Co-expression analysis

Gene ID At5g52230
Gene name MBD13
Module size 19 genes
NF 0.34
%ile 44.6



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
0.3541.61.00At5g52230835299MBD13Protein containing methyl-CpG-binding domain.Has sequence similarity to human MBD proteins.O.I.H.G.S.X.
0.6075.70.89At1g55970842048HAC4 (HISTONE ACETYLTRANSFERASE OF THE CBP FAMILY 4)HAC4 is most likely to be an expressed pseudogene that lacks HAT function. there is a single nucleotide deletion in both the HAC4 genomic and cDNA sequences relative to its homologs. The resulting frameshift within the open reading frame causes a stop codon to occur within the predicted acetyltransferase catalytic domain.O.I.H.G.S.X.
0.5368.60.87At4g14590827107emb2739 (embryo defective 2739)F:molecular_function unknown;P:embryonic development ending in seed dormancy;C:cellular_component unknown;MPOO.I.H.G.S.X.
0.4761.20.90At4g29560829077unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMO.I.H.G.S.X.
0.4659.80.88At5g08230830719PWWP domain-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOBFVAO.I.H.G.S.X.
0.4457.20.89At2g47820819394unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMBFPVO.I.H.G.S.X.
0.4253.90.88At2g33760817942pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:unknown;C:cellular_component unknown;POMFBAO.I.H.G.S.X.
0.4050.80.87At1g32610840156hydroxyproline-rich glycoprotein family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPOVBO.I.H.G.S.X.
0.4050.80.87At5g40820834082ATRAD3Encodes a Arabidopsis ortholog of the ATR protein kinase that is involved in a wide range of responses to DNA damage and plays a central role in cell-cycle regulation. Dominant loss of function alleles identified as suppressors of ALS also exhibit increased tolerance to aluminum. This may be due to the inhibition of terminal differentiation of the root apex upon exposure to Al.O.I.H.G.S.X.
0.3643.60.88At4g25270828630pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:biological_process unknown;C:chloroplast;POMFBO.I.H.G.S.X.
0.3643.60.87At5g55840835678pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:unknown;C:cellular_component unknown;POMFBAO.I.H.G.S.X.
0.3541.60.89At5g04050830284-F:molecular_function unknown;P:RNA splicing;C:cellular_component unknown;BPOFMAO.I.H.G.S.X.
0.3032.10.87At4g16570827358PRMT7 (PROTEIN ARGININE METHYLTRANSFERASE 7)F:methyltransferase activity;P:protein amino acid methylation;C:chloroplast;MFOPBAO.I.H.G.S.X.
0.2830.30.89At3g09370820094MYB3R-3 (myb domain protein 3R-3)putative c-myb-like transcription factor (MYB3R3) mRNA,O.I.H.G.S.X.
0.2726.20.87At3g12940820479unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.2624.40.88At4g20060827751EMB1895 (EMBRYO DEFECTIVE 1895)F:binding;P:embryonic development ending in seed dormancy;C:cellular_component unknown;MPOO.I.H.G.S.X.
0.2522.60.87At1g52620841694pentatricopeptide (PPR) repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMFBAO.I.H.G.S.X.
0.2420.70.88At1g63730842677disease resistance protein (TIR-NBS-LRR class), putativeF:protein binding, transmembrane receptor activity, nucleoside-triphosphatase activity, nucleotide binding, ATP binding;P:defense response;C:intrinsic to membrane;PMBOAFO.I.H.G.S.X.
0.1912.70.87At1g78930844232mitochondrial transcription termination factor-related / mTERF-relatedF:molecular_function unknown;P:biological_process unknown;C:chloroplast;PMOO.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
57.699.8GSM133303RIKEN-NAKABAYASHI1AGSE5700AtGenExpress: Effect of ABA during seed imbibitionLink to GEO
55.399.8GSM133304RIKEN-NAKABAYASHI1BGSE5700AtGenExpress: Effect of ABA during seed imbibitionLink to GEO
42.899.8GSM133117RIKEN-YAMAUCHI1AGSE5687AtGenExpress: Different temperature treatment of seedsLink to GEO
37.999.8GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
30.599.7GSM184922Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
27.799.7GSM184923Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
27.599.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
26.099.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
24.599.6GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
23.999.6GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
23.699.6GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
23.499.6GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
22.899.6GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
22.699.6GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
22.499.6GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
22.099.6GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
21.999.6GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
21.599.6GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
21.399.6GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
21.299.6GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
20.799.6GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
19.999.6GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
19.999.6GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
19.899.6GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
19.599.6GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
19.499.6GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
18.399.5GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
17.399.5GSM131318AtGen_6-3322_Saltstress-Roots-3.0h_Rep2GSE5623AtGenExpress: Stress Treatments (Salt stress)Link to GEO
17.199.5GSM184912Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
16.999.5GSM131321AtGen_6-3421_Saltstress-Roots-6.0h_Rep1GSE5623AtGenExpress: Stress Treatments (Salt stress)Link to GEO
14.699.4GSM184893Arabidopsis, root cells, columella root cap, standard conditions, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
14.299.4GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
13.699.4GSM131322AtGen_6-3422_Saltstress-Roots-6.0h_Rep2GSE5623AtGenExpress: Stress Treatments (Salt stress)Link to GEO
13.199.4GSM131317AtGen_6-3321_Saltstress-Roots-3.0h_Rep1GSE5623AtGenExpress: Stress Treatments (Salt stress)Link to GEO
12.799.3GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
11.999.3GSM184924Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
10.399.2GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
10.099.2GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
9.699.1GSM133957Fukuda_1-2_0B_Rep2_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0951GO:0007004The maintenance of proper telomeric length by the addition of telomeric repeats by telomerase.Link to AmiGO
0.0951GO:0032204Any process that modulates the frequency, rate or extent of a process that affects and monitors the activity of telomeric proteins and the length of telomeric DNA.Link to AmiGO
0.0951GO:0033044Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a chromosome.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG

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



Back to the CoP portal site

Back to the KAGIANA project homepage