Co-expression analysis

Gene ID At2g19810
Gene name zinc finger (CCCH-type) family protein
Module size 70 genes
NF 0.22
%ile 21.1

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
1.00100.01.00At2g19810816500zinc finger (CCCH-type) family proteinF:transcription factor activity, nucleic acid binding;P:regulation of transcription;C:unknown;POMO.I.H.G.S.X.
0.4152.40.78At1g75800843913pathogenesis-related thaumatin family proteinF:molecular_function unknown;P:response to other organism;C:endomembrane system;PMFBOVAO.I.H.G.S.X.
0.3745.00.83At1g67340843055zinc finger (MYND type) family protein / F-box family proteinF:binding, zinc ion binding;P:biological_process unknown;C:nucleus;BMFPOVO.I.H.G.S.X.
0.3439.80.78At4g00335828093RHB1AF:protein binding, zinc ion binding;P:N-terminal protein myristoylation;C:unknown;PMOFVO.I.H.G.S.X.
0.3235.70.78At1g68490843178unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;PO.I.H.G.S.X.
0.3235.70.80At4g29820829104CFIM-25Encodes a homolog of the protein CFI-25, a polyadenylation factor subunit.O.I.H.G.S.X.
0.3235.70.81At5g35330833487MBD02 (METHYL-CPG-BINDING DOMAIN PROTEIN 02)Protein containing methyl-CpG-binding domain.Has sequence similarity to human MBD proteins.O.I.H.G.S.X.
0.3032.10.79At3g14100820626oligouridylate-binding protein, putativeF:mRNA 3'-UTR binding;P:unknown;C:unknown;MPFOBO.I.H.G.S.X.
0.2930.30.80At5g16380831499unknown proteinF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;POO.I.H.G.S.X.
0.2930.30.78At1g56280842081ATDI19Encodes a gene whose transcript level in root and leaves increases to progressive drought stress. The increase in transcript level is independent from abscisic acid level. Sequence is not similar to any protein of known function. It appears to be a member of plant-specific gene family. It's phosphorylated by AtCPK11 in a Ca(2+)-dependent manner at Thr105 and Ser107 within the AtDi19 bipartite nuclear localization signalO.I.H.G.S.X.
0.2930.30.78At5g10860830953CBS domain-containing proteinF:unknown;P:response to salt stress;C:mitochondrion;BOAPFMO.I.H.G.S.X.
0.2930.30.78At2g01570814686RGA1 (REPRESSOR OF GA1-3 1)Member of the VHIID/DELLA regulatory family. Contains homopolymeric serine and threonine residues, a putative nuclear localization signal, leucine heptad repeats, and an LXXLL motif. Putative transcriptional regulator repressing the gibberellin response and integration of phytohormone signalling. DELLAs repress cell proliferation and expansion that drives plant growth. The protein undergoes degradation in response to GA via the 26S proteasome. RGA1 binds to PIF3 and inhibits its DNA binding activity and thus affects the expression of PIF3 regulated genes. RGA may be involved in reducing ROS accumulation in response to stress by up-regulating the transcription of superoxide dismutases. Represses GA-induced vegetative growth and floral initiation. Rapidly degraded in response to GA. Involved in fruit and flower development.O.I.H.G.S.X.
0.2830.30.80At1g01820839257PEX11C (PEROXIN 11C)member of the peroxin11 (PEX11) gene family, integral to peroxisome membrane, controls peroxisome proliferation.O.I.H.G.S.X.
0.2830.30.80At1g49850841408zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:unknown;C:unknown;PMOFVBO.I.H.G.S.X.
0.2726.20.80At1g76185843951unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.2624.40.80At2g21240816663BPC4 (BASIC PENTACYSTEINE 4)F:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:nucleus;PMBO.I.H.G.S.X.
0.2624.40.78At5g05950830480MEE60 (maternal effect embryo arrest 60)F:molecular_function unknown;P:embryonic development ending in seed dormancy;C:endomembrane system;PO.I.H.G.S.X.
0.2624.40.78At4g05150825863octicosapeptide/Phox/Bem1p (PB1) domain-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMFOBO.I.H.G.S.X.
