Co-expression analysis

Gene ID At2g46780
Gene name RNA binding / nucleic acid binding / nucleotide binding
Module size 58 genes
NF 0.26
%ile 28.1



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
1.00100.01.00At2g46780819291RNA binding / nucleic acid binding / nucleotide bindingF:RNA binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MPFOBAO.I.H.G.S.X.
0.4457.20.87At2g05810815132armadillo/beta-catenin repeat family proteinF:binding;P:unknown;C:cellular_component unknown;PMFOO.I.H.G.S.X.
0.4355.30.88At2g31340817692emb1381 (embryo defective 1381)F:molecular_function unknown;P:embryonic development ending in seed dormancy;C:cellular_component unknown;PO.I.H.G.S.X.
0.4152.40.87At5g65830836712leucine-rich repeat family proteinF:protein binding;P:signal transduction;C:endomembrane system;POMBFAO.I.H.G.S.X.
0.4152.40.88At1g13170837875ORP1D (OSBP(OXYSTEROL BINDING PROTEIN)-RELATED PROTEIN 1D)F:oxysterol binding;P:steroid metabolic process;C:unknown;MFOPO.I.H.G.S.X.
0.3846.70.88At3g27325822352hydrolase, acting on ester bondsF:hydrolase activity, acting on ester bonds;P:intracellular protein transport, GPI anchor metabolic process;C:endoplasmic reticulum, plasma membrane;FMPBOO.I.H.G.S.X.
0.3541.60.87At3g63290825504unknown proteinF:molecular_function unknown;P:pollen development;C:cellular_component unknown;FPOBO.I.H.G.S.X.
0.3541.60.86At2g17970816307oxidoreductase, 2OG-Fe(II) oxygenase family proteinF:oxidoreductase activity;P:biological_process unknown;C:cellular_component unknown;PMOBO.I.H.G.S.X.
0.3541.60.86At4g16320--O.I.H.G.S.X.
0.3541.60.87At1g23980839010zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:unknown;C:unknown;PMOFVBO.I.H.G.S.X.
0.3439.80.88At1g30970839984SUF4 (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.
0.3439.80.86At1g30010839880intron maturase, type II family proteinF:RNA binding, RNA-directed DNA polymerase activity;P:RNA-dependent DNA replication, RNA splicing;C:unknown;BPOFAMVO.I.H.G.S.X.
0.3439.80.87At3g44530823578HIRA (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.
0.3338.10.87At1g09800837510tRNA pseudouridine synthase family proteinF:pseudouridine synthase activity;P:tRNA processing, pseudouridine synthesis;C:cellular_component unknown;BOMAPO.I.H.G.S.X.
0.3338.10.88At5g04270830306zinc ion bindingF:zinc ion binding;P:biological_process unknown;C:endomembrane system;MOFPO.I.H.G.S.X.
0.3133.80.86At5g15790831435zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:unknown;C:chloroplast;MPOFVO.I.H.G.S.X.
0.3133.80.87At1g08960837416CAX11member of Potassium-dependent sodium-calcium exchanger like-familyO.I.H.G.S.X.
0.3133.80.87At4g11450826749unknown proteinF:unknown;P:biological_process unknown;C:chloroplast;PMOO.I.H.G.S.X.
0.3032.10.86At4g15180827183SDG2 (SET DOMAIN-CONTAINING PROTEIN 2)F:unknown;P:unknown;C:unknown;MOPFBVO.I.H.G.S.X.
0.2930.30.86At4g28990829020RNA-binding protein-relatedF:zinc ion binding;P:biological_process unknown;C:intracellular;MPFOBVO.I.H.G.S.X.
0.2930.30.86At5g05310830413unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OBPO.I.H.G.S.X.
0.2930.30.87At3g09370820094MYB3R-3 (myb domain protein 3R-3)putative c-myb-like transcription factor (MYB3R3) mRNA,O.I.H.G.S.X.
0.2830.30.88At1g06850837197AtbZIP52 (Arabidopsis thaliana basic leucine zipper 52)F:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:nucleus;PMFOBVO.I.H.G.S.X.
0.2830.30.86At2g32760817836unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPOBO.I.H.G.S.X.
0.2830.30.86At4g29560829077unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMO.I.H.G.S.X.
