Co-expression analysis

Gene ID At3g06740
Gene name zinc finger (GATA type) family protein
Module size 31 genes
NF 0.18
%ile 14.8



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
0.6781.61.00At3g06740819859zinc finger (GATA type) family proteinF:transcription factor activity;P:regulation of transcription, DNA-dependent;C:nucleus;PFMOO.I.H.G.S.X.
0.4355.30.82At5g65360836661histone H3F:DNA binding;P:nucleosome assembly;C:nucleus, chloroplast, nucleosome;MFPOO.I.H.G.S.X.
0.3948.40.81At3g20670821614HTA13Encodes HTA13, a histone H2A protein.O.I.H.G.S.X.
0.3338.10.83At3g62060825379pectinacetylesterase family proteinF:carboxylesterase activity;P:biological_process unknown;C:endomembrane system;PMOBO.I.H.G.S.X.
0.3338.10.83At5g08020830696RPA70B (RPA70-KDA SUBUNIT B)Encodes a homolog of Replication Protein A. rpa70b mutants are hypersensitive to UV-B radiation and MMS treatments suggesting a role for this protein in DNA damage repair.O.I.H.G.S.X.
0.3235.70.82At5g61000836221replication protein, putativeF:DNA binding, nucleic acid binding;P:DNA replication;C:nucleus;PMOFAO.I.H.G.S.X.
0.2726.20.81At1g65900842902unknown proteinF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;BPAOO.I.H.G.S.X.
0.2624.40.83At3g24495822040MSH7 (MUTS HOMOLOG 7)encodes a DNA mismatch repair homolog of human MutS gene, MSH6. There are four MutS genes in Arabidopsis, MSH2, MSH3, MSH6, and MSH7, which all act as heterodimers and bind to 51-mer duplexes. MSH2*MSH7 exhibit moderate affinity for a (T/G) substrate and weak binding of (+T), suggesting MSH2*MSH7 may be specialized for lesions/base mispairs not tested or for (T/G) mispairs in special contexts.O.I.H.G.S.X.
0.2522.60.82At5g48600834917ATSMC3 (ARABIDOPSIS THALIANA STRUCTURAL MAINTENANCE OF CHROMOSOME 3)member of SMC subfamilyO.I.H.G.S.X.
0.2522.60.81At3g14740820702PHD finger family proteinF:protein binding, zinc ion binding;P:unknown;C:unknown;MFPOO.I.H.G.S.X.
0.2522.60.81At3g19590821496WD-40 repeat family protein / mitotic checkpoint protein, putativeF:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex;MBFOPAO.I.H.G.S.X.
0.2522.60.82At2g24490816985RPA2 (REPLICON PROTEIN A2)Encodes a component of Replication Protein A. Component of transcriptional gene silencing which does not affect endogenous small RNA accumulation nor DNA methylation. Localized in the nucleus. Involved in DNA repair. Interacts physically with ROS1.O.I.H.G.S.X.
0.2420.70.81At1g14180837977protein binding / zinc ion bindingF:protein binding, zinc ion binding;P:biological_process unknown;C:unknown;PO.I.H.G.S.X.
0.2420.70.82At1g07790837293HTB1Encodes a histone 2B (H2B) protein.O.I.H.G.S.X.
0.2217.50.83At5g01910831775unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;MPOFO.I.H.G.S.X.
0.2217.50.83At5g59690836090histone H4F:DNA binding;P:nucleosome assembly;C:thylakoid;MOPFVO.I.H.G.S.X.
0.2217.50.81At3g25100822101CDC45 (cell division cycle 45)Required for normal meiosis, may act in the last round of DNA replication prior to meiosis, sequence similar to yeast CDC45O.I.H.G.S.X.
0.2115.80.82At5g62710836392leucine-rich repeat family protein / protein kinase family proteinF:protein binding, protein serine/threonine kinase activity, protein kinase activity, ATP binding;P:protein amino acid phosphorylation;C:endomembrane system;PMOBFVAO.I.H.G.S.X.
0.2115.80.82At1g01370839104HTR12Encodes a centromere-identifying protein histone H3 variant. Localized at centromeres in both mitotic and meiotic cells.O.I.H.G.S.X.
0.2115.80.81At3g61610825334aldose 1-epimerase family proteinF:carbohydrate binding, isomerase activity, aldose 1-epimerase activity, catalytic activity;P:galactose metabolic process, N-terminal protein myristoylation, carbohydrate metabolic process;C:cellular_component unknown;BOPFMO.I.H.G.S.X.
0.1710.20.81At1g15570838127CYCA2A2-type cyclin. Negatively regulates endocycles and acts as a key regulator of ploidy levels in Arabidopsis endoreduplication. Interacts physically with CDKA;1. Expressed preferentially in trichomes and young developing tissues.O.I.H.G.S.X.
0.168.80.83At2g42120818812POLD2 (DNA POLYMERASE DELTA SMALL SUBUNIT)F:DNA binding, DNA-directed DNA polymerase activity;P:DNA replication;C:nucleus;OMFAPO.I.H.G.S.X.
0.146.80.81At1g16520838222unknown proteinF:molecular_function unknown;P:biological_process unknown;C:plasma membrane;PMOFAO.I.H.G.S.X.
