Co-expression analysis

Gene ID At4g13710
Gene name pectate lyase family protein
Module size 40 genes
NF 0.18
%ile 15.0



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
1.00100.01.00At4g13710827005pectate lyase family proteinF:lyase activity, pectate lyase activity;P:biological_process unknown;C:endomembrane system;PBFOO.I.H.G.S.X.
0.3643.60.82At2g20240816543unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOFBO.I.H.G.S.X.
0.3541.60.78At3g01140821209MYB106 (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.
0.3541.60.78At2g24230816957leucine-rich repeat transmembrane protein kinase, putativeF:protein binding, protein serine/threonine kinase activity, protein tyrosine kinase activity, protein kinase activity, ATP binding;P:transmembrane receptor protein tyrosine kinase signaling pathway, protein amino acid phosphorylation;C:endomembrane system;MPOBFVAO.I.H.G.S.X.
0.3032.10.79At1g108503766694ATP 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.
0.2930.30.77At5g54200835508WD-40 repeat family proteinF:signal transducer activity;P:signal transduction;C:heterotrimeric G-protein complex;MFBOPAVO.I.H.G.S.X.
0.2930.30.79At5g37020833672ARF8 (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.
0.2522.60.78At5g06940830585leucine-rich repeat family proteinF:kinase activity;P:protein amino acid phosphorylation;C:endomembrane system;PMOBFVAO.I.H.G.S.X.
0.2522.60.81At2g19170816434SLP3Encodes a novel subtilisin-like serine protease.O.I.H.G.S.X.
0.2319.30.77At5g67200836855leucine-rich repeat transmembrane protein kinase, putativeF: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:plasma membrane;PMOBFVAO.I.H.G.S.X.
0.2217.50.78At5g59020836019unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMFO.I.H.G.S.X.
0.2217.50.81At5g41060834108zinc finger (DHHC type) family proteinF:zinc ion binding;P:unknown;C:plasma membrane;MOFPO.I.H.G.S.X.
0.2014.40.77At2g24630816999ATCSLC08encodes a gene similar to cellulose synthaseO.I.H.G.S.X.
0.2014.40.80At4g11450826749unknown proteinF:unknown;P:biological_process unknown;C:chloroplast;PMOO.I.H.G.S.X.
0.2014.40.78At1g79820844321SGB1 (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.
0.1912.70.77At3g49250824086DMS3 (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.
0.1811.40.77At3g56270824793unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;PMOO.I.H.G.S.X.
0.1710.20.79At1g13170837875ORP1D (OSBP(OXYSTEROL BINDING PROTEIN)-RELATED PROTEIN 1D)F:oxysterol binding;P:steroid metabolic process;C:unknown;MFOPO.I.H.G.S.X.
0.168.80.77At5g40550834053unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPOO.I.H.G.S.X.
0.168.80.79At3g19570821494unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMBFPVAO.I.H.G.S.X.
0.157.80.77At2g17270816233mitochondrial substrate carrier family proteinF:binding;P:transport;C:mitochondrial inner membrane, membrane;MFPOO.I.H.G.S.X.
0.135.80.78At3g08680820015leucine-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.
0.135.80.80At1g08840837406emb2411 (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.
0.124.90.78At4g14920827150DNA binding / protein binding / zinc ion bindingF:protein binding, DNA binding, zinc ion binding;P:regulation of transcription, DNA-dependent;C:nucleus;MPFOO.I.H.G.S.X.
0.124.90.78At1g21480838746exostosin family proteinF:catalytic activity;P:biological_process unknown;C:Golgi apparatus, membrane;PMOBFO.I.H.G.S.X.
0.114.10.78At2g46000819208unknown proteinF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PMO.I.H.G.S.X.
0.103.40.78At1g16750838246-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PBMOFO.I.H.G.S.X.
0.103.40.77At2g30800817631HVT1 (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.
0.103.40.78At3g23900821973RNA recognition motif (RRM)-containing proteinF:nucleotide binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MOFBPVAO.I.H.G.S.X.
0.103.40.78At3g50780824242-F:unknown;P:biological_process unknown;C:cellular_component unknown;PMOO.I.H.G.S.X.
0.092.80.80At3g03690821186UNE7 (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.