0.2624.40.78At2g18170816330ATMPK7 (ARABIDOPSIS THALIANA MAP KINASE 7)F:MAP kinase activity, kinase activity;P:signal transduction, response to hydrogen peroxide, circadian rhythm;C:unknown;MOPFBVAO.I.H.G.S.X.
0.2522.60.78At4g08330826387unknown proteinF:molecular_function unknown;P:biological_process unknown;C:plasma membrane;PO.I.H.G.S.X.
0.2522.60.78At5g24890832558unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOPFBO.I.H.G.S.X.
0.2522.60.79At2g28370817385-F:molecular_function unknown;P:biological_process unknown;C:plasma membrane;PO.I.H.G.S.X.
0.2522.60.81At3g06170819791TMS membrane family protein / tumour differentially expressed (TDE) family proteinF:unknown;P:unknown;C:endomembrane system, membrane;MFPOBO.I.H.G.S.X.
0.2420.70.80At5g02800831285protein kinase family proteinF:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:unknown;MPOBFVAO.I.H.G.S.X.
0.2420.70.79At4g27000828808ATRBP45CF:RNA binding;P:unknown;C:unknown;MPFOBAVO.I.H.G.S.X.
0.2420.70.78At4g40040830165histone H3.2F:DNA binding;P:nucleosome assembly;C:nucleus, nucleosome;MFPOO.I.H.G.S.X.
0.2420.70.80At3g09880820146ATB' BETAEncodes B' regulatory subunit of PP2A (AtB'beta).O.I.H.G.S.X.
0.2319.30.80At2g19350816452unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPO.I.H.G.S.X.
0.2319.30.80At5g56520835753unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.2319.30.77At2g37480818325unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOFBO.I.H.G.S.X.
0.2319.30.78At2g28840817433ankyrin repeat family proteinF:protein binding, zinc ion binding;P:unknown;C:unknown;MOFBPVAO.I.H.G.S.X.
0.2319.30.80At1g66890843007-F:molecular_function unknown;P:biological_process unknown;C:chloroplast;PO.I.H.G.S.X.
0.2319.30.78At5g20900832214JAZ12 (JASMONATE-ZIM-DOMAIN PROTEIN 12)F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PFO.I.H.G.S.X.
0.2217.50.79At1g52740841707HTA9 (HISTONE H2A PROTEIN 9)Encodes HTA9, a histone H2A protein.O.I.H.G.S.X.
0.2217.50.78At2g23780816910zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:unknown;C:unknown;MPOFVO.I.H.G.S.X.
0.2217.50.78At5g46760834719basic helix-loop-helix (bHLH) family proteinF:transcription factor activity, DNA binding;P:regulation of transcription;C:nucleus;POMFBVO.I.H.G.S.X.
0.2115.80.77At4g39100830065SHL1 (short life)Putative transcription factor containing a PHD finger and BAH motif, required for normal developmentO.I.H.G.S.X.
0.2115.80.77At1g08110837330lactoylglutathione lyase, putative / glyoxalase I, putativeF:calmodulin binding, lactoylglutathione lyase activity;P:response to cadmium ion, carbohydrate metabolic process;C:chloroplast;BOFPMAO.I.H.G.S.X.
0.2115.80.78At4g02080827368ATSAR2 (ARABIDOPSIS THALIANA SECRETION-ASSOCIATED RAS SUPER FAMILY 2)A member of ARF-like GTPase family. A thaliana has 21 members, in two subfamilies, ARF and ARF-like (ARL) GTPases.O.I.H.G.S.X.
0.2115.80.79At4g21560828241VPS28-1 (VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 28 HOMOLOG 1)F:transporter activity;P:transport;C:ESCRT I complex;MFPOO.I.H.G.S.X.
0.2014.40.79At3g47620823916AtTCP14 (TEOSINTE BRANCHED1, CYCLOIDEA and PCF (TCP) 14)Encodes a transcription factor AtTCP14 that regulates seed germination. AtTCP14 shows elevated expression level just prior to germination. AtTCP14 is predominantly expressed in the vascular tissue of the embryo, and affects gene expression in radicles in a non-cell-autonomous manner.O.I.H.G.S.X.
