Co-expression analysis

Gene ID At4g35470
Gene name leucine-rich repeat family protein
Module size 46 genes
NF 0.29
%ile 34.6



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
1.00100.01.00At4g35470829699leucine-rich repeat family proteinF:protein binding;P:biological_process unknown;C:plasma membrane;MPBOFAVO.I.H.G.S.X.
0.5873.80.90At3g02540821195RAD23-3 (PUTATIVE DNA REPAIR PROTEIN RAD23-3)F:damaged DNA binding;P:protein modification process, proteasomal ubiquitin-dependent protein catabolic process, nucleotide-excision repair;C:nucleus;MBOPFVAO.I.H.G.S.X.
0.5570.60.91At3g16850820938glycoside hydrolase family 28 protein / polygalacturonase (pectinase) family proteinF:polygalacturonase activity;P:carbohydrate metabolic process;C:vacuole, plant-type cell wall;PBFOMAO.I.H.G.S.X.
0.5065.30.90At5g47390834786myb family transcription factorF:transcription factor activity, DNA binding;P:in 8 processes;C:unknown;POFMO.I.H.G.S.X.
0.4963.50.91At5g55910835689D6PK (D6 PROTEIN KINASE)D6PK is a protein kinase involved that plays a role in polar auxin transport. Most likely acts redundantly with the related proteins: D6PKL1,D6PKL2,and D6PKL3. PIN1 is a target of D6PK phosphorylation.O.I.H.G.S.X.
0.4963.50.91At1g61900842486unknown proteinF:molecular_function unknown;P:biological_process unknown;C:anchored to plasma membrane, plasma membrane, anchored to membrane;PO.I.H.G.S.X.
0.4963.50.89At1g72150843546PATL1 (PATELLIN 1)novel cell-plate-associated protein that is related in sequence to proteins involved in membrane trafficking in other eukaryotesO.I.H.G.S.X.
0.4761.20.89At1g22910838898RNA recognition motif (RRM)-containing proteinF:RNA binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MPFOBAO.I.H.G.S.X.
0.4457.20.89At1g01430837247unknown proteinF:unknown;P:biological_process unknown;C:cellular_component unknown;PFO.I.H.G.S.X.
0.4457.20.91At2g20230816542-F:unknown;P:unknown;C:plasma membrane, vacuole;POO.I.H.G.S.X.
0.4355.30.91At1g66150842930TMK1 (TRANSMEMBRANE KINASE 1)receptor-like transmembrane kinase I (TMK1)O.I.H.G.S.X.
0.4253.90.89At5g49720835035ATGH9A1 (ARABIDOPSIS THALIANA GLYCOSYL HYDROLASE 9A1)Encodes a membrane-bound endo-1,4-beta-D-glucanase, involved in cellulose biosynthesis. Loss-of-function mutants have severe cellulose-deficient phenotypes. During cell elongation, KOR1 is associated with Golgi apparatus and early endosome. Inhibition of cellulose biosynthesis promoted a redistribution of KOR1 in subcellular locations. These observations suggest that deposition of cellulose involves the intracellular cycling of KOR1.O.I.H.G.S.X.
0.3846.70.91At2g25800817122-F:unknown;P:biological_process unknown;C:unknown;POMFBO.I.H.G.S.X.
0.3745.00.90At5g10450830909GRF6 (G-box regulating factor 6)Encodes a member of the 14-3-3 gene family that is a lambda isoform (14-3-3λ). Interacts with APX3 (ascorbate peroxidase) and AKR2 , suggesting a role in mediating oxidative metabolism in stress response. This protein was shown to colocalize and interact with SERK1 by which it is phosphorylated. This protein is also reported to interact with the phosphorylated form of the BZR1 transcription factor involved in brassinosteroid signaling and may affect the nucleocytoplasmic shuttling of BZR1.O.I.H.G.S.X.
0.3643.60.89At3g26030822200ATB' DELTAprotein phosphatase 2A regulatory subunit isoform B' deltaO.I.H.G.S.X.
0.3643.60.89At4g18710827605BIN2 (BRASSINOSTEROID-INSENSITIVE 2)ATSK (shaggy-like kinase) family member that encodes an AtSK protein involved in the cross-talk between auxin and brassinosteroid signaling pathways. BR-INSENSITIVE 2 mutant indicated that the BR-insensitive dwarf phenotype was due to a semidominant mutation in the BIN2. BIN2 is not allelic to BRI1. BIN2-mediated phosphorylation appears to promote BZR1 export from the nucleus.O.I.H.G.S.X.
