Co-expression analysis

Gene ID At5g23520
Gene name -
Module size 45 genes
NF 0.36
%ile 49.2

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
0.5773.80.94At3g03740821170ATBPM4 (BTB-POZ and MATH domain 4)F:protein binding;P:biological_process unknown;C:unknown;MPOFVO.I.H.G.S.X.
0.5267.40.93At4g33890829532unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PFOO.I.H.G.S.X.
0.5267.40.93At3g56740824841ubiquitin-associated (UBA)/TS-N domain-containing proteinF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;FMPOBO.I.H.G.S.X.
0.5166.30.93At3g52120824376SWAP (Suppressor-of-White-APricot)/surp domain-containing protein / D111/G-patch domain-containing proteinF:RNA binding, nucleic acid binding;P:RNA processing;C:intracellular;MPFOO.I.H.G.S.X.
0.5065.30.93At4g00170828017vesicle-associated membrane family protein / VAMP family proteinF:structural molecule activity;P:biological_process unknown;C:cellular_component unknown;MPFOO.I.H.G.S.X.
0.4761.20.92At4g39370830092UBP27 (UBIQUITIN-SPECIFIC PROTEASE 27)Encodes a ubiquitin-specific protease.O.I.H.G.S.X.
0.4659.80.93At5g07270830618ankyrin repeat family proteinF:ubiquitin-protein ligase activity, protein binding;P:N-terminal protein myristoylation;C:unknown;MOFBPVAO.I.H.G.S.X.
0.4659.80.93At5g55500835643XYLT (ARABIDOPSIS THALIANA BETA-1,2-XYLOSYLTRANSFERASE)Encodes a beta-1,2-xylosyltransferase that is glycosylated at two positions.O.I.H.G.S.X.
0.4558.30.92At3g12100820384cation efflux family protein / metal tolerance protein, putativeF:cation transmembrane transporter activity, efflux transmembrane transporter activity;P:cation transport, response to nematode;C:membrane;BMFOPAO.I.H.G.S.X.
0.4558.30.92At1g66340842951ETR1 (ETHYLENE RESPONSE 1)Similar to prokaryote sensory transduction proteins. Contains a histidine kinase and a response regulator domain. Homodimer. Membrane component. Binds ethylene. Mutations affect ethylene binding and metabolism of other plant hormones such as auxin, cytokinins, ABA and gibberellic acid. Ethylene receptor. Has histidine kinase activity. Is regulated by RTE1.O.I.H.G.S.X.
0.4355.30.93At5g49950835059embryogenesis-associated protein-relatedF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;BOMFPO.I.H.G.S.X.
0.4253.90.93At3g06540819832GDP dissociation inhibitor family protein / Rab GTPase activator family proteinF:RAB GDP-dissociation inhibitor activity;P:intracellular protein transport, regulation of GTPase activity, protein transport;C:cellular_component unknown;MFOPBO.I.H.G.S.X.
0.4152.40.93At1g77140844050VPS45 (VACUOLAR PROTEIN SORTING 45)A peripheral membrane protein that associates with microsomal membranes, likely to function in the transport of proteins to the vacuole. It is a member of Sec1p protein family. It may be involved in the regulation of vesicle fusion reactions through interaction with t-SNAREs at the Golgi trans face.O.I.H.G.S.X.
0.4152.40.93At1g16010838171magnesium transporter CorA-like family protein (MRS2-1)F:metal ion transmembrane transporter activity;P:metal ion transport;C:vacuole, membrane;PFOMBAO.I.H.G.S.X.
0.4152.40.92At2g22090816744UBP1 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.
0.4050.80.93At4g33650829506DRP3A (DYNAMIN-RELATED PROTEIN 3A)Encodes a protein with high sequence similarity to the dynamin superfamily. Among those members ADL2 was most closely related to Dnm1p of yeast and likely a member of the Vps1p subfamily. Widely expressed in various tissues with highest expression in flower tissues. Localizes to the chloroplast, mitochondrion and peroxisome. Involved in peroxisome and mitochondria fission in combination with DRP3B.O.I.H.G.S.X.
0.3948.40.93At3g01150821129PTB1 (POLYPYRIMIDINE TRACT-BINDING PROTEIN 1)Encodes one of the two polypyrimidine tract-binding (PTB) protein homologs in the Arabidopsis genome. Double mutants have defects in pollen germination.O.I.H.G.S.X.
0.3846.70.92At3g16270820873-F:unknown;P:intracellular protein transport;C:membrane;MOPBFO.I.H.G.S.X.
0.3846.70.93At3g17880821056ATTDX (TETRATICOPEPTIDE DOMAIN-CONTAINING THIOREDOXIN)Encodes a thioredoxin-like disulfide reductase. The protein interacts with the yeast Hsp70 protein Ssb2 in vitro. This interaction is sensitive to the redox status of the thioredoxin domain of AtTDX.O.I.H.G.S.X.
0.3745.00.93At5g18190831937protein kinase family proteinF:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cellular_component unknown;MBOPFVAO.I.H.G.S.X.
0.3745.00.92At4g23460828445beta-adaptin, putativeF:protein transporter activity, protein binding, clathrin binding, binding;P:intracellular protein transport, vesicle-mediated transport, protein transport;C:plasma membrane;MFOPBAO.I.H.G.S.X.
0.3643.60.92At5g64813836603LIP1 (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.
0.3643.60.92At1g54115841851CCX4 (CATION CALCIUM EXCHANGER 4)Involved in cation (Na and K) homeostasis.O.I.H.G.S.X.
0.3541.60.92At1g78800844216glycosyl transferase family 1 proteinF:transferase activity, transferring glycosyl groups;P:biosynthetic process;C:cellular_component unknown;BOAPMFO.I.H.G.S.X.
0.3541.60.92At1g22020838807SHM6 (serine hydroxymethyltransferase 6)Encodes a putative serine hydroxymethyltransferase.O.I.H.G.S.X.
0.3541.60.93At5g22770832340alpha-ADR (alpha-adaptin)F:protein transporter activity, protein binding, binding;P:intracellular protein transport, vesicle-mediated transport, protein transport;C:plasma membrane, membrane;MOFPO.I.H.G.S.X.
0.3439.80.92At3g63270825502unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPFOO.I.H.G.S.X.
0.3439.80.93At3g05090819671transducin family protein / WD-40 repeat family proteinF:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex;MFOBPAVO.I.H.G.S.X.
