Co-expression analysis

Gene ID At3g06010
Gene name ATCHR12
Module size 17 genes
NF 0.63
%ile 83.9



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
0.6781.61.00At3g06010819772ATCHR12Encodes AtCHR12, a SNF2/Brahma-type chromatin-remodeling protein. AtCHR12 mediates temporary growth arrest in Arabidopsis upon perceiving environmental stress.O.I.H.G.S.X.
0.7788.00.87At2g06210815177ELF8 (EARLY FLOWERING 8)Encodes a yeast CTR9 homolog that is involved in the control of flowering time by elevating FLC expression to a level that creates the vernalization-responsive, winter-annual habit. Yeast CTR9 is a component of a five-member PAF1 complex that associates with RNA pol II and is thought to regulate gene expression by recruiting SET1 (a histone 3 Lys 4 [H3-K4] methyl transferase) to the initially transcribed [5'] regions of target chromatin. Mutants display reduced H3-K4 methylation in both FLC and FLM chromatin.O.I.H.G.S.X.
0.7586.90.88At3g02760820930ATP binding / aminoacyl-tRNA ligase/ histidine-tRNA ligase/ nucleotide bindingF:histidine-tRNA ligase activity, aminoacyl-tRNA ligase activity, nucleotide binding, ATP binding;P:histidyl-tRNA aminoacylation, translation, tRNA aminoacylation for protein translation;C:chloroplast, cytoplasm;OBMFAPO.I.H.G.S.X.
0.7385.50.87At3g24490822039transcription factorF:transcription factor activity;P:regulation of transcription;C:cellular_component unknown;MOPFBVO.I.H.G.S.X.
0.6982.90.88At1g18950838476aminoacyl-tRNA synthetase familyF:aminoacyl-tRNA ligase activity;P:biological_process unknown;C:unknown;MOFBPVAO.I.H.G.S.X.
0.6882.20.88At5g05210830403nucleolar matrix protein-relatedF:unknown;P:unknown;C:cellular_component unknown;MOFBPVAO.I.H.G.S.X.
0.6781.60.88At1g74250843765DNAJ heat shock N-terminal domain-containing proteinF:heat shock protein binding, zinc ion binding, nucleic acid binding;P:protein folding;C:intracellular;MOBFPVAO.I.H.G.S.X.
0.6579.60.84At1g68790843210LINC3 (LITTLE NUCLEI3)F:unknown;P:biological_process unknown;C:nucleolus;MOBFPAVO.I.H.G.S.X.
0.6478.90.84At5g61310836252cytochrome c oxidase subunit Vc, putative / COX5C, putativeF:cytochrome-c oxidase activity;P:unknown;C:mitochondrial respiratory chain, endomembrane system;PO.I.H.G.S.X.
0.6478.90.89At2g40650818660pre-mRNA splicing factor PRP38 family proteinF:binding;P:RNA processing;C:cellular_component unknown;MBOFPVAO.I.H.G.S.X.
0.6378.10.88At2g29210817470splicing factor PWI domain-containing proteinF:unknown;P:RNA splicing;C:unknown;MOFBPVAO.I.H.G.S.X.
0.6176.70.87At3g19650821502cyclin-relatedF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFPBVO.I.H.G.S.X.
0.5873.80.82At1g53720841810CYP59 (CYCLOPHILIN 59)Encodes a cyclophilin, member of a family modular proteins consisting of a peptidyl-prolyl cis– trans isomerase (PPIase) domain, followed by an RNA recognition motif (RRM), and a C-terminal domain enriched in charged amino acids. Interacts with with SCL33/SR33 and with a majority of Arabidopsis SR proteins and the largest subunit of RNA polymerase II. Localizes to the nucleus, but it does not significantly colocalize with SR proteins in nuclear speckles.O.I.H.G.S.X.
0.5873.80.86At3g51270824290ATP binding / catalytic/ protein serine/threonine kinaseF:protein serine/threonine kinase activity, catalytic activity, ATP binding;P:protein amino acid phosphorylation;C:cellular_component unknown;MOFBPVAO.I.H.G.S.X.
