Co-expression analysis

Gene ID At4g24780
Gene name pectate lyase family protein
Module size 6 genes
NF 0.07
%ile 3.9



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
1.00100.01.00At4g24780828580pectate lyase family proteinF:lyase activity, pectate lyase activity;P:biological_process unknown;C:membrane;PBFOO.I.H.G.S.X.
0.4457.20.82At4g30020829125subtilase family proteinF:identical protein binding, serine-type endopeptidase activity;P:proteolysis, negative regulation of catalytic activity;C:endomembrane system, cell wall, membrane;BPOFAMO.I.H.G.S.X.
0.3338.10.82At5g65700836699BAM1 (BARELY ANY MERISTEM 1)Encodes a CLAVATA1-related receptor kinase-like protein required for both shoot and flower meristem function. Very similar to BAM2,with more than 85% a.a. identity. It has a broad expression pattern and is involved in vascular strand development in the leaf, control of leaf shape, size and symmetry, male gametophyte development and ovule specification and function. Anthers of double mutants (bam1bam2) appeared abnormal at a very early stage and lack the endothecium, middle, and tapetum layers. Further analyses revealed that cells interior to the epidermis (in anther tissue) acquire some characteristics of pollen mother cells (PMCs), suggesting defects in cell fate specification. The pollen mother-like cells degenerate before the completion of meiosis, suggesting that these cells are defective. In addition, the BAM1 expression pattern supports both an early role in promoting somatic cell fates and a subsequent function in the PMCs.O.I.H.G.S.X.
0.2217.50.82At3g57030824870strictosidine synthase family proteinF:strictosidine synthase activity;P:alkaloid biosynthetic process, biosynthetic process;C:endoplasmic reticulum, plasma membrane, plant-type cell wall;PBMOFAO.I.H.G.S.X.
0.146.80.83At5g62890836409permease, putativeF:transmembrane transporter activity;P:transport;C:cell wall, vacuole, membrane;BOMPFAVO.I.H.G.S.X.
0.010.20.82At1g60070842301binding / clathrin binding / protein binding / protein transporterF:protein transporter activity, protein binding, clathrin binding, binding;P:intracellular protein transport, vesicle-mediated transport, protein transport;C:membrane coat, Golgi apparatus part, Golgi apparatus, clathrin adaptor complex;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
126.799.9GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
114.399.9GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
113.999.9GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
106.699.9GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
103.799.9GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
93.499.9GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
91.799.9GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
76.199.9GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
72.399.9GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
62.299.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
56.699.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
56.199.8GSM184519Pericycle root cells 2hr continuous KNO3 and MSX treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
53.699.8E-MEXP-849-raw-cel-1181981030
52.999.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
52.699.8GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
52.199.8GSM133959Fukuda_1-4_2B_Rep2_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
51.899.8GSM133958Fukuda_1-3_2A_Rep1_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
51.799.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
50.999.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
50.399.8E-MEXP-849-raw-cel-1181981046
49.199.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
48.799.8GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
48.199.8E-MEXP-849-raw-cel-1181981022
47.899.8E-MEXP-849-raw-cel-1181981038
46.699.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
45.699.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
44.699.8GSM133961Fukuda_1-6_4B_Rep2_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
44.299.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
43.999.8GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
40.399.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.799.8GSM133960Fukuda_1-5_4A_Rep1_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
