Co-expression analysis

Gene ID At5g40250
Gene name zinc finger (C3HC4-type RING finger) family protein
Module size 37 genes
NF 0.14
%ile 10.8



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
1.00100.01.00At5g40250834023zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:unknown;C:unknown;PMOFVO.I.H.G.S.X.
0.3643.60.88At2g35330818100protein binding / zinc ion bindingF:protein binding, zinc ion binding;P:unknown;C:unknown;MOBFPAVO.I.H.G.S.X.
0.3133.80.88At1g03280838581transcription initiation factor IIE (TFIIE) alpha subunit family protein / general transcription factor TFIIE family proteinF:RNA polymerase II transcription factor activity, transcription initiation factor activity;P:transcription initiation from RNA polymerase II promoter;C:endomembrane system, transcription factor TFIIE complex;MFOPVBAO.I.H.G.S.X.
0.2726.20.87At3g54010824568PAS1 (PASTICCINO 1)Immunophilin-like protein similar to the p59 FK506-binding protein (FKBP52). Shows rotamase activity and contains an FKBP-like domain and three tetratricopeptide repeat units. Members of this class of mutation show ectopic cell proliferation in cotyledons. Gene may be alternatively spliced.O.I.H.G.S.X.
0.2522.60.86At5g26600832730catalytic/ pyridoxal phosphate bindingF:pyridoxal phosphate binding, catalytic activity;P:metabolic process;C:chloroplast;BOFAPMVO.I.H.G.S.X.
0.2522.60.86At5g60570836178kelch repeat-containing F-box family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOBVAFO.I.H.G.S.X.
0.2319.30.87At5g09410830800EICBP.B (ETHYLENE INDUCED CALMODULIN BINDING PROTEIN)calmodulin-binding protein, similar to another ethylene-upregulated calmodulin-binding protein ER1 GI:11612392 from (Nicotiana tabacum)O.I.H.G.S.X.
0.2319.30.86At1g61040842395VIP5 (vernalization independence 5)Encodes a yeast Paf1C subunit homolog required for the expression of the MADS box gene FLC and other members of the FLC/MAF MADS-box gene family.O.I.H.G.S.X.
0.2115.80.87At1g26830839226ATCUL3 (ARABIDOPSIS THALIANA CULLIN 3)Cullin, putative, similar to Cullin homolog 3 (CUL-3) SP:Q13618, GI:3639052 from (Homo sapiens); contains Pfam profile PF00888: Cullin family. Interacts with other components of E3 ligase complex suggesting it functions in RUB-modification. Forms complexes with BTB domain proteins forming a novel class of E3-based ubiquitin protein-ligase complexes. Mutant is early flowering and has a reduced sensitivity to far-red light. cul3a/cul3b homozygous/heterozygous plants are embryo lethal.O.I.H.G.S.X.
0.2014.40.86At1g59650842255CW14Encodes CW14.O.I.H.G.S.X.
0.2014.40.86At5g37370833711ATSRL1encodes a putative splicing factor. Over-expression in yeast and Arabidopsis result in increased tolerance to high salt.O.I.H.G.S.X.
0.1912.70.87At5g66950836829catalytic/ pyridoxal phosphate bindingF:pyridoxal phosphate binding, catalytic activity;P:biological_process unknown;C:plasma membrane;PMFOBAO.I.H.G.S.X.
0.1811.40.87At3g06400819814CHR11 (CHROMATIN-REMODELING PROTEIN 11)Encodes a SWI2/SNF2 chromatin remodeling protein belonging to the ISWI family. Involved in nuclear proliferation during megagametogenesis and cell expansion in the sporophyte. Constitutively expressed. RNAi induced loss of function in megagametogenesis results in female sterility.35S:RNAi plants have reduced stature.O.I.H.G.S.X.
0.1710.20.86At3g51390824302zinc finger (DHHC type) family proteinF:zinc ion binding;P:biological_process unknown;C:plasma membrane;MOFPO.I.H.G.S.X.
0.1710.20.86At5g42560834262abscisic acid-responsive HVA22 family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPFOBVO.I.H.G.S.X.
0.157.80.86At3g18990821432VRN1 (REDUCED VERNALIZATION RESPONSE 1)Required for vernalization. Essential for the complete repression of FLC in vernalized plants. Required for the methylation of histone H3O.I.H.G.S.X.
0.146.80.87At5g26610832729D111/G-patch domain-containing proteinF:zinc ion binding, nucleic acid binding;P:biological_process unknown;C:intracellular;MOFPBVAO.I.H.G.S.X.
0.146.80.86At4g11860826793-F:molecular_function unknown;P:biological_process unknown;C:cytosol, nucleus, plasma membrane;MFOPBO.I.H.G.S.X.
0.146.80.87At5g43320834350ckl8 (Casein Kinase I-like 8)F:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cellular_component unknown;MOPBFVAO.I.H.G.S.X.
0.146.80.86At3g12950820480catalyticF:catalytic activity;P:biological_process unknown;C:cellular_component unknown;PBOFO.I.H.G.S.X.
0.146.80.87At3g21865821741PEX22 (peroxin 22)Interacts with PEX4 in a yeast two-hybrid. The PEX4 and PEX22 pair may be important during the remodeling of peroxisome matrix contents as glyoxysomes transition to leaf peroxisomes.O.I.H.G.S.X.
0.135.80.86At5g08080830702SYP132 (SYNTAXIN OF PLANTS 132)member of SYP13 Gene FamilyO.I.H.G.S.X.
0.135.80.88At5g42470834254-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOO.I.H.G.S.X.
0.124.90.86At1g47330841136-F:molecular_function unknown;P:biological_process unknown;C:plasma membrane;BOMFPAO.I.H.G.S.X.