0.2726.20.86At3g60310825202unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.2624.40.86At3g03690821186UNE7 (unfertilized embryo sac 7)F:transferase activity, transferring glycosyl groups, acetylglucosaminyltransferase activity;P:carbohydrate biosynthetic process, double fertilization forming a zygote and endosperm, pollen tube development;C:endomembrane system, membrane;MPBVOO.I.H.G.S.X.
0.2522.60.86At5g64390836560HEN4 (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.
0.2522.60.87At4g19490827690protein bindingPutative homolog of yeast Vps54. Thought to associate with POK and ATVPS53 in a plant GARP-like complex involved in the membrane trafficking system.O.I.H.G.S.X.
0.2522.60.86At2g22530816786catalytic/ transferaseF:transferase activity, catalytic activity;P:metabolic process, phospholipid biosynthetic process;C:endomembrane system;MFOBPAO.I.H.G.S.X.
0.2319.30.87At3g19570821494unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMBFPVAO.I.H.G.S.X.
0.2319.30.86At2g35230818090VQ motif-containing proteinF:unknown;P:unknown;C:unknown;MFPOBVAO.I.H.G.S.X.
0.2319.30.86At3g06600819839unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.2319.30.87At3g12590820439unknown proteinF:unknown;P:biological_process unknown;C:chloroplast;POMO.I.H.G.S.X.
0.2319.30.86At4g37630829917CYCD5core cell cycle genesO.I.H.G.S.X.
0.2217.50.86At1g25570839144leucine-rich repeat protein-relatedF:protein binding;P:unknown;C:plasma membrane, vacuole;POBMFAO.I.H.G.S.X.
0.2217.50.86At5g45300834566BMY2 (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.
0.2115.80.86At3g27320822351hydrolaseF:hydrolase activity;P:metabolic process;C:unknown;BOPFMAVO.I.H.G.S.X.
0.2115.80.86At4g24760828578unknown proteinF:unknown;P:unknown;C:unknown;OBMPFVAO.I.H.G.S.X.
0.2014.40.86At2g44440819051emsy N terminus domain-containing protein / ENT domain-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMFOBO.I.H.G.S.X.
0.2014.40.86At5g19420832062Ran 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.
0.1912.70.86At1g11060837647unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MBPOFO.I.H.G.S.X.
0.1912.70.86At2g22090816744UBP1 interacting protein 1a (UBA1a)encodes a nuclear protein that binds to RNA with a specificity for oligouridylates in vitro. As with UBP1, transient overexpression of UBA1a in protoplasts increases the steady-state levels of reporter mRNAs in a promoter-dependent manner. Along with UBP1 and UBA2a, it may act as a component of a complex recognizing U-rich sequences in plant 3'-UTRs and contributing to the stabilization of mRNAs in the nucleus.O.I.H.G.S.X.
0.1912.70.87At5g48520834908unknown proteinF:molecular_function unknown;P:biological_process unknown;C:nucleus;MOPFBO.I.H.G.S.X.
0.1811.40.86At3g19460821480reticulon family protein (RTNLB11)F:molecular_function unknown;P:biological_process unknown;C:endoplasmic reticulum;MPOFO.I.H.G.S.X.
0.1811.40.87At3g48040823959ROP10 (RHO-RELATED PROTEIN FROM PLANTS 10)Encodes a member of the Rop subfamily of Rho GTPases in Arabidopsis that contains a putative farnesylation motif. It is localized to the plasma membrane and involved in the negative regulation of ABA signalling.O.I.H.G.S.X.
0.168.80.86At2g40980818698-F:unknown;P:unknown;C:plasma membrane;BPOO.I.H.G.S.X.
0.168.80.86At3g02290821179zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:N-terminal protein myristoylation;C:unknown;MPOFVBO.I.H.G.S.X.
0.157.80.86At1g32150840107bZIP transcription factor family proteinF:transcription factor activity;P:transcription, DNA-dependent, regulation of transcription, DNA-dependent, regulation of transcription;C:nucleus, chloroplast;MOPFBVAO.I.H.G.S.X.
0.157.80.86At3g26935822311zinc finger (DHHC type) family proteinF:zinc ion binding;P:biological_process unknown;C:plasma membrane;MOFPO.I.H.G.S.X.
0.157.80.86At5g41060834108zinc finger (DHHC type) family proteinF:zinc ion binding;P:unknown;C:plasma membrane;MOFPO.I.H.G.S.X.