0.2014.40.78At1g14400838002UBC1 (UBIQUITIN CARRIER PROTEIN 1)ubiquitin carrier proteinO.I.H.G.S.X.
0.2014.40.80At3g15040820733unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMPFBO.I.H.G.S.X.
0.1912.70.78At2g45980819206unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.1912.70.78At4g22750828372zinc finger (DHHC type) family proteinF:zinc ion binding;P:unknown;C:endomembrane system;MOFPO.I.H.G.S.X.
0.1912.70.78At5g59950836117RNA and export factor-binding protein, putativeF:nucleotide binding, nucleic acid binding;P:biological_process unknown;C:chloroplast;MPFOBVAO.I.H.G.S.X.
0.1912.70.77At3g07360819924PUB9 (PLANT U-BOX 9)Encodes a protein containing a U-box and an ARM domain. This protein has E3 ubiquitin ligase activity based on in vitro assays.O.I.H.G.S.X.
0.1912.70.77At5g25760832645PEX4 (PEROXIN4)mutant displays sucrose-dependent seedling development and reduced lateral root production. PEX4 interacts with PEX22 in a yeast two-hybrid. Necessary for peroxisome biogenesis. 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.
0.1912.70.79At2g37410818317ATTIM17-2Mitochondrial inner membrane translocase. Together with AtTIM17-1, TIM17-2 has a long C-terminal extension not present in other TIMs. The extension is located in the outer membrane and so TIM17-2 links the inner and outer mitochondrial membranes. The C-terminal region is essential for protein import into mitochondria via the general import pathway but is not necessary for import via the carrier pathway.O.I.H.G.S.X.
0.1912.70.80At4g25970828703PSD3 (phosphatidylserine decarboxylase 3)Encodes the major form of the two non-mitochondrail phosphatidylserine decarboxylase. Located at the ER.O.I.H.G.S.X.
0.1912.70.79At3g55460824712SCL30encodes an SC35-like splicing factor that is localized to nuclear specks.O.I.H.G.S.X.
0.1912.70.79At5g16550831517unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POBO.I.H.G.S.X.
0.1811.40.79At4g05000825842VPS28-2F:transporter activity;P:transport;C:ESCRT I complex;MFPOO.I.H.G.S.X.
0.1710.20.78At2g46550819267unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;PMO.I.H.G.S.X. (SCARECROW-LIKE 14)Encodes a member of the GRAS family of transcription factors. The protein interacts with the TGA2 transcription factor and affects the transcription of stress-responsive genes. The protein is found in the nucleus and is also exported to the cytoplasm.O.I.H.G.S.X. unknown;P:biological_process unknown;C:chloroplast;PO.I.H.G.S.X. (CELL DIVISION CONTROL 2)A-type cyclin-dependent kinase. Together with its specific inhibitor, the Kip-related protein, KRP2 they regulate the mitosis-to-endocycle transition during leaf development. Dominant negative mutations abolish cell division. Loss of function phenotype has reduced fertility with failure to transmit via pollen. Pollen development is arrested at the second mitotic division. Expression is regulated by environmental and chemical signals. Part of the promoter is responsible for expression in trichomes. Functions as a positive regulator of cell proliferation during development of the male gametophyte, embryo and endosperm. Phosphorylation of threonine 161 is required for activation of its associated kinase.O.I.H.G.S.X. (PB1) domain-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFPBVO.I.H.G.S.X. (PLANT U-BOX 8)Encodes a U-box/ARM repeat protein required fore self-incompatibility.O.I.H.G.S.X. (ZEITLUPE)Encodes clock-associated PAS protein ZTL; Also known as FKF1-like protein 2 or ADAGIO1(ADO1). A protein containing a PAS domain ZTL contributes to the plant fitness (carbon fixation, biomass) by influencing the circadian clock period. ZTL is the F-box component of an SCF complex implicated in the degradation of TOC1.O.I.H.G.S.X. unknown;P:biological_process unknown;C:cellular_component unknown;PBMO.I.H.G.S.X. stress protein (USP) family proteinContains a universal stress protein domain. Protein is phosphorylated in response to Phytophthora infestans zoospores and xylanase.O.I.H.G.S.X. (DERLIN-2.2)F:unknown;P:proteolysis;C:cellular_component unknown;MOFPO.I.H.G.S.X. (AUXIN RESPONSE FACTOR 2)Encodes an auxin response factor. Mutants have many defects including enlarged rosette leaves, reduced fertility, later senescence, hypocotyl elongation defects, enlarged seeds and enlarged cotyledons. May not mediate auxin effects. Increase in seed size due to increased cell proliferation.O.I.H.G.S.X. (LOV KELCH PROTEIN 2)encodes a member of F-box proteins that includes two other proteins in Arabidopsis (ZTL and FKF1). These proteins contain a unique structure containing a PAS domain at their N-terminus, an F-box motif, and 6 kelch repeats at their C-terminus. Overexpression results in arrhythmic phenotypes for a number of circadian clock outputs in both