Co-expression analysis

Gene ID At3g06290
Gene name -
Module size 26 genes
NF 0.34
%ile 45.4



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
0.7788.01.00At3g06290819803-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMFPBO.I.H.G.S.X.
0.5065.30.91At1g24460839062unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPAVO.I.H.G.S.X.
0.4862.50.93At2g40770818674ATP binding / DNA binding / helicase/ nucleic acid binding / protein binding / zinc ion bindingF:in 6 functions;P:unknown;C:unknown;MFBOPVAO.I.H.G.S.X.
0.4761.20.91At4g16320--O.I.H.G.S.X.
0.4558.30.91At1g08060837322MOM (MORPHEUS MOLECULE)F:unknown;P:chromatin silencing;C:nucleus;MFOBPVAO.I.H.G.S.X.
0.4457.20.91At5g41580834160zinc ion bindingF:zinc ion binding;P:unknown;C:unknown;MOFPBVAO.I.H.G.S.X.
0.4253.90.92At1g30970839984SUF4 (suppressor of FRIGIDA4)Encodes SUF4 (SUPPRESSOR of FRI 4), a putative zinc-finger-containing transcription factor that is required for delayed flowering in winter-annual Arabidopsis. suf4 mutations strongly suppress the late-flowering phenotype of FRI (FRIGIDA) mutants. suf4 mutants also show reduced H3K4 trimethylation at FLC (FLOWERING LOCUS C), a floral inhibitor. SUF4 may act to specifically recruit a putative histone H3 methyltransferase EFS (EARLY FLOWERING IN SHORT DAYS) and the PAF1-like complex to the FLC locus.O.I.H.G.S.X.
0.4253.90.92At4g38180829974FRS5 (FAR1-related sequence 5)F:zinc ion binding;P:response to red or far red light;C:cellular_component unknown;PFAOMO.I.H.G.S.X.
0.4152.40.91At4g10070826598KH domain-containing proteinF:RNA binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MFOPBVAO.I.H.G.S.X.
0.4152.40.92At1g13940837954unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOBO.I.H.G.S.X.
0.4050.80.91At4g18600827594WAVE5Encodes a member of the SCAR family.These proteins are part of a complex (WAVE) complex.The SCAR subunit activates the ARP2/3 complex which in turn act as a nucleator for actin filaments.O.I.H.G.S.X.
0.3948.40.91At1g20670838655DNA-binding bromodomain-containing proteinF:DNA binding;P:biological_process unknown;C:cellular_component unknown;OMFPBVO.I.H.G.S.X.
0.3948.40.91At5g23150832379HUA2 (ENHANCER OF AG-4 2)Putative transcription factor. Member of the floral homeotic AGAMOUS pathway.Mutations in HUA enhance the phenotype of mild ag-4 allele. Single hua mutants are early flowering and have reduced levels of FLC mRNA. Other MADS box flowering time genes such as FLM and MAF2 also appear to be regulated by HUA2. HUA2 normally activates FLC expression and enhances AG function.O.I.H.G.S.X.
0.3846.70.91At3g50430824207unknown proteinF:unknown;P:unknown;C:unknown;MPO.I.H.G.S.X.
0.3541.60.91At4g15180827183SDG2 (SET DOMAIN-CONTAINING PROTEIN 2)F:unknown;P:unknown;C:unknown;MOPFBVO.I.H.G.S.X.
0.3439.80.91At3g44530823578HIRA (Arabidopsis homolog of histone chaperone HIRA)Encodes a nuclear localized WD-repeat containing protein involved in negative regulation of knox gene expression via epigenetic mechanism of chromatin re-organization. Interacts physically and genetically with AS1. Expressed in meristem and leaf primordia. Homozygous mutants are embryo lethal. Phenotype of cosuppressed lines is variable but show effects on leaf development similar to as1/as2.O.I.H.G.S.X.
0.3235.70.91At2g32000817760DNA topoisomerase family proteinF:DNA topoisomerase activity, DNA topoisomerase type I activity, DNA binding, nucleic acid binding;P:DNA topological change, DNA unwinding during replication, DNA metabolic process;C:endomembrane system, chromosome;BOMAFPVO.I.H.G.S.X.
0.3032.10.91At1g24706839081unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFPBVAO.I.H.G.S.X.
0.2930.30.91At2g32760817836unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPOBO.I.H.G.S.X.
0.2726.20.92At1g11060837647unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MBPOFO.I.H.G.S.X.
