Co-expression analysis

Gene ID At3g25185
Gene name -
Module size 54 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
1.00100.01.00At3g25185--O.I.H.G.S.X.
0.8693.10.86At2g13900815874DC1 domain-containing proteinF:protein binding, zinc ion binding;P:unknown;C:unknown;PMOO.I.H.G.S.X.
0.8693.10.87At1g54880841927unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.8693.10.85At5g26620832728unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.8391.40.86At3g49170824078EMB2261 (embryo defective 2261)F:unknown;P:embryonic development ending in seed dormancy;C:chloroplast;POMFBO.I.H.G.S.X.
0.8391.40.89At1g46912841119F-box family protein-relatedF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.8391.40.88At4g02970828121AT7SL-1 (Arabidopsis 7SL RNA 1)Signal recognition particle. Type 4 of RNA polymerase III dependent genes.O.I.H.G.S.X.
0.8391.40.92At5g27810832843sequence-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.
0.8391.40.88At4g26020828708-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPAVO.I.H.G.S.X.
0.8089.80.85At4g14670827117CLPB2This 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.
0.8089.80.87At4g21950828284unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.7989.10.87At5g66370836769unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POFO.I.H.G.S.X.
0.7989.10.86At5g44330834458male sterility MS5 family proteinF:binding;P:biological_process unknown;C:unknown;POBAO.I.H.G.S.X.
0.7989.10.87At2g24410816977-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPOO.I.H.G.S.X.
0.7888.60.88At3g57900824959unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.7888.60.86At5g14560831307unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.7888.60.84At1g18050838385SWAP (Suppressor-of-White-APricot)/surp domain-containing proteinF:RNA binding;P:RNA processing;C:cellular_component unknown;MPOFO.I.H.G.S.X.
0.7888.60.86At2g30430817594unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.7888.60.88At1g52430841674ubiquitin carboxyl-terminal hydrolase-relatedF:ubiquitin thiolesterase activity;P:ubiquitin-dependent protein catabolic process;C:cellular_component unknown;POBMFO.I.H.G.S.X.
0.7788.00.88At1g29730839851ATP 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.
0.7788.00.87At2g40440818638BTB/POZ domain-containing proteinF:protein binding;P:biological_process unknown;C:cellular_component unknown;PMOO.I.H.G.S.X.
0.7687.40.86At5g18160831934F-box family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.7687.40.85At4g16050827290unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMFPBVAO.I.H.G.S.X.
0.7586.90.85At2g17960816306unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.7586.90.89At3g04990819659-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPAVO.I.H.G.S.X.
0.7586.90.86At1g59630842253F-box family protein-relatedF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.7486.10.84At2g13640815849Golgi GDP mannose transporter (GONST1)F:unknown;P:transcription;C:nucleus;OMBPFVAO.I.H.G.S.X.
0.7486.10.86At2g33160817877glycoside 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.
0.7385.50.83At3g06970819882RNA 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.
0.7385.50.87At1g32650840159unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknownO.I.H.G.S.X.
0.7284.80.85At4g220653769974transposable element geneF:unknown;P:unknown;C:unknownO.I.H.G.S.X.
0.7284.80.87At3g28280822454-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.7083.50.85At2g01500814678PFS2 (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.
0.7083.50.85At1g09410837463pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:biological_process unknown;C:unknown;POMFBO.I.H.G.S.X.
0.7083.50.84At2g33010817863ubiquitin-associated (UBA)/TS-N domain-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMFO.I.H.G.S.X.
0.6982.90.83At5g37860833764copper-binding family proteinF:copper ion binding, metal ion binding;P:copper ion transport, metal ion transport;C:cellular_component unknown;POBFMO.I.H.G.S.X.
0.6882.20.83At5g44470834474-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.6882.20.85At1g11690837713unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPAVO.I.H.G.S.X.
0.6882.20.84At2g36610818233ATHB22 (ARABIDOPSIS THALIANA HOMEOBOX PROTEIN 22)Encodes a homeodomain leucine zipper class I (HD-Zip I) protein.O.I.H.G.S.X.
0.6882.20.92At1g65210842828-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PBO.I.H.G.S.X.
0.6882.20.84At4g05340825882ATP bindingF:ATP binding;P:biological_process unknown;C:cellular_component unknown;PFMOBVO.I.H.G.S.X.
0.6781.60.87At1g50800841502unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PBOMFVO.I.H.G.S.X.
0.6579.60.85At1g76780844012-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFBPVAO.I.H.G.S.X.
0.5974.70.83At1g33820840277unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBPO.I.H.G.S.X.
0.5974.70.83At5g38500833838DNA bindingF:DNA binding;P:regulation of transcription, DNA-dependent;C:cellular_component unknown;OMPFBO.I.H.G.S.X.
0.5974.70.87At3g45570823699zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:unknown;C:unknown;MPOFVO.I.H.G.S.X.
