Co-expression analysis

Gene ID At2g15580
Gene name zinc finger (C3HC4-type RING finger) family protein
Module size 33 genes
NF 0.23
%ile 23.2



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
1.00100.01.00At2g15580816051zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:unknown;C:unknown;PMOFBVO.I.H.G.S.X.
0.4050.80.85At1g31170840004SRX (SULFIREDOXIN)encodes a cysteine-sulfinic acid reductase (sulfiredoxin - EC 1.8.98.2) capable of reducing overoxidized plastidic 2-Cys-Prx involved in peroxide detoxification and response to oxidative stressO.I.H.G.S.X.
0.3643.60.85At3g13062820493-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOO.I.H.G.S.X.
0.3439.80.86At2g20920816626unknown proteinF:unknown;P:unknown;C:membrane;BPOO.I.H.G.S.X.
0.3133.80.84At5g11840831057unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;OBPO.I.H.G.S.X.
0.2930.30.84At1g60010842295unknown proteinF:molecular_function unknown;P:N-terminal protein myristoylation;C:cellular_component unknown;PFOO.I.H.G.S.X.
0.2930.30.83At1g13090837866CYP71B28putative cytochrome P450O.I.H.G.S.X.
0.2930.30.84At4g27990828912YGGT family proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast, chloroplast envelope;BOPO.I.H.G.S.X.
0.2830.30.84At1g02475839236-F:molecular_function unknown;P:biological_process unknown;C:chloroplast;BOPO.I.H.G.S.X.
0.2726.20.85At5g13720831217-F:unknown;P:unknown;C:chloroplast, chloroplast inner membrane, chloroplast envelope;BOPAO.I.H.G.S.X.
0.2726.20.85At3g53470824515unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast thylakoid membrane, chloroplast;PO.I.H.G.S.X.
0.2726.20.84At4g27800828893protein phosphatase 2C PPH1 / PP2C PPH1 (PPH1)F:protein serine/threonine phosphatase activity, catalytic activity;P:protein amino acid dephosphorylation;C:nucleolus, nucleus, chloroplast, protein serine/threonine phosphatase complex, cytoplasm;PMOFBVAO.I.H.G.S.X.
0.2624.40.86At5g23440832410FTRA1 (ferredoxin/thioredoxin reductase subunit A (variable subunit) 1)F:ferredoxin:thioredoxin reductase activity, lipoate synthase activity, catalytic activity, ferredoxin reductase activity;P:photosynthesis, light reaction, lipoate biosynthetic process, photosynthesis;C:chloroplast;BPFOO.I.H.G.S.X.
0.2624.40.83At4g08920826470CRY1 (CRYPTOCHROME 1)Encodes CRY1, a flavin-type blue-light photoreceptor with ATP binding and autophosphorylation activity. The photoreceptor may be involved in electron transport. Mutant phenotype displays a blue light-dependent inhibition of hypocotyl elongation. Photoreceptor activity requires light-induced homodimerisation of the N-terminal CNT1 domains of CRY1. Involved in blue-light induced stomatal opening. The C-terminal domain of the protein undergoes a light dependent conformational change. Also involved in response to circadian rhythm. Mutants exhibit long hypocotyl under blue light and are out of phase in their response to circadian rhythm. CRY1 is present in the nucleus and cytoplasm. Different subcellular pools of CRY1 have different functions during photomorphogenesis of Arabidopsis seedlings.O.I.H.G.S.X.
0.2420.70.83At1g77930844128DNAJ heat shock N-terminal domain-containing proteinF:heat shock protein binding;P:protein folding;C:chloroplast;BOMFPAVO.I.H.G.S.X.
0.2420.70.86At2g14910815980unknown proteinF:unknown;P:unknown;C:chloroplast;BOPMO.I.H.G.S.X.
0.2420.70.85At2g39000818486GCN5-related N-acetyltransferase (GNAT) family proteinF:N-acetyltransferase activity;P:metabolic process;C:chloroplast;BPOAFMO.I.H.G.S.X.
0.2217.50.84At1g10500837590ATCPISCA (chloroplast-localized IscA-like protein)Involved in chloroplast Fe-S cluster assembly. Located in the chloroplast stroma. Expressed preferentially in green tissues.O.I.H.G.S.X.
0.2115.80.83At1g043508395422-oxoglutarate-dependent dioxygenase, putativeencodes a protein whose sequence is similar to 2-oxoglutarate-dependent dioxygenaseO.I.H.G.S.X.
0.2115.80.84At4g23890828489unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast thylakoid membrane, chloroplast;OBPMFO.I.H.G.S.X.
0.2014.40.84At1g55000841942peptidoglycan-binding LysM domain-containing proteinF:molecular_function unknown;P:cell wall macromolecule catabolic process;C:endomembrane system;MPOBO.I.H.G.S.X.
0.1811.40.85At1g49970841420CLPR1Encodes a ClpP-related sequence. Though similar to ClpP proteins, this does not contains the highly conserved catalytic triad of Ser-type proteases (Ser-His-Asp). The name reflects nomenclature described in Adam et. al (2001).O.I.H.G.S.X.
0.1811.40.83At5g02790831798In2-1 protein, putativeF:unknown;P:response to cadmium ion;C:unknown;PBMOFAO.I.H.G.S.X.
0.1710.20.85At3g19800821517unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.168.80.84At4g25910828697NFU3Encodes 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 NFU1 and 2 than to NFU4 and 5. Targeted to the chloroplast.O.I.H.G.S.X.
0.146.80.84At1g74880843827NDH-O (NAD(P)H:plastoquinone dehydrogenase complex subunit O)Encodes subunit NDH-O 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.
0.146.80.84At1g68660843196-F:molecular_function unknown;P:protein catabolic process;C:unknown;BOPO.I.H.G.S.X.
