Co-expression analysis

Gene ID At5g05210
Gene name nucleolar matrix protein-related
Module size 15 genes
NF 0.64
%ile 85.1



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
0.5673.01.00At5g05210830403nucleolar matrix protein-relatedF:unknown;P:unknown;C:cellular_component unknown;MOFBPVAO.I.H.G.S.X.
0.7989.10.90At3g02760820930ATP 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.
0.7989.10.90At1g74250843765DNAJ 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.
0.7184.20.88At3g06010819772ATCHR12Encodes 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.
0.7083.50.88At1g18950838476aminoacyl-tRNA synthetase familyF:aminoacyl-tRNA ligase activity;P:biological_process unknown;C:unknown;MOFBPVAO.I.H.G.S.X.
0.6982.90.85At3g24490822039transcription factorF:transcription factor activity;P:regulation of transcription;C:cellular_component unknown;MOPFBVO.I.H.G.S.X.
0.6982.90.87At2g06210815177ELF8 (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.
0.6781.60.84At1g53720841810CYP59 (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.
0.6781.60.87At3g19650821502cyclin-relatedF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFPBVO.I.H.G.S.X.
0.6579.60.89At2g40650818660pre-mRNA splicing factor PRP38 family proteinF:binding;P:RNA processing;C:cellular_component unknown;MBOFPVAO.I.H.G.S.X.
0.6277.30.88At5g61310836252cytochrome 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.
0.6176.70.85At3g50690824233leucine-rich repeat family proteinF:protein binding;P:biological_process unknown;C:cellular_component unknown;MOFBPVAO.I.H.G.S.X.
0.5974.70.87At2g29210817470splicing factor PWI domain-containing proteinF:unknown;P:RNA splicing;C:unknown;MOFBPVAO.I.H.G.S.X.
0.5065.30.87At1g68790843210LINC3 (LITTLE NUCLEI3)F:unknown;P:biological_process unknown;C:nucleolus;MOBFPAVO.I.H.G.S.X.
0.4963.50.88At5g55670835661RNA 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
44.399.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
43.399.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
41.399.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
39.299.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
38.299.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.899.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.899.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.399.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.299.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.599.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.799.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.999.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.499.7GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
30.499.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
29.999.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
28.699.7GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
28.699.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
26.799.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
26.799.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
25.099.6GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
22.499.6GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
21.499.6GSM311289Laser 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
20.399.6GSM311290Laser 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
17.599.5E-MEXP-807-raw-cel-1173273252
15.499.5GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
13.699.4E-MEXP-1725-raw-cel-1669614623
13.399.4GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
13.299.4E-MEXP-807-raw-cel-1173273144
13.299.4E-MEXP-98-raw-cel-320188969
12.199.3E-MEXP-98-raw-cel-320188859
11.999.3GSM142751MJ001_ATH1_A2-jones-WT2GSE6165The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.Link to GEO
11.899.3GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
11.899.3E-MEXP-98-raw-cel-320188804
11.699.3GSM131453AtGen_6-9321_Heatstress-Roots-3.0h_Rep1GSE5628AtGenExpress: Stress Treatments (Heat stress)Link to GEO
11.699.3GSM131149AtGen_B-35_3-7-1_REP3_ATH1GSE5615AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitorsLink to GEO
11.399.3E-MEXP-1474-raw-cel-1593932705
11.299.2GSM142750MJ001_ATH1_A1-jones-WT1GSE6165The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.Link to GEO
11.299.2E-MEXP-98-raw-cel-320189024
11.199.2GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
11.099.2E-MEXP-98-raw-cel-320189079
10.599.2GSM142593DB001_ATH1_A3-Brown-calGSE6148The trans-differentiation of cultured Arabidopsis cellsLink to GEO
10.499.2GSM131131AtGen_B-17_2-3-1_REP2_ATH1GSE5615AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitorsLink to GEO
10.499.2GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
10.299.2GSM131454AtGen_6-9322_Heatstress-Roots-3.0h_Rep2GSE5628AtGenExpress: Stress Treatments (Heat stress)Link to GEO
10.099.2GSM270868Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep2GSE10719Response of Arabidopsis cell culture to phytoprostane A1Link to GEO
9.899.1E-MEXP-1474-raw-cel-1593932609
9.899.1GSM133720Deeken_A-2-Deeke-Inf_SLD_REP1GSE5725Agrobacterium tumefaciens-induced tumour development of Arabidopsis thalianaLink to GEO
9.699.1GSM184518Pericycle root cells 2hr continuous KCl and MSX control treated, biological rep3GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.699.1GSM270870Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep3GSE10719Response of Arabidopsis cell culture to phytoprostane A1Link to GEO
9.399.1E-MEXP-1725-raw-cel-1669614634
9.399.1E-MEXP-1474-raw-cel-1593932513
9.299.1GSM131135AtGen_B-21_2-7-1_REP2_ATH1GSE5615AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitorsLink to GEO
9.199.1GSM75510Col-0 6h NAA replicate 1GSE3350SLR/IAA14-dependent auxin induced lateral root initiationLink to GEO
8.999.0GSM131452AtGen_6-9312_Heatstress-Shoots-3.0h_Rep2GSE5628AtGenExpress: Stress Treatments (Heat stress)Link to GEO
8.899.0GSM131145AtGen_B-31_3-3-1_REP3_ATH1GSE5615AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitorsLink to GEO
8.699.0GSM131147AtGen_B-33_3-5-1_REP3_ATH1GSE5615AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitorsLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1111GO: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
0.0911GO:0045893Any process that activates or increases the frequency, rate or extent of DNA-dependent transcription.Link to AmiGO
0.0801GO: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
0.032100970Aminoacyl-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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