0.5873.80.84At1g65120842819ubiquitin carboxyl-terminal hydrolase-relatedF:ubiquitin thiolesterase activity, zinc ion binding;P:ubiquitin-dependent protein catabolic process;C:intracellular;OPMFBVO.I.H.G.S.X.
0.5570.60.84At1g29570839834zinc finger protein-relatedF:zinc ion binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MOBFPVAO.I.H.G.S.X.
0.5469.50.83At1g47730841184F-box family proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;POO.I.H.G.S.X.
0.5267.40.84At3g19070821441cell wall protein-relatedF:transcription factor activity;P:regulation of transcription;C:unknown;OMFPBVAO.I.H.G.S.X.
0.4963.50.84At1g18310838411glycosyl hydrolase family 81 proteinF:hydrolase activity, acting on glycosyl bonds, endo-1,3(4)-beta-glucanase activity;P:cell wall macromolecule catabolic process;C:unknown;FOBPMO.I.H.G.S.X.
0.4862.50.85At2g077373768151transposable element geneF:unknown;P:unknown;C:unknownO.I.H.G.S.X.
0.4761.20.86At1g57906842163-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.4457.20.83At2g43730818975lectin-relatedF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.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
48.099.8GSM133766Lindsey_1-18_torpedo-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
45.799.8GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
44.599.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
44.499.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.699.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.299.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
39.199.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.999.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.999.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.999.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.999.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.699.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.799.7GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
35.299.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.099.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.099.7GSM284393Arabidopsis GCE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
33.699.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.399.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.099.7GSM311276Laser capture microdissected (LCM) micropylar endospermr at the pre-globular stage, biological replicate 2GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
31.299.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.699.7GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
30.599.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
28.899.7GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
28.399.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
28.299.7GSM311275Laser capture microdissected (LCM) micropylar endosperm at the pre-globular stage, biological replicate 1GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
26.699.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
25.899.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
24.999.6GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
22.199.6GSM284394Arabidopsis GCE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
22.099.6GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
21.999.6GSM284392Arabidopsis GCE1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
19.099.5GSM142736DH001_ATH1_A3-TCP1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
18.899.5GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
17.899.5GSM142625MC002_ATH1_A1.3-dubos-wtxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
17.899.5GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
17.199.5GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
16.199.5GSM284389Arabidopsis GMPE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
16.099.5GSM142630MC002_ATH1_A3.2-dubos-6kxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
14.399.4GSM142629MC002_ATH1_A3.1-dubos-6kxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
14.199.4GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
13.999.4GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
13.799.4E-MEXP-1138-raw-cel-1432773290
13.299.4GSM131707ATGE_84_BGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
12.699.3E-MEXP-1138-raw-cel-1432773258
11.999.3E-MEXP-1138-raw-cel-1432773322
11.799.3GSM142631MC002_ATH1_A3.3-dubos-6kxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
11.699.3GSM142623MC002_ATH1_A1.1-dubos-wtxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
11.199.2GSM131708ATGE_84_DGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
10.999.2GSM131706ATGE_84_AGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
9.899.1GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.399.1GSM184552Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.199.1GSM142740DH001_ATH1_A7-MPG1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0361GO: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
0.0361GO:0048446The process by which the anatomical structures of the petal are generated and organized. Morphogenesis pertains to the creation of form.Link to AmiGO
0.0361GO: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



Back to the CoP portal site

Back to the KAGIANA project homepage