Co-expression analysis

Gene ID At4g13210
Gene name lyase/ pectate lyase
Module size 46 genes
NF 0.14
%ile 10.3



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
1.00100.01.00At4g13210826936lyase/ pectate lyaseF:lyase activity, pectate lyase activity;P:biological_process unknown;C:unknown;PBFOO.I.H.G.S.X.
0.4963.50.77At4g13710827005pectate lyase family proteinF:lyase activity, pectate lyase activity;P:biological_process unknown;C:endomembrane system;PBFOO.I.H.G.S.X.
0.2726.20.67At5g06940830585leucine-rich repeat family proteinF:kinase activity;P:protein amino acid phosphorylation;C:endomembrane system;PMOBFVAO.I.H.G.S.X.
0.2624.40.73At3g01140821209MYB106 (myb domain protein 106)Encodes a putative transcription factor that is a member of the MYB family. Loss of function mutations show an increased number of branchpoints in leaf trichomes suggesting a role in negative regulation of trichome branching.O.I.H.G.S.X.
0.2522.60.71At2g20240816543unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOFBO.I.H.G.S.X.
0.2420.70.66At1g65620842873AS2 (ASYMMETRIC LEAVES 2)required for formation of a symmetric flat leaf lamina, encodes a member of a family of proteins characterized by cysteine repeats and a leucine zipper; involved in KNOX gene regulation. Acts together with ASL1 in proximal-distal symmetry determination. Forms a complex with AS1 that binds to the BP promoter and leads to silencing of BP.O.I.H.G.S.X.
0.2217.50.66At3g05980819769unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOFO.I.H.G.S.X.
0.2014.40.68At4g11450826749unknown proteinF:unknown;P:biological_process unknown;C:chloroplast;PMOO.I.H.G.S.X.
0.1912.70.66At4g39790830137unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PBFMOO.I.H.G.S.X.
0.1912.70.68At4g38950830050kinesin motor family proteinF:microtubule motor activity, ATP binding;P:microtubule-based process, microtubule-based movement;C:microtubule associated complex;MOPFO.I.H.G.S.X.
0.1912.70.67At5g37020833672ARF8 (AUXIN RESPONSE FACTOR 8)Encodes a member of the auxin response factor family. Mediates auxin response via expression of auxin regulated genes. Acts redundantly with ARF6 to control stamen elongation and flower maturation. Expression of ARF8 is controlled by miR167.O.I.H.G.S.X.
0.1811.40.68At4g13990827035exostosin family proteinF:catalytic activity;P:biological_process unknown;C:cell wall, membrane;POMO.I.H.G.S.X.
0.1710.20.67At1g108503766694ATP binding / protein binding / protein kinase/ protein serine/threonine kinaseF:protein binding, protein serine/threonine kinase activity, protein kinase activity, ATP binding;P:transmembrane receptor protein tyrosine kinase signaling pathway, protein amino acid phosphorylation;C:endomembrane system;PMOBFVAO.I.H.G.S.X.
0.1710.20.70At1g01600839347CYP86A4Encodes a member of the CYP86A subfamily of cytochrome p450 genes. Expressed significantly at highest level in mature stems and flowers.O.I.H.G.S.X.
0.168.80.68At1g79820844321SGB1 (SUPPRESSOR OF G PROTEIN BETA1)F:carbohydrate transmembrane transporter activity, sugar:hydrogen symporter activity;P:transport, transmembrane transport;C:integral to membrane, membrane;BFMPOAVO.I.H.G.S.X.
0.168.80.66At5g59020836019unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMFO.I.H.G.S.X.
0.168.80.66At2g17270816233mitochondrial substrate carrier family proteinF:binding;P:transport;C:mitochondrial inner membrane, membrane;MFPOO.I.H.G.S.X.
0.157.80.67At4g12840826896unknown proteinF:unknown;P:unknown;C:unknown;POO.I.H.G.S.X.
0.157.80.66At4g18470827577SNI1Negative regulator of systemic acquired resistance (SAR), repressor of pathogenesis-related PR gene expression which is removed by NPR1 upon induction of SAR. Encodes leucine-rich nuclear protein. Conserved in plants, with putative orthologs found in several plant species. Many NPR1-dependent PR gene are specifically derepressed in the sni1 mutant. The structural similarity of SNI1 to Armadillo repeat proteins implies that SNI1 may form a scaffold for interaction with proteins that modulate transcription. Histone modification may be involved in SNI1-mediated repression of PR genes.O.I.H.G.S.X.
0.157.80.66At2g45870819195unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;BFPOO.I.H.G.S.X.
0.146.80.71At2g19170816434SLP3Encodes a novel subtilisin-like serine protease.O.I.H.G.S.X.
0.146.80.69At4g33800829522unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.146.80.67At5g41060834108zinc finger (DHHC type) family proteinF:zinc ion binding;P:unknown;C:plasma membrane;MOFPO.I.H.G.S.X.
0.146.80.69At5g42280834233DC1 domain-containing proteinF:unknown;P:unknown;C:unknown;POMO.I.H.G.S.X.
0.146.80.66At5g49330834993AtMYB111 (myb domain protein 111)Member of the R2R3 factor gene family.O.I.H.G.S.X.
0.146.80.66At3g49250824086DMS3 (DEFECTIVE IN MERISTEM SILENCING 3)Similar to hinge-domain region of structural maintenance of chromosomes (SMC)proteins.Putative chromosome architecture protein that can potentialy link nucleic acids in facilitating an RNA1-mediated epigenetic modification involving secondary siRNA and spreading of DNA methylation.O.I.H.G.S.X.
0.135.80.66At1g60860842378AGD2 (ARF-GAP DOMAIN 2)A member of ARF GAP domain (AGD), A thaliana has 15 members, grouped into four classes. AGD2 belongs to the class 1, together with AGD1, AGD3, and AGD4.O.I.H.G.S.X.
0.124.90.74At3g44610823587protein kinase family proteinF:kinase activity;P:protein amino acid phosphorylation;C:chloroplast;MOPFBVAO.I.H.G.S.X.
0.124.90.68At1g08840837406emb2411 (embryo defective 2411)F:ATP-dependent DNA helicase activity, DNA binding, ATP binding;P:embryonic development ending in seed dormancy, DNA replication;C:chloroplast;MBOFPAVO.I.H.G.S.X.
0.124.90.66At3g50050824167aspartyl protease family proteinF:aspartic-type endopeptidase activity;P:proteolysis;C:endomembrane system;MPFOO.I.H.G.S.X.
