Co-expression analysis

Gene ID At5g38500
Gene name DNA binding
Module size 37 genes
NF 0.65
%ile 85.9



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
0.8290.91.00At5g38500833838DNA bindingF:DNA binding;P:regulation of transcription, DNA-dependent;C:cellular_component unknown;OMPFBO.I.H.G.S.X.
0.7788.00.89At1g50680841490AP2 domain-containing transcription factor, putativeF:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:nucleus;POVO.I.H.G.S.X.
0.7586.90.88At1g76780844012-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFBPVAO.I.H.G.S.X.
0.7586.90.89At5g66370836769unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POFO.I.H.G.S.X.
0.7385.50.89At1g65120842819ubiquitin carboxyl-terminal hydrolase-relatedF:ubiquitin thiolesterase activity, zinc ion binding;P:ubiquitin-dependent protein catabolic process;C:intracellular;OPMFBVO.I.H.G.S.X.
0.7385.50.88At2g33010817863ubiquitin-associated (UBA)/TS-N domain-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMFO.I.H.G.S.X.
0.7385.50.87At5g14560831307unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.7284.80.87At1g32390840132transposable element geneF:unknown;P:unknown;C:unknownO.I.H.G.S.X.
0.7184.20.88At3g49170824078EMB2261 (embryo defective 2261)F:unknown;P:embryonic development ending in seed dormancy;C:chloroplast;POMFBO.I.H.G.S.X.
0.7083.50.89At5g18160831934F-box family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.6982.90.89At1g18050838385SWAP (Suppressor-of-White-APricot)/surp domain-containing proteinF:RNA binding;P:RNA processing;C:cellular_component unknown;MPOFO.I.H.G.S.X.
0.6982.90.86At1g54880841927unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.6982.90.89At1g65210842828-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PBO.I.H.G.S.X.
0.6982.90.88At2g40440818638BTB/POZ domain-containing proteinF:protein binding;P:biological_process unknown;C:cellular_component unknown;PMOO.I.H.G.S.X.
0.6882.20.89At4g02970828121AT7SL-1 (Arabidopsis 7SL RNA 1)Signal recognition particle. Type 4 of RNA polymerase III dependent genes.O.I.H.G.S.X.
0.6882.20.87At5g37640833742UBQ9polyubiquitin gene with 4 ubiquitin repeats. The first ubiquitin repeat has 16 amino acid replacements.O.I.H.G.S.X.
0.6781.60.90At1g46912841119F-box family protein-relatedF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.6781.60.88At2g30430817594unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.6781.60.87At4g16050827290unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMFPBVAO.I.H.G.S.X.
0.6781.60.88At4g25510828655unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.6781.60.86At4g26020828708-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPAVO.I.H.G.S.X.
0.6781.60.89At5g401303771383-F:unknown;P:unknown;C:unknownO.I.H.G.S.X.
0.6579.60.89At2g34580818022unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMBFPAVO.I.H.G.S.X.
0.6478.90.87At4g23580828458kelch repeat-containing F-box family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOBVFO.I.H.G.S.X.
0.6378.10.88At2g43730818975lectin-relatedF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.6378.10.87At3g59180825087-F:molecular_function unknown;P:biological_process unknown;C:unknown;PO.I.H.G.S.X.
0.6277.30.88At2g13640815849Golgi GDP mannose transporter (GONST1)F:unknown;P:transcription;C:nucleus;OMBPFVAO.I.H.G.S.X.
0.6277.30.87At2g33160817877glycoside hydrolase family 28 protein / polygalacturonase (pectinase) family proteinF:polygalacturonase activity, nucleic acid binding;P:carbohydrate metabolic process;C:endomembrane system;PFBOMAO.I.H.G.S.X.
0.6075.70.87At5g44330834458male sterility MS5 family proteinF:binding;P:biological_process unknown;C:unknown;POBAO.I.H.G.S.X.
0.5974.70.87At3g04990819659-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPAVO.I.H.G.S.X.
0.5974.70.87At2g01500814678PFS2 (PRETTY FEW SEEDS 2)PFS2 encodes a homeodomain gene that is a member of the WUS clade of transcription factors. It delays differentiation and maturation of primordia and regulates ovule patterning. The pfs2 mutant exhibits developmental defects in the maternal integuments and gametophyte, specifically, the boundary between the chalaza and the nucellus shifted towards the distal end of pfs2 ovule primordia. In addition, leaves displayed curling and petals were wavy and crenulated. Overexpression of PFS2 affects floral organ and leaf development. Single- and double-mutant analyses reveal that PFS2 activity represses AGAMOUS expression in young floral primordia. Also involved in regulation of response to low temperature.O.I.H.G.S.X.
0.5974.70.88At1g09410837463pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:biological_process unknown;C:unknown;POMFBO.I.H.G.S.X.