0.146.80.86At5g01460831815LMBR1 integral membrane family proteinF:unknown;P:unknown;C:membrane;MOFPO.I.H.G.S.X.
0.146.80.86At5g11040830971-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOPO.I.H.G.S.X.
0.135.80.87At5g64813836603LIP1 (Light Insensitive Period1)The LIP1 gene encodes a small GTPase that influences the light input pathway of the plant circadian network. An MBP:LIP1 fusion protein has GTP hydrolyzing abilities in vitro. In plants, LIP1 seems to play a negative role in regulating circadian period that can be suppressed by light. LIP1 also seems to negatively affect light-pulse-dependent resetting of the clock, especially during the first portion of the subjective evening. LIP1 expression levels are not significantly affected by the circadian clock in seedlings grown under LL conditions. The levels of the YFP:LIP1 protein expressed under the control of the 35S promoter, shows a low amplitude variation, with protein levels peaking near the beginning of subjective night under LL conditions. In hypocotyl epidermal cells of dark and light-grown seedlings, a YFP:LIP1 fusion protein can be seen in the cytoplasm and the nucleus, and does not cluster in nuclear speckles. LIP1 may also be involved in photomorphogenesis.O.I.H.G.S.X.
0.124.90.86At2g35100818076ARAD1 (ARABINAN DEFICIENT 1)Putative glycosyltransferase, similar to other CAZy Family 47 proteins. The protein is predicted to be a type 2 membrane protein with a signal anchor and is predicted to be targeted to the secretory pathway and to have a single transmembrane helix near the N terminus; hence, the protein has the features expected for a type II membrane protein targeted to the Golgi vesicles. The gene was shown to be expressed in all tissues but particularly in vascular tissues of leaves and stems.O.I.H.G.S.X.
0.114.10.87At4g09630826549-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMPFBVAO.I.H.G.S.X.
0.114.10.86At1g16190838188DNA repair protein RAD23, putativeF:damaged DNA binding;P:protein modification process, proteasomal ubiquitin-dependent protein catabolic process, base-excision repair, nucleotide-excision repair;C:nucleus;MPOFVBAO.I.H.G.S.X.
0.103.40.86At3g58580825027hydrolaseF:hydrolase activity;P:unknown;C:cellular_component unknown;MFOPBO.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
47.899.8GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
47.099.8GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
45.299.8GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
43.099.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
42.299.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
40.199.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
39.899.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
39.599.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.499.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.099.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.199.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.099.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.699.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.199.7GSM311296Laser capture microdissected (LCM) general seed coat at the linear-cotyledon stage, biological replicate 2GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
34.999.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.899.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.299.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.099.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
33.499.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.999.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.499.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.899.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.699.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
28.299.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
27.099.7GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
17.099.5GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
16.999.5GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
15.399.4GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
13.499.4GSM133117RIKEN-YAMAUCHI1AGSE5687AtGenExpress: Different temperature treatment of seedsLink to GEO
12.099.3GSM311274Laser 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
11.399.3GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.399.1E-MEXP-1725-raw-cel-1669614623
9.199.1GSM311295Laser capture microdissected (LCM) general seed coat at the linear-cotyledon stage, biological replicate 1GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
8.899.0GSM311273Laser 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

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0331GO:0032922Any process that modulates the frequency, rate or extent of gene expression such that an expression pattern recurs with a regularity of approximately 24 hours.Link to AmiGO
0.0331GO:0048255Prevention of degradation of mRNA molecules. In the absence of compensating changes in other processes, the slowing of mRNA degradation can result in an overall increase in the population of active mRNA molecules.Link to AmiGO
0.0331GO:0006505The chemical reactions and pathways involving glycosylphosphatidylinositol anchors, molecular mechanisms for attaching membrane proteins to the lipid bilayer of cell membranes. Structurally they consist of a molecule of phosphatidylinositol to which is linked, via the C-6 hydroxyl of the inositol, a carbohydrate chain. This chain is in turn linked to the protein through an ethanolamine phosphate moiety, the amino group of which is in amide linkage with the C-terminal carboxyl of the protein chain, the phosphate group being esterified to the C-6 hydroxyl of the terminal mannose of the core carbohydrate chain.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.018103420Nucleotide 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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