0.135.80.83At5g51020835175CRL (CRUMPLED LEAF)Encodes CRL (CRUMPLED LEAF), a protein localized in the outer envelope membrane of plastids. Mutation in this gene affects the pattern of cell division, cell differentiation and plastid division.O.I.H.G.S.X.
0.124.90.84At2g26340817174unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast thylakoid membrane, chloroplast thylakoid lumen, chloroplast;PO.I.H.G.S.X.
0.114.10.83At1g23310838940GGT1 (GLUTAMATE:GLYOXYLATE AMINOTRANSFERASE)Identified by cloning the gene that corresponded to a purified protein having glyoxylate aminotransferase activity. Localized to the peroxisome and thought to be involved in photorespiration/ metabolic salvage pathway.O.I.H.G.S.X.
0.103.40.84At1g35420840434dienelactone hydrolase family proteinF:hydrolase activity;P:biological_process unknown;C:chloroplast, chloroplast stroma;BFOPMAO.I.H.G.S.X.
0.071.90.83At4g03520825653ATHM2chloroplast localized thioredoxin, similar to prokaryotic types.O.I.H.G.S.X.
0.061.40.84At1g01490839440heavy-metal-associated domain-containing proteinF:metal ion binding;P:metal ion transport;C:cellular_component unknown;MOPBFVAO.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
59.599.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
56.399.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
53.999.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
52.499.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
52.299.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
49.799.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
49.699.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
48.699.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
48.199.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
46.599.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
46.399.8GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
44.199.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
44.099.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.399.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
42.999.8GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
42.999.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.099.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.099.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.699.8GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
38.099.8GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
35.199.7GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
34.499.7GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
31.399.7GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
29.499.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
29.299.7GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
29.199.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
26.199.7GSM265423Arabidopsis, root, longitudinal zone 3, standard conditions, rep 2GSE10497Expression analysis of root developmental zones after iron deficiency (-Fe) treatmentLink to GEO
26.199.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
21.499.6E-MEXP-1443-raw-cel-1581869573
20.799.6GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
16.799.5GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
16.299.5GSM265431Arabidopsis, root, longitudinal zone 3, -Fe conditions, rep 2GSE10497Expression analysis of root developmental zones after iron deficiency (-Fe) treatmentLink to GEO
13.599.4GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
13.399.4E-MEXP-807-raw-cel-1173273144
12.399.3GSM265430Arabidopsis, root, longitudinal zone 3, -Fe conditions, rep 1GSE10497Expression analysis of root developmental zones after iron deficiency (-Fe) treatmentLink to GEO
11.799.3GSM184911Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
11.599.3E-MEXP-807-raw-cel-1173273252
10.999.2GSM184922Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
10.399.2GSM265422Arabidopsis, root, longitudinal zone 3, standard conditions, rep1GSE10497Expression analysis of root developmental zones after iron deficiency (-Fe) treatmentLink to GEO
9.699.1GSM131577ATGE_31_B2GSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
9.599.1GSM131607ATGE_42_CGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
9.399.1GSM131578ATGE_31_C2GSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
9.299.1GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
9.099.1GSM131576ATGE_31_A2GSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
9.099.1GSM39198RRE1_Chitin4GSE2169rre1 and rre2 mutantsLink to GEO
8.699.0E-MEXP-807-raw-cel-1173273170
8.699.0GSM184920Arabidopsis, root cells, stele, 140 mM NaCls, 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
0.0752GO:0016226The incorporation of iron and exogenous sulfur into a metallo-sulfur cluster.Link to AmiGO
0.0591GO:0010343Programmed cell death induced by singlet oxygen. Programmed cell death is the cell death resulting from activation of endogenous cellular processes.Link to AmiGO
0.0561GO: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

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.032104712Circadian rhythm - plantLink to KEGG PATHWAY
0.027100250Alanine, aspartate and glutamate metabolismLink to KEGG PATHWAY
0.020100945Stilbenoid, diarylheptanoid and gingerol biosynthesisLink 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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