0.5065.30.89At5g55660835660-F:unknown;P:unknown;C:mitochondrion;MOFBPVAO.I.H.G.S.X.
0.4761.20.83At5g53800835461unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPVAO.I.H.G.S.X.
0.4761.20.92At5g55670835661RNA recognition motif (RRM)-containing proteinF:RNA binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MBOFPVAO.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
48.499.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
45.299.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
44.499.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.599.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
42.599.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.399.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.199.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
41.099.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.099.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
39.499.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
38.299.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.599.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.799.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.499.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.199.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.599.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.499.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.599.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
26.799.7GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
25.799.7GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
24.999.6GSM131593ATGE_36_CGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
23.999.6GSM142736DH001_ATH1_A3-TCP1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
21.499.6GSM131591ATGE_36_AGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
21.099.6GSM131592ATGE_36_BGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
20.299.6GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
19.399.6GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
19.099.5GSM311289Laser capture microdissected (LCM) cellularized endosperm at the linear-cotyledon stage, biological replicate 1GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
17.999.5GSM311290Laser capture microdissected (LCM) cellularized endosperm at the linear-cotyledon stage, biological replicate 2GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
17.599.5GSM106913opr3_JA_8 hrs_Rep2GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
16.699.5GSM142739DH001_ATH1_A6-TCP2GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
15.599.5E-MEXP-807-raw-cel-1173273252
14.999.4GSM106967opr3_OPDA_22 hrs_Rep1GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
14.599.4GSM106969opr3_OPDA_22 hrs_Rep2GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
13.899.4GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
12.499.3GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
12.099.3E-MEXP-1725-raw-cel-1669614623
11.799.3E-MEXP-807-raw-cel-1173273144
11.799.3E-MEXP-98-raw-cel-320188969
10.799.2E-MEXP-98-raw-cel-320188859
10.499.2GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
10.499.2E-MEXP-98-raw-cel-320188804
10.499.2GSM142751MJ001_ATH1_A2-jones-WT2GSE6165The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.Link to GEO
10.299.2GSM131149AtGen_B-35_3-7-1_REP3_ATH1GSE5615AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitorsLink to GEO
10.099.2E-MEXP-1474-raw-cel-1593932705
9.999.1E-MEXP-98-raw-cel-320189024
9.899.1GSM142750MJ001_ATH1_A1-jones-WT1GSE6165The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.Link to GEO
9.899.1E-MEXP-98-raw-cel-320189079
9.799.1GSM106923opr3_OPDA_2 hrs_Rep2GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
9.699.1GSM284394Arabidopsis GCE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
9.499.1GSM131453AtGen_6-9321_Heatstress-Roots-3.0h_Rep1GSE5628AtGenExpress: Stress Treatments (Heat stress)Link to GEO
9.499.1GSM106910opr3_JA_2 hrs_rep2GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
9.499.1GSM142593DB001_ATH1_A3-Brown-calGSE6148The trans-differentiation of cultured Arabidopsis cellsLink to GEO
9.499.1GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
9.299.1GSM131131AtGen_B-17_2-3-1_REP2_ATH1GSE5615AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitorsLink to GEO
8.799.0GSM133720Deeken_A-2-Deeke-Inf_SLD_REP1GSE5725Agrobacterium tumefaciens-induced tumour development of Arabidopsis thalianaLink to GEO
8.799.0E-MEXP-1474-raw-cel-1593932609
8.699.0GSM270868Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep2GSE10719Response of Arabidopsis cell culture to phytoprostane A1Link to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1001GO:0006427The process of coupling histidine to histidyl-tRNA, catalyzed by histidyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA.Link to AmiGO
0.0831GO:0045893Any process that activates or increases the frequency, rate or extent of DNA-dependent transcription.Link to AmiGO
0.0741GO:0016571The modification of histones by addition of methyl groups.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.031100970Aminoacyl-tRNA 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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