0.114.10.69At4g14750827130IQD19 (IQ-domain 19)F:calmodulin binding;P:unknown;C:unknown;PMOFBVAO.I.H.G.S.X.
0.114.10.66At4g22250828320zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:unknown;C:unknown;MPOFVO.I.H.G.S.X.
0.114.10.67At4g23440828443nucleoside-triphosphatase/ nucleotide binding / transmembrane receptorF:transmembrane receptor activity, nucleoside-triphosphatase activity, nucleotide binding;P:signal transduction, innate immune response;C:plasma membrane;BPFOMAO.I.H.G.S.X.
0.114.10.67At3g19570821494unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMBFPVAO.I.H.G.S.X.
0.114.10.67At1g13170837875ORP1D (OSBP(OXYSTEROL BINDING PROTEIN)-RELATED PROTEIN 1D)F:oxysterol binding;P:steroid metabolic process;C:unknown;MFOPO.I.H.G.S.X.
0.092.80.66At2g27340817277-F:molecular_function unknown;P:biological_process unknown;C:unknown;FMOBPO.I.H.G.S.X.
0.092.80.67At1g270708395965'-AMP-activated protein kinase-relatedF:unknown;P:unknown;C:unknown;MFPOBAO.I.H.G.S.X.
0.082.30.66At3g08680820015leucine-rich repeat transmembrane protein kinase, putativeF:protein serine/threonine kinase activity, kinase activity, ATP binding;P:transmembrane receptor protein tyrosine kinase signaling pathway, protein amino acid phosphorylation;C:plasma membrane, plant-type cell wall;PMOBFVAO.I.H.G.S.X.
0.082.30.68At3g03690821186UNE7 (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.
0.071.90.68At1g16750838246-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PBMOFO.I.H.G.S.X.
0.071.90.66At3g06600819839unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.061.40.66At1g78810844217unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOFO.I.H.G.S.X.
0.051.10.67At1g14820838047SEC14 cytosolic factor family protein / phosphoglyceride transfer family proteinF:transporter activity;P:transport;C:cellular_component unknown;PFMOO.I.H.G.S.X.
0.040.90.66At1g29550839832eukaryotic translation initiation factor 4E, putative / eIF-4E, putative / eIF4E, putative / mRNA cap-binding protein, putativeF:RNA binding, translation initiation factor activity;P:translational initiation;C:cytoplasm;MOPFO.I.H.G.S.X.
0.030.60.66At1g73970843735unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POO.I.H.G.S.X.
0.020.40.69At2g41830818782cyclin-relatedF:unknown;P:unknown;C:plasma membrane;MPOFO.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
59.199.8GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
51.599.8GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
42.099.8GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
41.199.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
39.199.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.299.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.599.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.199.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.999.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
35.399.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.399.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.699.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.499.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.199.7GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
33.999.7GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
33.899.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
33.799.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.599.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.399.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
32.299.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
31.599.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.499.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.699.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
25.899.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
22.799.6E-MEXP-1474-raw-cel-1593932513
22.699.6GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
19.499.6GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
17.999.5E-MEXP-1474-raw-cel-1593932609
17.099.5GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
15.599.5GSM10451WT Mature Green Seed 1GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
15.299.4GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
13.199.4GSM184917Arabidopsis, root cells, endodermis and quiescent center, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
12.399.3GSM133766Lindsey_1-18_torpedo-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
11.899.3E-MEXP-1474-raw-cel-1593932705
11.899.3GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
10.599.2GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.799.1GSM133304RIKEN-NAKABAYASHI1BGSE5700AtGenExpress: Effect of ABA during seed imbibitionLink to GEO
9.499.1E-ATMX-1-raw-cel-1112746154
8.999.0E-ATMX-1-raw-cel-1112746209

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0431GO:0009799The establishment of an organism's body plan or part of an organism such that a similar arrangement in form and relationship of parts around a common axis, or around each side of a plane is created.Link to AmiGO
0.0431GO:0010113Any process that stops, prevents or reduces the frequency, rate or extent of systemic acquired resistance.Link to AmiGO
0.0401GO:0009954The regionalization process by which specific areas of cell differentiation are determined along a proximal/distal axis. The proximal/distal axis is defined by a line that runs from main body (proximal end) of an organism outward (distal end).Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.026100040Pentose and glucuronate interconversionsLink to KEGG PATHWAY
0.024103030DNA replicationLink to KEGG PATHWAY
0.018100945Stilbenoid, diarylheptanoid and gingerol biosynthesisLink 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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