0.3338.10.93At5g05700830454ATE1 (ARGININE-TRNA PROTEIN TRANSFERASE 1)Encodes an arginyl-tRNA:protein transferase (ATE1), a component of the N-end rule pathway that targets protein degradation through the identity of the amino-terminal residue of specific protein substrates. Arabidopsis contains two ATE genes: At5g05700/ATE1, At3g11240/ATE2. Another component of the N-end rule pathway is At5g02310/PROTEOLYSIS6 (PRT6). PRT6 and ATE were shown to regulate seed after-ripening, seedling sugar sensitivity, seedling lipid breakdown, and abscisic acid (ABA) sensitivity of germination. Mutants of ATE1 also display delayed leaf senescence.O.I.H.G.S.X.
0.3338.10.93At3g03570821234-F:molecular_function unknown;P:biological_process unknown;C:cytosol;MPOO.I.H.G.S.X.
0.3235.70.92At1g22870838892protein kinase family proteinF:in 6 functions;P:protein amino acid phosphorylation;C:cellular_component unknown;MOFPBVAO.I.H.G.S.X.
0.3133.80.93At3g25800822171PP2AA2 (PROTEIN PHOSPHATASE 2A SUBUNIT A2)one of three genes encoding the protein phosphatase 2A regulatory subunitO.I.H.G.S.X.
0.3032.10.93At5g46190834661KH domain-containing proteinF:RNA binding, nucleic acid binding;P:biological_process unknown;C:unknown;MPFOBO.I.H.G.S.X.
0.3032.10.92At5g51340835208unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOBO.I.H.G.S.X.
0.2930.30.92At2g27900817335unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOO.I.H.G.S.X.
0.2930.30.92At2g36360818209kelch repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOPFBAO.I.H.G.S.X.
0.2930.30.92At3g59770825146SAC9Encodes a phosphoinositide phosphatase. The sac9 null mutant accumulates elevated levels of PtdIns(4,5)P2 and Ins(1,4,5)P3. The mutant plants have characteristics of constitutive stress responses.O.I.H.G.S.X.
0.2830.30.92At4g37880829944protein binding / zinc ion bindingF:protein binding, zinc ion binding;P:biological_process unknown;C:cellular_component unknown;MFOPO.I.H.G.S.X.
0.2420.70.93At1g16970838268KU70 (ARABIDOPSIS THALIANA KU70 HOMOLOG)Ku80 and ku70 form the heterodimer complex Ku, required for proper maintenance of the telomeric C strand. Ku regulates the extension of the telomeric G strand. Interacts with WEX, and this interaction stimulates the WEX exonuclease activity.O.I.H.G.S.X.
0.2420.70.92At1g17730838349VPS46.1 (VACUOLAR PROTEIN SORTING 46.1)F:unknown;P:vesicle-mediated transport;C:cellular_component unknown;MPFOAO.I.H.G.S.X.
0.2319.30.92At4g05000825842VPS28-2F:transporter activity;P:transport;C:ESCRT I complex;MFPOO.I.H.G.S.X.
0.2014.40.93At3g22170821781FHY3 (FAR-RED ELONGATED HYPOCOTYLS 3)A component of the PHYA signaling network, mediates the FR-HIR response to far-red light in concert with FAR1.O.I.H.G.S.X. box RNA helicase, putative (RH20)F:helicase activity, ATP-dependent helicase activity, ATP binding, nucleic acid binding;P:unknown;C:cellular_component unknown;BOMFPAVO.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
76.599.9GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
51.999.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
51.799.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
48.899.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
47.199.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
46.999.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
46.799.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
44.099.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
43.699.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.299.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
42.799.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
42.799.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.999.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
41.599.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
39.099.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
38.799.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.199.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.499.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
35.799.7GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
32.799.7GSM184905Arabidopsis, root cells, protophloem, standard conditions, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
32.299.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.199.7GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
26.799.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
23.299.6GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
22.899.6GSM184906Arabidopsis, root cells, protophloem, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
17.199.5GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
14.199.4GSM284394Arabidopsis GCE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
14.099.4GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
12.899.3GSM142734DH001_ATH1_A1-UNM1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
11.099.2GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
10.799.2GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
10.499.2GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
10.299.2GSM133766Lindsey_1-18_torpedo-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
9.499.1GSM142737DH001_ATH1_A4-UNM2GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
9.099.1GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
8.999.0GSM284385Arabidopsis GEP6GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
8.899.0GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
8.899.0GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0495GO:0006886The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.Link to AmiGO
0.0431GO:0031204The process by which a protein translocates through the ER membrane posttranslationally.Link to AmiGO
0.0431GO:0000578The establishment, maintenance and elaboration of a pattern along a line or a point in an embryo.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.055304144EndocytosisLink to KEGG PATHWAY
0.053200510N-Glycan biosynthesisLink to KEGG PATHWAY
0.038103450Non-homologous end-joiningLink to KEGG PATHWAY

Inter-species module comparison

Select a plant to compare co-expressed genes between species.

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