0.5873.80.87At1g52430841674ubiquitin carboxyl-terminal hydrolase-relatedF:ubiquitin thiolesterase activity;P:ubiquitin-dependent protein catabolic process;C:cellular_component unknown;POBMFO.I.H.G.S.X.
0.5773.80.88At3g28280822454-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.5469.50.89At1g11690837713unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPAVO.I.H.G.S.X.
0.5368.60.87At2g076863768051transposable element geneF:unknown;P:unknown;C:unknownO.I.H.G.S.X.
0.4558.30.88At2g077373768151transposable element geneF:unknown;P:unknown;C:unknownO.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
39.099.8GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
37.699.7GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
37.399.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.399.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.999.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.999.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.499.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
34.099.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.899.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
33.799.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.599.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.499.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.999.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.699.7GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
32.599.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.899.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.499.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.399.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.799.7GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
29.799.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
29.699.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
29.599.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
28.499.7GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
27.499.7GSM142736DH001_ATH1_A3-TCP1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
24.799.6GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
24.599.6GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
21.399.6GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
20.699.6GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
19.599.6E-MEXP-1138-raw-cel-1432773290
19.299.6GSM131707ATGE_84_BGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
18.299.5GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
17.899.5E-MEXP-1138-raw-cel-1432773258
17.299.5GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
16.899.5E-MEXP-1138-raw-cel-1432773322
16.699.5GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
16.199.5GSM131708ATGE_84_DGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
15.899.5GSM131706ATGE_84_AGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
12.399.3GSM142740DH001_ATH1_A7-MPG1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
11.499.3GSM131703ATGE_83_AGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
10.899.2GSM131705ATGE_83_CGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
10.599.2GSM131704ATGE_83_BGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
10.499.2GSM142739DH001_ATH1_A6-TCP2GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
10.499.2GSM131593ATGE_36_CGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
9.199.1GSM10480lec1-1 Cotyledon Stage Seed 2GSE1051Seed development in LEAFY COTYLEDON1 mutantsLink to GEO
9.199.1GSM131701ATGE_82_BGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
9.199.1GSM142634MC002_ATH1_A4.3-dubos-6kcGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
9.099.1GSM106916opr3_JA_22 hrs_Rep2GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
8.899.0GSM147966lec1-1 Globular Stage Seed 2GSE1051Seed development in LEAFY COTYLEDON1 mutantsLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0511GO:0048314The process by which the anatomical structures of the embryo sac are generated and organized. Morphogenesis pertains to the creation of form. The embryo sac develops from the megaspore in heterosporous plants.Link to AmiGO
0.0511GO:0048446The process by which the anatomical structures of the petal are generated and organized. Morphogenesis pertains to the creation of form.Link to AmiGO
0.0511GO:0048482The process by which the anatomical structures of the ovule are generated and organized. Morphogenesis pertains to the creation of form. The ovule is the structure in seed plants enclosing the female gametophyte, and is composed of the nucellus, one or two integuments, and the funiculus; it develops into the seed.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



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