Co-expression analysis

Gene ID At3g05060
Gene name SAR DNA-binding protein, putative
Module size 28 genes
NF 0.50
%ile 71.0



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
0.7083.51.00At3g05060819668SAR DNA-binding protein, putativeSAR DNA-binding protein, putative, strong similarity to SAR DNA-binding protein-1 (Pisum sativum) GI:3132696; contains Pfam profile PF01798: Putative snoRNA binding domain; encodes NOP58-like proteinO.I.H.G.S.X.
0.8190.40.92At4g25340828637immunophilin-related / FKBP-type peptidyl-prolyl cis-trans isomerase-relatedF:FK506 binding, peptidyl-prolyl cis-trans isomerase activity;P:protein folding;C:nucleolus;MOBFPVAO.I.H.G.S.X.
0.7284.80.91At3g12270820407PRMT3 (PROTEIN ARGININE METHYLTRANSFERASE 3)F:methyltransferase activity, zinc ion binding;P:metabolic process;C:intracellular;MBOFPAO.I.H.G.S.X.
0.6781.60.95At1g56110842063NOP56 (Arabidopsis homolog of nucleolar protein Nop56)NOP56-like proteinO.I.H.G.S.X.
0.6680.10.93At3g11964820370RNA bindingF:RNA binding;P:mRNA processing, RNA processing;C:nucleolus, plasma membrane;BOMFPAO.I.H.G.S.X.
0.6680.10.92At4g32720829408AtLa1 (Arabidopsis thaliana La protein 1)Encodes AtLa1, a member of the highly abundant phosphoprotein La proteins. Predominantly localized to the nucleoplasm and was also detected in the nucleolar cavity. Has RNA binding activity. Required for normal ribosome biogenesis and embryogenesis.O.I.H.G.S.X.
0.6378.10.92At5g38720833863unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMFBPVAO.I.H.G.S.X.
0.6176.70.92At5g14050831254transducin family protein / WD-40 repeat family proteinF:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex;BMOFPAVO.I.H.G.S.X.
0.6075.70.91At5g62440836365-Encodes a protein DOMINO1 that belongs to a plant-specific gene family sharing a common motif present in the tomato DEFECTIVE CHLOROPLASTS AND LEAVES (LeDCL) protein. DOMINO1 is located in the nucleus. Arabidopsis embryos carrying the domino1 mutation grow slowly in comparison with wild type embryos and reach only the globular stage at desiccation. The primary defect of the mutation at the cellular level is the large size of the nucleolus that can be observed soon after fertilization in the nuclei of both the embryo and the endosperm. DOMINO1 might have a role in ribosome biogenesis and in determining the rate of cell division.O.I.H.G.S.X.
0.6075.70.91At1g03360839521ATRRP4 (ARABIDOPSIS THALIANA RIBOSOMAL RNA PROCESSING 4)F:RNA binding, exonuclease activity;P:unknown;C:mitochondrion;OMAFPO.I.H.G.S.X.
0.5673.00.93At3g18600821391DEAD/DEAH box helicase, putativeF:helicase activity, ATP binding, ATP-dependent helicase activity, nucleic acid binding;P:unknown;C:nucleolus;BOMFPAVO.I.H.G.S.X.
0.5673.00.91At5g57280835833methyltransferaseF:methyltransferase activity;P:metabolic process;C:unknown;BOMFPAO.I.H.G.S.X.
0.5469.50.91At4g04940825833transducin family protein / WD-40 repeat family proteinF:nucleotide binding;P:rRNA processing;C:CUL4 RING ubiquitin ligase complex;MFBOPAO.I.H.G.S.X.
0.5368.60.90At1g52930841726brix domain-containing proteinF:unknown;P:unknown;C:cellular_component unknown;MFOPO.I.H.G.S.X.
0.5267.40.92At3g21540821708transducin family protein / WD-40 repeat family proteinF:nucleotide binding;P:rRNA processing;C:nucleolus, heterotrimeric G-protein complex;MFOPBAO.I.H.G.S.X.
