Co-expression analysis

Gene ID At1g02960
Gene name unknown protein
Module size 30 genes
NF 0.36
%ile 48.2



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
0.5570.61.00At1g02960839363unknown proteinF:unknown;P:unknown;C:cellular_component unknown;OMPFBO.I.H.G.S.X.
0.5570.60.92At2g32000817760DNA 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.
0.5166.30.92At2g41020818702WW domain-containing proteinF:protein binding;P:biological_process unknown;C:cellular_component unknown;MOFPO.I.H.G.S.X.
0.5065.30.91At2g40770818674ATP 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.
0.5065.30.91At5g14620831315DRM2 (DOMAINS REARRANGED METHYLTRANSFERASE 2)A putative DNA methyltransferase with rearranged catalytic domains; similar to mammalian DNMT3 methyltransferases; contains UBA domains. The 3'-end proximal part of the gene coding region is highly methylated at both adenine and cytosine residues.O.I.H.G.S.X.
0.4558.30.93At1g33400840233tetratricopeptide repeat (TPR)-containing proteinF:binding;P:biological_process unknown;C:cellular_component unknown;MOPBFAO.I.H.G.S.X.
0.4355.30.91At4g18600827594WAVE5Encodes 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.
0.4355.30.92At1g73970843735unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POO.I.H.G.S.X.
0.4253.90.91At4g23840828483leucine-rich repeat family proteinF:protein binding;P:unknown;C:cellular_component unknown;BMPOFVAO.I.H.G.S.X.
0.4253.90.91At4g31010829228RNA bindingF:RNA binding;P:biological_process unknown;C:mitochondrion;PO.I.H.G.S.X.
0.4152.40.91At4g38180829974FRS5 (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.
0.4050.80.91At2g31450817703endonuclease-relatedF:4 iron, 4 sulfur cluster binding, sequence-specific DNA binding, DNA binding, catalytic activity, endonuclease activity;P:DNA repair, base-excision repair;C:intracellular;BOAMFPO.I.H.G.S.X.
0.3948.40.91At4g31200829247SWAP (Suppressor-of-White-APricot)/surp domain-containing proteinF:RNA binding;P:RNA processing;C:cellular_component unknown;MPFOBVAO.I.H.G.S.X.
0.3846.70.90At4g38170829973FRS9 (FAR1-related sequence 9)F:zinc ion binding;P:response to red or far red light;C:cellular_component unknown;PMFO.I.H.G.S.X.
0.3745.00.91At1g24706839081unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFPBVAO.I.H.G.S.X.
0.3643.60.92At5g64390836560HEN4 (HUA ENHANCER 4)encodes a K homology (KH) domain-containing, putative RNA binding protein that interacts with HUA1, a CCCH zinc finger RNA binding protein in the nucleus. HEN4 acts redundantly with HUA1 and HUA2 in the specification of floral organ identity in the third whorl.O.I.H.G.S.X.
0.3643.60.91At2g30800817631HVT1 (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.
0.3541.60.91At5g45300834566BMY2 (BETA-AMYLASE 2)F:cation binding, beta-amylase activity, catalytic activity;P:cellulose biosynthetic process, carbohydrate metabolic process, polysaccharide catabolic process;C:cellular_component unknown;PMBOFO.I.H.G.S.X.
0.3338.10.92At4g31150829243endonuclease V family proteinF:endonuclease activity;P:DNA repair;C:cellular_component unknown;BAOMPFO.I.H.G.S.X.
0.3338.10.92At3g56830824850unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POBO.I.H.G.S.X.
0.3235.70.91At1g30970839984SUF4 (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.
0.3133.80.91At2g39910818578bindingF:binding;P:biological_process unknown;C:unknown;MPO.I.H.G.S.X.
0.3032.10.91At4g16280827323FCAInvolved in the promotion of the transition of the vegetative meristem to reproductive development. Four forms of the protein (alpha, beta, delta and gamma) are produced by alternative splicing. Involved in RNA-mediated chromatin silencing.O.I.H.G.S.X.
0.2930.30.91At2g26350817175PEX10Zinc-binding peroxisomal integral membrane protein (PEX10). Inserted directly from the cytosol into peroxisomes and is involved in importing proteins into the peroxisome. Required for embryogenesis.O.I.H.G.S.X.
0.2830.30.92At5g55390835632EDM2Encodes 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.
0.2830.30.91At1g11060837647unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MBPOFO.I.H.G.S.X.
0.2726.20.92At1g04950839370TAF6 (TBP-ASSOCIATED FACTOR 6)Encodes one of two Arabidopsis proteins with significant similarity to the histone fold TBP-associated factor TAF6. Mutants are embryo lethal and transmission of the mutant allele through the male gametophyte is significantly reduced. This is due to reduced pollen tube growth of the mutant.O.I.H.G.S.X.
0.2726.20.91At2g27110817253FRS3 (FAR1-related sequence 3)F:zinc ion binding;P:response to red or far red light;C:cellular_component unknown;PFMO.I.H.G.S.X.
0.2522.60.91At1g22870838892protein kinase family proteinF:in 6 functions;P:protein amino acid phosphorylation;C:cellular_component unknown;MOFPBVAO.I.H.G.S.X.
0.2217.50.90At3g17450821009hAT dimerisation domain-containing proteinF:protein dimerization activity, DNA binding;P:biological_process unknown;C:cellular_component unknown;POMVFBO.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
84.199.9GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
83.499.9GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
67.999.9GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
66.199.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
39.199.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.599.8GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
37.699.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.299.7GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
35.099.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.399.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
33.799.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.499.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.399.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.099.7GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
31.099.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.299.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
29.899.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
29.499.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
29.299.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
29.299.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
28.999.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
27.999.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
27.899.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
27.099.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
24.499.6GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
24.299.6GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
22.999.6GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
22.999.6GSM184905Arabidopsis, root cells, protophloem, standard conditions, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
20.799.6GSM284394Arabidopsis GCE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
19.299.6GSM184906Arabidopsis, root cells, protophloem, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
18.399.5E-ATMX-35-raw-cel-1574334832
18.099.5GSM266667Arabidopsis, root cells, columella root cap, -Fe, replicate 2GSE10501Expression analysis of root cell-types after iron deficiency (-Fe) treatmentLink to GEO
17.999.5E-ATMX-35-raw-cel-1574334816
17.699.5E-MEXP-1725-raw-cel-1669614623
16.799.5GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
15.599.5GSM266668Arabidopsis, root cells, columella root cap, -Fe, replicate 3GSE10501Expression analysis of root cell-types after iron deficiency (-Fe) treatmentLink to GEO
15.499.5GSM266666Arabidopsis, root cells, columella root cap, -Fe, replicate 1GSE10501Expression analysis of root cell-types after iron deficiency (-Fe) treatmentLink to GEO
14.899.4GSM184894Arabidopsis, root cells, columella root cap, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
14.799.4E-MEXP-1725-raw-cel-1669614634
13.799.4GSM284392Arabidopsis GCE1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
11.899.3GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
11.799.3GSM133759Lindsey_1-9_heart-stage-cotyledon_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
10.699.2GSM311279Laser capture microdissected (LCM) chalazal endosperm at the pre-globular stage, biological replicate 1GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
10.399.2E-MEXP-1725-raw-cel-1669614562
10.399.2E-MEXP-1725-raw-cel-1669614582
9.799.1GSM131303AtGen_6-2611_Osmoticstress-Shoots-24.0h_Rep1GSE5622AtGenExpress: Stress Treatments (Osmotic stress)Link to GEO
8.799.0E-ATMX-35-raw-cel-1574334800