0.124.90.88At4g27040828812VPS22F:molecular_function unknown;P:vesicle-mediated transport;C:ESCRT II complex;MFOPO.I.H.G.S.X.
0.124.90.86At4g10050826596hydrolase, alpha/beta fold family proteinF:hydrolase activity;P:unknown;C:vacuole;BOMFPAVO.I.H.G.S.X.
0.114.10.86At1g79030844244DNAJ heat shock N-terminal domain-containing protein / S-locus protein, putativeF:unfolded protein binding, heat shock protein binding;P:protein folding;C:cellular_component unknown;BOMFPAVO.I.H.G.S.X.
0.103.40.89At1g17210838292zinc ion bindingF:zinc ion binding;P:unknown;C:cytosol, nucleus, phragmoplast;OMPFBAO.I.H.G.S.X.
0.103.40.86At2g42700818870-F:molecular_function unknown;P:vesicle-mediated transport, vesicle docking during exocytosis;C:cellular_component unknown;MPOO.I.H.G.S.X.
0.103.40.86At5g05980830484ATDFB (A. THALIANA DHFS-FPGS HOMOLOG B)F:tetrahydrofolylpolyglutamate synthase activity;P:one-carbon compound metabolic process;C:chloroplast stroma;BOFMPAO.I.H.G.S.X.
0.092.80.86At1g17760838354CSTF77Encodes a homolog of the mammalian protein CstF77, a polyadenylation factor subunit.O.I.H.G.S.X.
0.092.80.86At1g22860838891unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOPBO.I.H.G.S.X.
0.082.30.86At4g16440827338ferredoxin hydrogenaseEncodes a [FeFe]-hydrogenase-like protein named Gollum (for Growth in different Oxygen LeveLs inflUences Morphogenesis). Heterologous expression of Gollum in E. coli indicates that it probably contains two [Fe-S] clusters with different magnetic properties. Sequence alignment analysis indicates that these two clusters would be topologically equivalent to the mesial and proximal [Fe-S] centers of [FeFe]-hydrogenases. Knockdown mutants (RNAi) show a dwarf phenotype at the normal atmospheric partial oxygen pressure of 21 kPa. This dwarf phenotype could be rescued by growing the plant under low oxygen pressure (5kPa), suggesting a role for this gene in oxygen sensing.O.I.H.G.S.X.
0.082.30.87At5g61840836306GUT1F:glucuronoxylan glucuronosyltransferase activity, catalytic activity;P:secondary cell wall biogenesis, glucuronoxylan biosynthetic process;C:Golgi apparatus, membrane;PMOBFO.I.H.G.S.X.
0.071.90.87At1g12470837804Pep3/Vps18/deep orange family proteinF:protein binding, zinc ion binding;P:unknown;C:unknown;MFOPBO.I.H.G.S.X.
0.071.90.86At4g24550828557clathrin adaptor complexes medium subunit family proteinF:protein binding;P:intracellular protein transport, transport, vesicle-mediated transport;C:membrane coat, clathrin vesicle coat, clathrin adaptor complex;MFOPO.I.H.G.S.X.
0.040.90.87At1g68070843135zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:unknown;C:plasma membrane;PMOFVBO.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
96.099.9GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
67.399.8GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
57.399.8GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
54.299.8GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
43.799.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.499.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.099.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.899.8GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
41.899.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.299.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.199.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.099.8GSM154508Arabidopsis growing pollen tubes rep2GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
40.999.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
39.699.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
38.299.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.799.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.799.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.599.7GSM284394Arabidopsis GCE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
37.099.7GSM184900Arabidopsis, root cells, endodermis and quiescent center, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
36.599.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.999.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
35.399.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.499.7GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
31.899.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
28.699.7GSM133775Lindsey_1-27_torpedo-meristem_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
28.399.7GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
25.299.6GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
24.799.6GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
24.099.6GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
17.399.5GSM184477Lateral Root Cap root cells 2hr KCl control treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
15.799.5GSM13779Dexamethasone plus cycloheximideGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
14.499.4GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
14.399.4GSM13780CycloheximideGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
13.799.4GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
13.399.4GSM284392Arabidopsis GCE1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
13.399.4GSM311280Laser 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
12.899.3GSM284393Arabidopsis GCE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
12.599.3GSM154507Arabidopsis growing pollen tubes rep1GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
12.099.3GSM13783Dexamethasone plus cycloheximide - replicateGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
11.999.3GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
11.899.3E-MEXP-1443-raw-cel-1581869515
11.599.3GSM133766Lindsey_1-18_torpedo-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
10.599.2GSM311292Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 2GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
10.499.2GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
10.399.2GSM13784Cycloheximide - replicateGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
10.099.2GSM184480Lateral Root Cap root cells 2hr transitory KNO3 treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.899.1GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
9.699.1GSM184483Lateral Root Cap root cells 2hr continuous KNO3 treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.299.1GSM184898Arabidopsis, root cells, endodermis and quiescent center, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
8.699.0GSM311279Laser capture microdissected (LCM) chalazal endosperm at the pre-globular stage, biological replicate 1GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0451GO:0045893Any process that activates or increases the frequency, rate or extent of DNA-dependent transcription.Link to AmiGO
0.0441GO:0010417The chemical reactions and pathways resulting in the formation of glucuronoxylan, a polymer containing a beta-1,4-linked D-xylose backbone substituted with glucuronic acid residues.Link to AmiGO
0.0421GO:0050826A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a freezing stimulus, temperatures below 0 degrees Celsius.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.029103022Basal transcription factorsLink to KEGG PATHWAY
0.020104144EndocytosisLink to KEGG PATHWAY
0.015104120Ubiquitin mediated proteolysisLink 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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