0.3541.60.90At1g04400839529CRY2 (CRYPTOCHROME 2)Blue light receptor mediating blue-light regulated cotyledon expansion and flowering time. Positive regulator of the flowering-time gene CONSTANS. This gene possesses a light-induced CNT2 N-terminal homodimerisation domain.Involved in blue-light induced stomatal opening. Involved in triggering chromatin decondensation. An 80-residue motif (NC80) is sufficient to confer CRY2's physiological function. It is proposed that the PHR domain and the C-terminal tail of the unphosphorylated CRY2 form a "closed" conformation to suppress the NC80 motif in the absence of light. In response to blue light, the C-terminal tail of CRY2 is phosphorylated and electrostatically repelled from the surface of the PHR domain to form an "open" conformation, resulting in derepression of the NC80 motif and signal transduction to trigger photomorphogenic responses. Cry2 phosphorylation and degradation both occur in the nucleus.O.I.H.G.S.X.
0.3439.80.88At1g76920844027F-box family protein (FBX3)F:ubiquitin-protein ligase activity;P:ubiquitin-dependent protein catabolic process;C:unknown;PO.I.H.G.S.X.
0.3338.10.88At3g18060821331transducin family protein / WD-40 repeat family proteinF:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex;MFBOPAO.I.H.G.S.X.
0.3338.10.89At4g02440828008EID1 (EMPFINDLICHER IM DUNKELROTEN LICHT 1)EID1 is an F-box protein that functions as a negative regulator in phytochrome A (phyA)-specific light signalling. Expressed at all stages of plant development independently of light conditions, localizes to the nucleus, and forms nuclear speckles under continuous far-red light. Forms stable dimeric and trimeric complexes with several ASK proteins and Cullin1 in yeast and in planta.O.I.H.G.S.X.
0.3338.10.89At1g05850837095POM1 (POM-POM1)Encodes an endo chitinase-like protein AtCTL1. Essential for tolerance to heat, salt and drought stresses. Also involved in root hair development, cell expansion and response to cytokinin. Allelic to erh2. 11 alleles described in Hauser (1995). Mutant is defective in acquired thermotolerance, appears semidwarf throughout its life cycle and has extra lateral branches. There are two EMS alleles. Expression of AtHSP101 is not affected in the mutants.O.I.H.G.S.X.
0.3235.70.89At5g65430836668GRF8 (GENERAL REGULATORY FACTOR 8)member of 14-3-3 proteins. This protein is reported to interact with the BZR1 transcription factor involved in brassinosteroid signaling and may affect the nucleocytoplasmic shuttling of BZR1O.I.H.G.S.X.
0.2930.30.89At1g06060837115RanBPM-relatedF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPFOO.I.H.G.S.X.
0.2930.30.89At4g32410829376CESA1 (CELLULOSE SYNTHASE 1)Encodes a cellulose synthase isomer. CESA1 mutants have cellulose defect in the primary cell wall. Multiple lines of evidence suggest that CESA1, along with CESA3 and CESA6 are present in the same plasma membrane complex for cellulose biosynthesis. lasma membrane complex for cellulose biosynthesis.O.I.H.G.S.X.
0.2830.30.89At3g61180825290zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:unknown;C:plasma membrane;PMOFVBO.I.H.G.S.X.
0.2624.40.88At4g25570828662ACYB-2Encodes cytochrome b561.O.I.H.G.S.X.
0.2624.40.89At3g59090825078-F:unknown;P:unknown;C:unknown;POFO.I.H.G.S.X.
0.2420.70.89At2g20120816531COV1 (CONTINUOUS VASCULAR RING)Encodes an integral membrane protein of unknown function, highly conserved between plants and bacteria; is likely to be involved in a mechanism that negatively regulates the differentiation of vascular tissue in the stem. Mutants display a dramatic increase in vascular tissue development in the stem in place of the interfascicular region that normally separates the vascular bundles.O.I.H.G.S.X.
0.2319.30.88At5g05170830399CEV1 (CONSTITUTIVE EXPRESSION OF VSP 1)Encodes a cellulose synthase isomer. CESA3 mutants have cellulose defect in the primary cell wall. Multiple lines of evidence suggest that CESA3, along with CESA1 and CESA6 are present in the same plasma membrane complex for cellulose biosynthesis.O.I.H.G.S.X.
0.2319.30.88At1g32410840134vacuolar protein sorting 55 family protein / VPS55 family proteinF:transporter activity;P:transport;C:vacuole;MFPOO.I.H.G.S.X.
0.2319.30.88At4g24800828582MA3 domain-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOFO.I.H.G.S.X.
0.2319.30.88At4g22750828372zinc finger (DHHC type) family proteinF:zinc ion binding;P:unknown;C:endomembrane system;MOFPO.I.H.G.S.X.
0.2217.50.89At4g03560825655ATTPC1 (TWO-PORE CHANNEL 1)Encodes a depolarization-activated Ca(2+) channel. Anti-sense experiments with this gene as well as Sucrose-H(+) symporters and complementation of yeast sucrose uptake mutant cch1 suggest that this protein mediates a voltage-activated Ca(2+ )influx. Mutants lack detectable SV channel activity suggesting TPC1 is essential component of the SV channel. Patch clamp analysis of loss of function mutation indicates TPC1 does not affect Ca2+ signaling in response to abiotic and biotic stress.O.I.H.G.S.X.