0.082.30.77At1g74690843808IQD31 (IQ-domain 31)F:calmodulin binding;P:biological_process unknown;C:cytosol, plasma membrane;MOFPBVAO.I.H.G.S.X.
0.082.30.77At3g52290824394IQD3 (IQ-domain 3)F:calmodulin binding;P:biological_process unknown;C:plasma membrane;POFMO.I.H.G.S.X.
0.082.30.78At1g80900844430magnesium transporter CorA-like family protein (MGT1) (MRS2)F:metal ion transmembrane transporter activity;P:metal ion transport;C:membrane;PFOMBO.I.H.G.S.X.
0.082.30.78At3g60740825245TTN1 (TITAN 1)Encodes tubulin-folding cofactor D. Mutants arrest during embryogenesis with embryos that are small, mushroom-shaped ('pilz') and consist of only one or few large cells each containing one or more variably enlarged nuclei and often cell wall stubs. Gene product necessary for continuous microtubule organization.O.I.H.G.S.X.
0.071.90.77At1g30300839910unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OBPAFO.I.H.G.S.X.
0.071.90.79At1g55130841956endomembrane protein 70, putativeF:unknown;P:unknown;C:integral to membrane, Golgi apparatus;MPOFBO.I.H.G.S.X.
0.061.40.77At1g29550839832eukaryotic 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.
0.061.40.78At2g41830818782cyclin-relatedF:unknown;P:unknown;C:plasma membrane;MPOFO.I.H.G.S.X.
0.030.60.78At3g53520824520UXS1 (UDP-GLUCURONIC ACID DECARBOXYLASE 1)Encodes an isoform of UDP-glucuronic acid decarboxylase, which is predicted to be membrane-bound by PSORT analysis. This enzyme produces UDP-xylose, which is a substrate for many cell wall carbohydrates including hemicellulose and pectin. UDP-xylose is also known to feedback regulate several cell wall biosynthetic enzymes.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
80.299.9GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
77.999.9GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
64.199.8GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
61.999.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
58.799.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
58.399.8GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
56.999.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
54.299.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
53.999.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
53.599.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
51.199.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
50.199.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
48.899.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
48.499.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
47.799.8GSM253645High_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
46.999.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
46.999.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
45.999.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
45.699.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
44.099.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
41.499.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.199.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
38.499.8GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
36.699.7GSM184906Arabidopsis, root cells, protophloem, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
36.499.7GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
35.499.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
32.399.7GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
31.999.7GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
28.699.7GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
27.099.7GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
25.999.7E-MEXP-1474-raw-cel-1593932513
24.899.6GSM184923Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
20.599.6E-MEXP-1474-raw-cel-1593932609
17.399.5GSM184905Arabidopsis, root cells, protophloem, standard conditions, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
17.299.5GSM10451WT Mature Green Seed 1GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
14.399.4GSM184917Arabidopsis, root cells, endodermis and quiescent center, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
13.599.4E-MEXP-1474-raw-cel-1593932705
13.099.4E-ATMX-1-raw-cel-1112746154
11.799.3E-ATMX-1-raw-cel-1112746209
11.199.2GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
10.799.2E-ATMX-1-raw-cel-1112746267
9.699.1GSM67086Arabidopsis_Stigma02GSE3056Arabidopsis Pollination StudyLink to GEO
9.599.1GSM226547Slice5JWGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
9.499.1GSM266668Arabidopsis, root cells, columella root cap, -Fe, replicate 3GSE10501Expression analysis of root cell-types after iron deficiency (-Fe) treatmentLink to GEO
9.199.1GSM184900Arabidopsis, root cells, endodermis and quiescent center, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
9.099.1GSM10453WT Mature Green Seed 2GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
9.099.1GSM258002LMPC-derived phloem_1GSE10247Transcriptome analysis of the Arabidopsis phloemLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0474GO:0007169The series of molecular signals generated as a consequence of a transmembrane receptor tyrosine kinase binding to its physiological ligand.Link to AmiGO
0.0441GO:0042732The chemical reactions and pathways involving D-xylose, a naturally occurring plant polysaccharide.Link to AmiGO
0.0431GO:0007021The aggregation and bonding together of alpha- and beta-tubulin to form a tubulin heterodimer.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.028100040Pentose and glucuronate interconversionsLink to KEGG PATHWAY
0.026103030DNA replicationLink 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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