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0953GO:0009639A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a red or far red light stimulus. Red light is electromagnetic radiation of wavelength of 580-700nm. Far red light is electromagnetic radiation of wavelength 700-800nm. An example of this response is seen at the beginning of many plant species developmental stages. These include germination, and the point when cotyledon expansion is triggered. In certain species these processes take place in response to absorption of red light by the pigment molecule phytochrome, but the signal can be reversed by exposure to far red light. During the initial phase the phytochrome molecule is only present in the red light absorbing form, but on absorption of red light it changes to a far red light absorbing form, triggering progress through development. An immediate short period of exposure to far red light entirely returns the pigment to its initial state and prevents triggering of the developmental process. A thirty minute break between red and subsequent far red light exposure renders the red light effect irreversible, and development then occurs regardless of whether far red light exposure subsequently occurs.Link to AmiGO
0.0651GO:0010381The process by which a peroxisome is transported to, and/or maintained in, a location adjacent to the chloroplast.Link to AmiGO
0.0591GO:0031048Repression of transcription by conversion of large regions of DNA into heterochromatin, directed by small RNAs sharing sequence identity to the repressed region.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.036103440Homologous recombinationLink to KEGG PATHWAY
0.032103022Basal transcription factorsLink to KEGG PATHWAY
0.029103410Base excision repairLink 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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