0.135.80.81At4g09510826535beta-fructofuranosidase, putative / invertase, putative / saccharase, putative / beta-fructosidase, putativeF:catalytic activity, beta-fructofuranosidase activity;P:biological_process unknown;C:cellular_component unknown;OPBO.I.H.G.S.X.
0.124.90.81At1g21560838757unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PBMO.I.H.G.S.X.
0.114.10.82At3g13560820558glycosyl hydrolase family 17 proteinF:cation binding, hydrolase activity, hydrolyzing O-glycosyl compounds, catalytic activity;P:carbohydrate metabolic process;C:anchored to plasma membrane, plasma membrane, anchored to membrane;PFOO.I.H.G.S.X.
0.082.30.82At3g45980823741HTB9Encodes a histone 2B (H2B) protein. This protein can be ubiquitinated in planta, and this modification depends on the HUB1 and HUB2 E3 ubiquitin ligases as well as the UBC1 and UBC2 E2 ubiquitin conjugating enzymes. Lysine 146 appears to be the site of the ubiquitin addition.O.I.H.G.S.X.
0.071.90.83At2g48120819424PAC (PALE CRESS)The pale cress (pac) mutant affects chloroplast and leaf development; mutants are ABA-deficient and accumulate lower levels of carotenoids and chlorophyll compared to wild type. PAC is probably involved in chloroplast mRNA maturation. Three alternative transcripts of this gene exist.O.I.H.G.S.X.
0.061.40.83At4g26840828791SUMO1 (SMALL UBIQUITIN-LIKE MODIFIER 1)Encodes a small ubiquitin-like modifier (SUMO) polypeptide that becomes covalently attached to various intracellular protein targets, much like ubiquitination, leading to post-translational modification of those targets.O.I.H.G.S.X.
0.040.90.84At1g33040840199NACA5 (NASCENT POLYPEPTIDE-ASSOCIATED COMPLEX SUBUNIT ALPHA-LIKE PROTEIN 5)F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFPBVAO.I.H.G.S.X.
0.030.60.84At5g10320830896unknown proteinF:molecular_function unknown;P:unknown;C:unknown;PBO.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
96.899.9GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
66.699.8GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
49.699.8GSM284392Arabidopsis GCE1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
48.199.8GSM284393Arabidopsis GCE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
43.799.8GSM284389Arabidopsis GMPE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
42.699.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
42.199.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
42.199.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.799.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
39.099.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.699.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
38.399.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.999.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.899.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.399.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.299.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
33.299.7GSM284394Arabidopsis GCE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
33.199.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.799.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.699.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.199.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
29.899.7GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
29.499.7GSM133861Beynon_1-4-cat-SpikeMix4_Rep1_ATH1GSE5739Comparison of CATMA, Affymetrix and Agilent arraysLink to GEO
29.499.7GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
29.399.7GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
26.799.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
25.199.6GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
24.999.6GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
24.299.6GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
23.999.6GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
23.199.6GSM284388Arabidopsis GMPE1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
21.099.6GSM184480Lateral Root Cap root cells 2hr transitory KNO3 treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
16.299.5GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
15.899.5GSM10479lec1-1 Cotyledon Stage Seed 1GSE1051Seed development in LEAFY COTYLEDON1 mutantsLink to GEO
15.899.5GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
15.599.5GSM184483Lateral Root Cap root cells 2hr continuous KNO3 treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
14.399.4GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
13.899.4GSM311280Laser 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
13.599.4GSM10480lec1-1 Cotyledon Stage Seed 2GSE1051Seed development in LEAFY COTYLEDON1 mutantsLink to GEO
13.499.4GSM184477Lateral Root Cap root cells 2hr KCl control treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
13.399.4GSM311279Laser 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
12.999.3GSM10448WT Cotyledon Stage Seed 1GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
12.599.3GSM184484Lateral Root Cap root cells 2hr continuous KNO3 treated, biological rep3GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
12.599.3GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
11.699.3GSM311276Laser 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
11.199.2GSM311294Laser capture microdissected (LCM) chalazal seed coat at the linear-cotyledon stage, biological replicate 2GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
11.099.2GSM142751MJ001_ATH1_A2-jones-WT2GSE6165The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.Link to GEO
10.999.2GSM184478Lateral Root Cap root cells 2hr KCl control treated, biological rep3GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
10.999.2GSM142750MJ001_ATH1_A1-jones-WT1GSE6165The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.Link to GEO
10.399.2GSM184481Lateral Root Cap root cells 2hr transitory KNO3 treated, biological rep3GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.499.1GSM311275Laser 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
9.299.1GSM284386Arabidopsis GSUS3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
9.299.1GSM133860Beynon_1-3-cat-SpikeMix3_Rep1_ATH1GSE5739Comparison of CATMA, Affymetrix and Agilent arraysLink to GEO
9.099.1GSM10449WT Cotyledon Stage Seed 2GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
8.899.0GSM133766Lindsey_1-18_torpedo-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1125GO:0006334The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.Link to AmiGO
0.1004GO:0006260The process whereby new strands of DNA are synthesized. The template for replication can either be an existing DNA molecule or RNA.Link to AmiGO
0.0631GO:0006279The replication of DNA that precedes meiotic cell division.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.071203440Homologous recombinationLink to KEGG PATHWAY
0.070203430Mismatch repairLink to KEGG PATHWAY
0.059203030DNA replicationLink 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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