3Encodes a Arabidopsis ortholog of the ATR protein kinase that is involved in a wide range of responses to DNA damage and plays a central role in cell-cycle regulation. Dominant loss of function alleles identified as suppressors of ALS also exhibit increased tolerance to aluminum. This may be due to the inhibition of terminal differentiation of the root apex upon exposure to Al.O.I.H.G.S.X.
0.3643.60.88At4g15240827190fringe-related proteinF:transferase activity, transferring glycosyl groups;P:biological_process unknown;C:Golgi apparatus;PMFOO.I.H.G.S.X.
0.3541.60.88At1g19010838482unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOPFBO.I.H.G.S.X.
0.3439.80.88At2g31340817692emb1381 (embryo defective 1381)F:molecular_function unknown;P:embryonic development ending in seed dormancy;C:cellular_component unknown;PO.I.H.G.S.X.
0.3439.80.90At4g31150829243endonuclease V family proteinF:endonuclease activity;P:DNA repair;C:cellular_component unknown;BAOMPFO.I.H.G.S.X.
0.3338.10.87At4g29560829077unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMO.I.H.G.S.X.
0.3338.10.87At4g14790827134ATSUV3encodes a nuclear-encoded DExH box RNA helicase, which is localized to mitochondria and whose in vitro ATPase activity is stimulated with mitochondrial RNA.O.I.H.G.S.X.
0.3338.10.89At3g50430824207unknown proteinF:unknown;P:unknown;C:unknown;MPO.I.H.G.S.X.
0.3235.70.88At3g63290825504unknown proteinF:molecular_function unknown;P:pollen development;C:cellular_component unknown;FPOBO.I.H.G.S.X.
0.3032.10.88At2g35540818119DNAJ heat shock N-terminal domain-containing proteinF:heat shock protein binding;P:protein folding;C:cellular_component unknown;BMOPFAO.I.H.G.S.X.
0.2830.30.89At1g08060837322MOM (MORPHEUS MOLECULE)F:unknown;P:chromatin silencing;C:nucleus;MFOBPVAO.I.H.G.S.X.
0.2522.60.87At5g51690835243ACS12Encodes an aminotransferase with broad specificity for aspartate and aromatic amino aids such as tyrosine and phenylalanine. It does not act on branched chain amino acids and does not have ACC synthase activity.O.I.H.G.S.X.
0.2420.70.87At2g17970816307oxidoreductase, 2OG-Fe(II) oxygenase family proteinF:oxidoreductase activity;P:biological_process unknown;C:cellular_component unknown;PMOBO.I.H.G.S.X.
0.2319.30.88At4g17895827513UBP20 (UBIQUITIN-SPECIFIC PROTEASE 20)Encodes a ubiquitin-specific protease.O.I.H.G.S.X.
0.2319.30.89At2g32760817836unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPOBO.I.H.G.S.X.
0.2319.30.87At1g30970839984SUF4 (suppressor of FRIGIDA4)Encodes SUF4 (SUPPRESSOR of FRI 4), a putative zinc-finger-containing transcription factor that is required for delayed flowering in winter-annual Arabidopsis. suf4 mutations strongly suppress the late-flowering phenotype of FRI (FRIGIDA) mutants. suf4 mutants also show reduced H3K4 trimethylation at FLC (FLOWERING LOCUS C), a floral inhibitor. SUF4 may act to specifically recruit a putative histone H3 methyltransferase EFS (EARLY FLOWERING IN SHORT DAYS) and the PAF1-like complex to the FLC locus.O.I.H.G.S.X.
0.2319.30.87At5g23150832379HUA2 (ENHANCER OF AG-4 2)Putative transcription factor. Member of the floral homeotic AGAMOUS pathway.Mutations in HUA enhance the phenotype of mild ag-4 allele. Single hua mutants are early flowering and have reduced levels of FLC mRNA. Other MADS box flowering time genes such as FLM and MAF2 also appear to be regulated by HUA2. HUA2 normally activates FLC expression and enhances AG function.O.I.H.G.S.X.
0.2115.80.88At1g08960837416CAX11member of Potassium-dependent sodium-calcium exchanger like-familyO.I.H.G.S.X.
0.2115.80.88At4g19490827690protein bindingPutative homolog of yeast Vps54. Thought to associate with POK and ATVPS53 in a plant GARP-like complex involved in the membrane trafficking system.O.I.H.G.S.X.
0.2014.40.89At2g23140816846binding / ubiquitin-protein ligaseF:ubiquitin-protein ligase activity, binding;P:protein ubiquitination;C:ubiquitin ligase complex;OPMFBVAO.I.H.G.S.X.
0.2014.40.90At1g74860843825unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOPFBVO.I.H.G.S.X.