0.4963.50.90At1g04870839393PRMT10Encodes a type I protein arginine methyltransferase based on the At1g04870.2 gene model. PRMT10 can catalyze the asymmetric dimethylation of arginine 3 on histone 4 and can also methylate myelin basic protein in vitro. Mutants lacking PRMT10 flower late due to defects in the autonomous pathway and they have elevated levels of FLC transcripts.O.I.H.G.S.X.
0.4862.50.90At2g40700818665DEAD/DEAH box helicase, putative (RH17)F:helicase activity, ATP binding, ATP-dependent helicase activity, nucleic acid binding;P:unknown;C:unknown;BOMFPAVO.I.H.G.S.X.
0.4659.80.93At5g61770836299PPAN (PETER PAN-LIKE PROTEIN)F:unknown;P:unknown;C:cellular_component unknown;MOFPVBO.I.H.G.S.X.
0.4558.30.90At3g55510824716RBL (REBELOTE)F:unknown;P:floral meristem determinacy;C:nucleus;MFOPO.I.H.G.S.X.
0.4558.30.91At1g8075084441460S ribosomal protein L7 (RPL7A)F:structural constituent of ribosome, transcription regulator activity;P:translation;C:cytosolic large ribosomal subunit, nucleolus, large ribosomal subunit;MOFPAO.I.H.G.S.X.
0.4457.20.91At3g09720820129DEAD/DEAH box helicase, putativeF:helicase activity, ATP-dependent helicase activity, nucleic acid binding, ATP binding;P:unknown;C:cellular_component unknown;BOMFPAVO.I.H.G.S.X.
0.4253.90.90At4g05410825889transducin family protein / WD-40 repeat family proteinF:nucleotide binding, nucleic acid binding;P:mitochondrial fission;C:nucleolus, small nucleolar ribonucleoprotein complex, anaphase-promoting complex, CUL4 RING ubiquitin ligase complex;MFOBPVAO.I.H.G.S.X.
0.4253.90.91At2g40430818636-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMFPBO.I.H.G.S.X.
0.3643.60.90At3g01160820504unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cytosol, nucleus;MOFBPVAO.I.H.G.S.X.
0.3541.60.90At5g45140834550NRPC2Encodes a subunit of RNA polymerase III (aka RNA polymerase C).O.I.H.G.S.X.
0.3133.80.91At3g57000824867nucleolar essential protein-relatedF:molecular_function unknown;P:unknown;C:nucleus;MOFAPBVO.I.H.G.S.X.
0.3133.80.91At3g13160820505pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:biological_process unknown;C:mitochondrion, membrane;POMFBAO.I.H.G.S.X.
0.2930.30.92At5g14520831303pescadillo-relatedF:transcription coactivator activity;P:cell proliferation;C:nucleolus, intracellular;MFOPO.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
120.899.9GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
100.199.9GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
87.699.9GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
80.399.9GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
74.599.9GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
70.099.9GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
66.899.8GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
66.399.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
65.699.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
65.399.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
64.599.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
64.499.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
64.299.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
63.799.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
63.599.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
63.099.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
60.299.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
58.799.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
57.499.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
55.499.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
50.399.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
49.499.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
48.899.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
31.099.7GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
30.299.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
29.899.7GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
15.199.4GSM131608ATGE_42_DGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
14.799.4GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
10.799.2GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
10.699.2GSM142647MC002_ATH1_A9.1-dubos-aahGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
10.599.2GSM142649MC002_ATH1_A9.3-dubos-aahGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
10.299.2GSM131606ATGE_42_BGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
9.599.1GSM142648MC002_ATH1_A9.2-dubos-aahGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
8.699.0GSM154508Arabidopsis growing pollen tubes rep2GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0691GO:0017126The process by which the nucleolus, a small, dense body one or more of which are present in the nucleus of eukaryotic cells, is formed and assembled.Link to AmiGO
0.0672GO:0006364Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.Link to AmiGO
0.0651GO:0019919The process of methylation of peptidyl-arginine to form peptidyl-N(omega),N(omega)-dimethyl-L-arginine.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.035103020RNA polymeraseLink to KEGG PATHWAY
0.026103018RNA degradationLink to KEGG PATHWAY
0.020100240Pyrimidine metabolismLink 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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