0.2522.60.92At5g55390835632EDM2Encodes EDM2 (enhanced downy mildew 2). The predicted protein bears typical features of transcriptional regulators. EDM2 contains two putative bipartite nuclear localization signals (NLS) two zinc-finger-like motifs, a Proline-rich region and a large aspartic acid-rich region. Both zinc-finger-like stretches resemble the PHD (plant homeodomain) finger motif. Mutations in EDM2 comprise RPP7 mediated resistance against Hyaloperonospora parasitica isolate Hiks1 (HpHiks1). EDM2 may function as a direct or indirect regulator of RPP7 expression.O.I.H.G.S.X.
0.2319.30.91At2g41020818702WW domain-containing proteinF:protein binding;P:biological_process unknown;C:cellular_component unknown;MOFPO.I.H.G.S.X.
0.2217.50.92At2g30800817631HVT1 (HELICASE IN VASCULAR TISSUE AND TAPETUM)Has RNA or DNA helicase activity and expressed specifically in tapetum and vascular tissue. First identified member of a new group of the mle helicase group of the DEAH family.O.I.H.G.S.X.
0.2115.80.92At5g19420832062Ran GTPase binding / chromatin binding / zinc ion bindingF:chromatin binding, zinc ion binding, Ran GTPase binding;P:unknown;C:unknown;MOPBFAVO.I.H.G.S.X.
0.2115.80.92At4g31010829228RNA bindingF:RNA binding;P:biological_process unknown;C:mitochondrion;PO.I.H.G.S.X.
0.1912.70.91At2g36960818270TKI1 (TSL-kinase interacting protein 1)Arabidopsis thaliana myb/SANT domain proteinO.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
77.399.9GSM133765Lindsey_1-17_torpedo-cotyledon_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
33.199.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.799.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.299.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
31.899.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
31.299.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.399.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.099.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
29.999.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
29.699.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
29.599.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
28.799.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
28.799.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
28.499.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
28.299.7GSM184905Arabidopsis, root cells, protophloem, standard conditions, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
27.999.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
27.799.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
26.199.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
25.399.6GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
25.199.6GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
23.599.6GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
23.599.6GSM184906Arabidopsis, root cells, protophloem, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
23.499.6GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
22.499.6GSM311274Laser capture microdissected (LCM) embryo proper at the pre-globular stage, biological replicate 2GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
22.099.6GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
20.599.6E-MEXP-1725-raw-cel-1669614623
20.299.6GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
19.099.5GSM131608ATGE_42_DGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
18.899.5GSM311273Laser capture microdissected (LCM) embryo proper at the pre-globular stage, biological replicate 1GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
17.199.5E-MEXP-1725-raw-cel-1669614634
16.099.5GSM131607ATGE_42_CGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
15.899.5GSM131609ATGE_43_AGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
15.799.5GSM131611ATGE_43_CGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
15.199.4GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
14.999.4GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
14.599.4GSM131606ATGE_42_BGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
14.399.4GSM131610ATGE_43_BGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
13.599.4GSM133759Lindsey_1-9_heart-stage-cotyledon_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
12.399.3GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
12.299.3GSM67086Arabidopsis_Stigma02GSE3056Arabidopsis Pollination StudyLink to GEO
11.999.3GSM131303AtGen_6-2611_Osmoticstress-Shoots-24.0h_Rep1GSE5622AtGenExpress: Stress Treatments (Osmotic stress)Link to GEO
11.999.3E-MEXP-1725-raw-cel-1669614562
11.899.3E-MEXP-1725-raw-cel-1669614582
11.099.2GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
10.699.2GSM67087Arabidopsis_Stigma03GSE3056Arabidopsis Pollination StudyLink to GEO
10.499.2GSM284395Arabidopsis GPSc1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
10.099.2GSM284396Arabidopsis GPSc2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
8.699.0GSM106916opr3_JA_22 hrs_Rep2GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
8.699.0GSM131448AtGen_6-9212_Heatstress-Shoots-1.0h_Rep2GSE5628AtGenExpress: Stress Treatments (Heat stress)Link to GEO
8.699.0GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0711GO:0048497The process by which the identity of a floral organ is maintained. Identity is considered to be the aggregate of characteristics by which a structure is recognized.Link to AmiGO
0.0652GO:0009910Any process that stops, prevents or reduces the frequency, rate or extent of flower development.Link to AmiGO
0.0611GO:0045814Any epigenetic process that stops, prevents or reduces the rate of gene expression.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.039103440Homologous recombinationLink 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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