0.1710.20.87At5g47400834787unknown proteinF:molecular_function unknown;P:unknown;C:endomembrane system;MPOO.I.H.G.S.X.
0.1710.20.88At5g64390836560HEN4 (HUA ENHANCER 4)encodes a K homology (KH) domain-containing, putative RNA binding protein that interacts with HUA1, a CCCH zinc finger RNA binding protein in the nucleus. HEN4 acts redundantly with HUA1 and HUA2 in the specification of floral organ identity in the third whorl.O.I.H.G.S.X.
0.1710.20.89At1g51390841563NFU5Encodes a protein containing the NFU domain that may be involved in iron-sulfur cluster assembly. Part of a five member gene family, more closely related to NFU4 than to NFU1,2, and 3. Targeted to the mitochondrion.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
104.999.9GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
74.599.9GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
73.299.9GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
68.899.9GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
68.399.9GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
59.399.8GSM133765Lindsey_1-17_torpedo-cotyledon_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
58.199.8GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
53.699.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
53.499.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
52.199.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
52.199.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
52.099.8GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
50.799.8GSM284389Arabidopsis GMPE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
50.499.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
50.099.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
48.999.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
48.499.8GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
48.299.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
47.099.8GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
45.799.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
45.199.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
44.799.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
44.499.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
40.799.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.299.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
39.199.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.699.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.399.7GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
35.999.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
35.199.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.299.7GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
25.299.6GSM184894Arabidopsis, root cells, columella root cap, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
25.199.6GSM266668Arabidopsis, root cells, columella root cap, -Fe, replicate 3GSE10501Expression analysis of root cell-types after iron deficiency (-Fe) treatmentLink to GEO
24.399.6GSM266667Arabidopsis, root cells, columella root cap, -Fe, replicate 2GSE10501Expression analysis of root cell-types after iron deficiency (-Fe) treatmentLink to GEO
23.699.6GSM266666Arabidopsis, root cells, columella root cap, -Fe, replicate 1GSE10501Expression analysis of root cell-types after iron deficiency (-Fe) treatmentLink to GEO
18.799.5GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
18.599.5GSM133766Lindsey_1-18_torpedo-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
18.299.5GSM67087Arabidopsis_Stigma03GSE3056Arabidopsis Pollination StudyLink to GEO
17.999.5GSM67086Arabidopsis_Stigma02GSE3056Arabidopsis Pollination StudyLink to GEO
15.799.5E-MEXP-1725-raw-cel-1669614623
13.699.4GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
13.199.4E-MEXP-1725-raw-cel-1669614634
12.299.3GSM184912Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
11.299.2GSM67084Arabidopsis_Stigma01GSE3056Arabidopsis Pollination StudyLink to GEO
11.199.2GSM67078Arabidopsis_Ovary01GSE3056Arabidopsis Pollination StudyLink to GEO
11.199.2GSM131303AtGen_6-2611_Osmoticstress-Shoots-24.0h_Rep1GSE5622AtGenExpress: Stress Treatments (Osmotic stress)Link to GEO
10.799.2GSM67080Arabidopsis_Ovary03GSE3056Arabidopsis Pollination StudyLink to GEO
10.599.2GSM133759Lindsey_1-9_heart-stage-cotyledon_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
10.199.2GSM133303RIKEN-NAKABAYASHI1AGSE5700AtGenExpress: Effect of ABA during seed imbibitionLink to GEO
10.199.2GSM67081Arabidopsis_Ovary04GSE3056Arabidopsis Pollination StudyLink to GEO
9.799.1GSM311276Laser capture microdissected (LCM) micropylar endospermr at the pre-globular stage, biological replicate 2GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
9.599.1GSM311275Laser 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
9.499.1GSM133304RIKEN-NAKABAYASHI1BGSE5700AtGenExpress: Effect of ABA during seed imbibitionLink to GEO
9.199.1GSM133117RIKEN-YAMAUCHI1AGSE5687AtGenExpress: Different temperature treatment of seedsLink to GEO
9.199.1E-MEXP-1725-raw-cel-1669614562
9.199.1GSM184893Arabidopsis, root cells, columella root cap, standard conditions, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
9.199.1E-MEXP-1725-raw-cel-1669614582
8.999.0GSM284388Arabidopsis GMPE1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
8.899.0GSM184892Arabidopsis, root cells, columella root cap, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
8.799.0GSM131706ATGE_84_AGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
8.799.0E-ATMX-35-raw-cel-1574334880

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0572GO:0009910Any process that stops, prevents or reduces the frequency, rate or extent of flower development.Link to AmiGO
0.0561GO:0007004The maintenance of proper telomeric length by the addition of telomeric repeats by telomerase.Link to AmiGO
0.0561GO:0032204Any process that modulates the frequency, rate or extent of a process that affects and monitors the activity of telomeric proteins and the length of telomeric DNA.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG

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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