Co-expression analysis

Gene ID At3g49170
Gene name EMB2261 (embryo defective 2261)
Module size 44 genes
NF 0.70
%ile 89.1



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
0.8391.41.00At3g49170824078EMB2261 (embryo defective 2261)F:unknown;P:embryonic development ending in seed dormancy;C:chloroplast;POMFBO.I.H.G.S.X.
0.8793.50.89At2g13900815874DC1 domain-containing proteinF:protein binding, zinc ion binding;P:unknown;C:unknown;PMOO.I.H.G.S.X.
0.8793.50.89At4g26020828708-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPAVO.I.H.G.S.X.
0.8190.40.86At5g26620832728unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.8089.80.87At4g14670827117CLPB2This locus was originally annotated as encoding ClpB2 (also referred to as Hsp92.7), which belongs to the Casein lytic proteinase/heat shock protein 100 (Clp/Hsp100) family. However, according to Lee et al. (2007, Plant Journal, 49:115-127), there is no evidence for expression of an appropriate-sized mRNA from this locus. Re-annotation of the genome indicates that this locus potentially encodes a 68.8-kDa protein, containing only the N-terminal two thirds of the originally predicted open reading frame. This locus contains a 626-bp deletion in WS ecotype compared with the Col ecotype, which eliminates residues 1-86 of the predicted protein.O.I.H.G.S.X.
0.8089.80.88At4g02970828121AT7SL-1 (Arabidopsis 7SL RNA 1)Signal recognition particle. Type 4 of RNA polymerase III dependent genes.O.I.H.G.S.X.
0.8089.80.91At1g46912841119F-box family protein-relatedF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.7989.10.87At5g14560831307unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.7788.00.85At2g32050817765cell cycle control protein-relatedF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOPO.I.H.G.S.X.
0.7687.40.87At2g40440818638BTB/POZ domain-containing proteinF:protein binding;P:biological_process unknown;C:cellular_component unknown;PMOO.I.H.G.S.X.
0.7687.40.87At5g27810832843sequence-specific DNA binding / transcription factorF:transcription factor activity, sequence-specific DNA binding;P:regulation of transcription, DNA-dependent;C:nucleus;PO.I.H.G.S.X.
0.7687.40.87At1g18050838385SWAP (Suppressor-of-White-APricot)/surp domain-containing proteinF:RNA binding;P:RNA processing;C:cellular_component unknown;MPOFO.I.H.G.S.X.
0.7687.40.88At2g30430817594unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.7586.90.86At1g54880841927unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.7586.90.86At2g24410816977-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPOO.I.H.G.S.X.
0.7586.90.86At4g16050827290unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMFPBVAO.I.H.G.S.X.
0.7586.90.87At3g57900824959unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.7486.10.87At5g18160831934F-box family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.7486.10.87At5g44330834458male sterility MS5 family proteinF:binding;P:biological_process unknown;C:unknown;POBAO.I.H.G.S.X.
0.7486.10.87At5g66370836769unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POFO.I.H.G.S.X.
0.7385.50.87At4g25510828655unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.7284.80.88At1g76780844012-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFBPVAO.I.H.G.S.X.
0.7284.80.88At2g17960816306unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.7284.80.85At3g06970819882RNA binding / nucleic acid binding / nucleotide bindingF:RNA binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MPOFBVO.I.H.G.S.X.
0.7284.80.87At1g29730839851ATP binding / kinase/ protein binding / protein kinase/ protein serine/threonine kinase/ protein tyrosine kinaseF:in 6 functions;P:protein amino acid phosphorylation;C:endomembrane system;PMOBFVAO.I.H.G.S.X.
0.7184.20.85At4g220653769974transposable element geneF:unknown;P:unknown;C:unknownO.I.H.G.S.X.
0.7184.20.87At2g34580818022unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMBFPAVO.I.H.G.S.X.
0.7083.50.87At1g52430841674ubiquitin carboxyl-terminal hydrolase-relatedF:ubiquitin thiolesterase activity;P:ubiquitin-dependent protein catabolic process;C:cellular_component unknown;POBMFO.I.H.G.S.X.
0.6982.90.88At2g33160817877glycoside 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.
0.6982.90.87At2g33010817863ubiquitin-associated (UBA)/TS-N domain-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMFO.I.H.G.S.X.
0.6882.20.85At2g13640815849Golgi GDP mannose transporter (GONST1)F:unknown;P:transcription;C:nucleus;OMBPFVAO.I.H.G.S.X.
0.6781.60.87At2g01500814678PFS2 (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.
0.6781.60.85At1g50680841490AP2 domain-containing transcription factor, putativeF:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:nucleus;POVO.I.H.G.S.X.
0.6680.10.85At5g44470834474-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.6579.60.87At1g65210842828-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PBO.I.H.G.S.X.
0.6478.90.87At1g09410837463pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:biological_process unknown;C:unknown;POMFBO.I.H.G.S.X.
0.6378.10.87At1g11690837713unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPAVO.I.H.G.S.X.
0.6176.70.86At1g65120842819ubiquitin carboxyl-terminal hydrolase-relatedF:ubiquitin thiolesterase activity, zinc ion binding;P:ubiquitin-dependent protein catabolic process;C:intracellular;OPMFBVO.I.H.G.S.X.
0.6176.70.88At5g38500833838DNA bindingF:DNA binding;P:regulation of transcription, DNA-dependent;C:cellular_component unknown;OMPFBO.I.H.G.S.X.
0.6075.70.85At5g401303771383-F:unknown;P:unknown;C:unknownO.I.H.G.S.X.
0.5773.80.87At1g50800841502unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PBOMFVO.I.H.G.S.X.
0.5065.30.84At1g29570839834zinc finger protein-relatedF:zinc ion binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MOBFPVAO.I.H.G.S.X.
0.4963.50.87At3g45570823699zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:unknown;C:unknown;MPOFVO.I.H.G.S.X.
0.4862.50.85At3g19070821441cell wall protein-relatedF:transcription factor activity;P:regulation of transcription;C:unknown;OMFPBVAO.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
34.899.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.299.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.899.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.599.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.499.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.299.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.099.7GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
31.599.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.199.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.899.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
29.999.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
29.999.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
29.699.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
29.299.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
28.799.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
28.699.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
28.099.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
27.199.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
26.799.7GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
26.799.7GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
26.299.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
24.899.6GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
24.299.6GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
23.099.6GSM142736DH001_ATH1_A3-TCP1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
20.799.6GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
18.199.5GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
17.099.5GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
16.499.5E-MEXP-1138-raw-cel-1432773290
16.199.5GSM131707ATGE_84_BGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
15.099.4E-MEXP-1138-raw-cel-1432773258
14.199.4E-MEXP-1138-raw-cel-1432773322
14.199.4GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
13.799.4GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
13.499.4GSM131708ATGE_84_DGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
13.299.4GSM131706ATGE_84_AGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
12.599.3GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
10.399.2GSM142740DH001_ATH1_A7-MPG1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
9.599.1GSM131703ATGE_83_AGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
9.099.1GSM131705ATGE_83_CGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
8.899.0GSM131593ATGE_36_CGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
8.799.0GSM131704ATGE_83_BGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
8.799.0GSM10480lec1-1 Cotyledon Stage Seed 2GSE1051Seed development in LEAFY COTYLEDON1 mutantsLink to GEO
8.799.0GSM142739DH001_ATH1_A6-TCP2GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0431GO: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
0.0431GO:0048446The process by which the anatomical structures of the petal are generated and organized. Morphogenesis pertains to the creation of form.Link to AmiGO
0.0431GO: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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