constant light and constant darkness, long hypocotyls under multiple fluences of both red and blue light, and a loss of photoperiodic control of flowering time. Although this the expression of this gene itself is not regulated by circadian clock, it physically interacts with Dof transcription factors that are transcriptionally regulated by circadian rhythm. LKP2 interacts with Di19, CO/COL family proteins.O.I.H.G.S.X. (NUCLEAR FACTOR Y, SUBUNIT C9)heme activated protein (HAP5c)O.I.H.G.S.X. family protein (FBW2)F:ubiquitin-protein ligase activity;P:ubiquitin-dependent protein catabolic process;C:cellular_component unknown;MPOFO.I.H.G.S.X. Phosphatase 2CO.I.H.G.S.X. (oligouridylate binding protein 1B)F:mRNA 3'-UTR binding;P:unknown;C:unknown;MPFOBO.I.H.G.S.X. (Ser/Arg-rich protein kinase 4)Encodes a protein kinase SRPK4 that specifically targets Arabidopsis Ser/Arg-rich (SR) slicing factors involved in RNA metabolism. In vitro kinase assay showed that SRPK4 phosphorylates the SR protein RSp31.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
39.699.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.999.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.099.7GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
36.899.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.199.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.299.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.199.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.199.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.899.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
33.599.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.599.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.199.7GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
32.799.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.299.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.699.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.399.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.399.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.399.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.099.7GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
30.099.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
29.099.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
24.199.6GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
21.999.6GSM311280Laser 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
21.799.6GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
21.799.6GSM133773Lindsey_1-25_torpedo-meristem_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
21.599.6GSM184906Arabidopsis, root cells, protophloem, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
21.099.6GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
20.899.6GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
18.899.5GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
18.399.5GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
17.799.5GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
16.799.5GSM284394Arabidopsis GCE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
14.399.4GSM142735DH001_ATH1_A2-BCP1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
13.499.4GSM142734DH001_ATH1_A1-UNM1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
12.799.3GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
11.899.3GSM311279Laser 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
10.799.2GSM184905Arabidopsis, root cells, protophloem, standard conditions, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
10.799.2GSM311296Laser capture microdissected (LCM) general seed coat at the linear-cotyledon stage, biological replicate 2GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
10.199.2GSM284392Arabidopsis GCE1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
9.199.1GSM226548Slice6JWGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink 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
0.0583GO:0007623Any biological process in an organism that recurs with a regularity of approximately 24 hours.Link to AmiGO
0.0492GO:0042752Any process that modulates the frequency, rate or extent of a circadian rhythm. A circadian rhythm is a biological process in an organism that recurs with a regularity of approximately 24 hours.Link to AmiGO
0.0472GO:0007031A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a peroxisome. A peroxisome is a small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.040204712Circadian rhythm - plantLink to KEGG PATHWAY
0.030204144EndocytosisLink to KEGG PATHWAY
0.015100620Pyruvate metabolismLink to KEGG PATHWAY

Inter-species module comparison

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

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