0.2217.50.88At3g03860821101ATAPRL5 (APR-like 5)Encodes a protein disulfide isomerase-like (PDIL) protein, a member of a multigene family within the thioredoxin (TRX) superfamily. This protein also belongs to the adenosine 5'-phosphosulfate reductase-like (APRL) group.O.I.H.G.S.X.
0.2115.80.89At3g28710822502H+-transporting two-sector ATPase, putativeF:hydrogen ion transmembrane transporter activity, proton-transporting ATPase activity, rotational mechanism;P:proton transport, ATP synthesis coupled proton transport;C:vacuolar membrane, plasma membrane, vacuole, plant-type vacuole;MFOPABO.I.H.G.S.X.
0.2014.40.88At2g21240816663BPC4 (BASIC PENTACYSTEINE 4)F:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:nucleus;PMBO.I.H.G.S.X.
0.2014.40.88At5g54540835542-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PBMO.I.H.G.S.X.
0.1811.40.88At1g04140839272transducin family protein / WD-40 repeat family proteinF:nucleotide binding;P:biological_process unknown;C:chloroplast;MBFOPAO.I.H.G.S.X.
0.1811.40.88At5g41260834127protein kinase family proteinF:protein tyrosine kinase activity, binding, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation, N-terminal protein myristoylation;C:plasma membrane;PMOBFVAO.I.H.G.S.X.
0.1710.20.88At3g09740820132SYP71 (SYNTAXIN OF PLANTS 71)syntaxin of plants 71 (SYP71)O.I.H.G.S.X.
0.1710.20.88At3g26935822311zinc finger (DHHC type) family proteinF:zinc ion binding;P:biological_process unknown;C:plasma membrane;MOFPO.I.H.G.S.X.
0.157.80.89At2g45810819189DEAD/DEAH box helicase, putativeF:helicase activity, ATP-dependent helicase activity, nucleic acid binding, ATP binding;P:unknown;C:cellular_component unknown;OMBFPAVO.I.H.G.S.X.
0.146.80.89At3g59110825080protein kinase family proteinF:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:plasma membrane;MPOBFVAO.I.H.G.S.X.
0.135.80.89At4g37880829944protein binding / zinc ion bindingF:protein binding, zinc ion binding;P:biological_process unknown;C:cellular_component unknown;MFOPO.I.H.G.S.X.
0.082.30.88At2g42590818859GRF9 (GENERAL REGULATORY FACTOR 9)14-3-3 gene. Binds calcium and displays induced structural changes.O.I.H.G.S.X.
0.082.30.88At2g20190816539CLASP (CLIP-ASSOCIATED PROTEIN)Encodes a microtubule-associated protein that is involved in both cell division and cell expansion. It likely promotes microtubule stability.O.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
38.299.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
35.299.7GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
34.799.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.699.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.299.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.099.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.799.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
33.499.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.099.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.499.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.199.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.999.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
31.399.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
31.299.7GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
31.099.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.999.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.799.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.599.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.199.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
29.599.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
28.899.7GSM311275Laser 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
28.899.7GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
28.399.7GSM311276Laser 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
25.399.6GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
25.299.6GSM184906Arabidopsis, root cells, protophloem, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
23.499.6GSM284388Arabidopsis GMPE1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
23.299.6GSM184923Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
22.999.6GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
21.599.6GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
20.299.6GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
17.499.5GSM184905Arabidopsis, root cells, protophloem, standard conditions, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
16.499.5E-MEXP-807-raw-cel-1173273088
15.999.5GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
15.399.4GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
14.799.4GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
14.699.4E-MEXP-807-raw-cel-1173273223
14.399.4GSM284389Arabidopsis GMPE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
14.199.4GSM133773Lindsey_1-25_torpedo-meristem_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
13.899.4GSM133759Lindsey_1-9_heart-stage-cotyledon_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
13.799.4E-MEXP-807-raw-cel-1173273196
13.099.4GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
13.099.4GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
11.999.3E-MEXP-807-raw-cel-1173273116
11.499.3E-MEXP-807-raw-cel-1173273060
11.299.2GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
10.199.2GSM131704ATGE_83_BGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
9.299.1E-MEXP-807-raw-cel-1173273170
9.199.1GSM131706ATGE_84_AGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
9.099.1GSM131708ATGE_84_DGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
8.899.0GSM131705ATGE_83_CGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0833GO:0009742A series of molecular signals mediated by the detection of brassinosteroid.Link to AmiGO
0.0813GO:0030244The chemical reactions and pathways resulting in the formation of cellulose, a linear beta1-4 glucan of molecular mass 50-400 kDa with the pyranose units in the -4C1 conformation.Link to AmiGO
0.0802GO:0009833The chemical reactions and pathways resulting in the formation of cellulose and pectin-containing cell walls that form adjacent to the middle lamella following cell division and during cell expansion. An example of this is found in Arabidopsis thaliana.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.027104712Circadian rhythm - plantLink to KEGG PATHWAY
0.021104130SNARE interactions in vesicular transportLink to KEGG PATHWAY
0.021103420Nucleotide 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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