34.199.7E-MEXP-849-raw-cel-1181981014
32.999.7GSM134299Penfield_1-1_endosperm-control_Rep1_ATH1GSE5751The early post-germinative embryo and endosperm transcriptomes in ArabidopsisLink to GEO
31.499.7GSM134301Penfield_1-3_endosperm-control_Rep3_ATH1GSE5751The early post-germinative embryo and endosperm transcriptomes in ArabidopsisLink to GEO
26.899.7GSM133967Fukuda_1-12_10B_Rep2_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
26.299.7GSM133120RIKEN-YAMAUCHI2BGSE5687AtGenExpress: Different temperature treatment of seedsLink to GEO
25.299.6GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
25.099.6GSM133964Fukuda_1-9_8A_Rep1_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
24.799.6GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
24.599.6GSM133773Lindsey_1-25_torpedo-meristem_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
23.599.6GSM133965Fukuda_1-10_8B_Rep2_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
22.199.6GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
21.999.6E-MEXP-849-raw-cel-1181981006
21.499.6GSM133979Birnbaum_1-9_StageII-2_Rep2_ATH1GSE5749A gene expression map of the Arabidopsis rootLink to GEO
20.999.6GSM133306RIKEN-NAKABAYASHI2BGSE5700AtGenExpress: Effect of ABA during seed imbibitionLink to GEO
20.899.6GSM133981Birnbaum_1-11_StageII-4_Rep4_ATH1GSE5749A gene expression map of the Arabidopsis rootLink to GEO
20.599.6GSM184517Pericycle root cells 2hr continuous KCl and MSX control treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
20.399.6GSM184520Pericycle root cells 2hr continuous KNO3 and MSX treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
20.099.6GSM184516Pericycle root cells 2hr continuous KCl and MSX control treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
18.499.5GSM134300Penfield_1-2_endosperm-control_Rep2_ATH1GSE5751The early post-germinative embryo and endosperm transcriptomes in ArabidopsisLink to GEO
18.499.5GSM176878AWP_AL_Txed_2GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
18.199.5GSM134304Penfield_1-6_endosperm-ABA_Rep3_ATH1GSE5751The early post-germinative embryo and endosperm transcriptomes in ArabidopsisLink to GEO
17.599.5GSM133980Birnbaum_1-10_StageII-3_Rep3_ATH1GSE5749A gene expression map of the Arabidopsis rootLink to GEO
17.099.5GSM13784Cycloheximide - replicateGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
16.399.5GSM133966Fukuda_1-11_10A_Rep1_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
16.199.5GSM134310Penfield_1-12_embryo-control_Rep3_ATH1GSE5751The early post-germinative embryo and endosperm transcriptomes in ArabidopsisLink to GEO
15.999.5GSM173628ARF10 rep2GSE7227microRNA160 resistant AUXIN RESPONSE FACTOR10 (mARF10) germinating seedsLink to GEO
15.699.5GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
15.399.4GSM133310RIKEN-NAKABAYASHI5BGSE5700AtGenExpress: Effect of ABA during seed imbibitionLink to GEO
14.999.4GSM299321Wild Type Germinating Seeds With Solvent Treatment Only Set 1 of 6GSE11852Effect of uniconazole on wt and pkl mutant germinating seedsLink to GEO
14.499.4GSM131106Broadley_1-4_A4-Bo-P3-phosphate-starved_Rep3_ATH1GSE5614Changes in Gene Expression in Brassica oleracea Shoots during Phosphate Starvation (Cross-species study)Link to GEO
14.499.4GSM133307RIKEN-NAKABAYASHI3AGSE5700AtGenExpress: Effect of ABA during seed imbibitionLink to GEO
14.199.4GSM173629ARF10 rep3GSE7227microRNA160 resistant AUXIN RESPONSE FACTOR10 (mARF10) germinating seedsLink to GEO
13.799.4GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
13.599.4GSM133308RIKEN-NAKABAYASHI4AGSE5700AtGenExpress: Effect of ABA during seed imbibitionLink to GEO
13.399.4GSM252678Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 13 hrs Taking 70 mm of Stump (4dpg) rep4GSE9996Organ regeneration in plants is independent of stem cell niche activityLink to GEO
13.399.4GSM252668Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 0 hrs Taking 70 mm of Stump (4dpg) rep2GSE9996Organ regeneration in plants is independent of stem cell niche activityLink to GEO
13.099.4GSM173623Col-0 rep2GSE7227microRNA160 resistant AUXIN RESPONSE FACTOR10 (mARF10) germinating seedsLink to GEO
12.799.3GSM226545Slice3JWGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
12.799.3GSM176879AWP_Control_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
12.799.3GSM133305RIKEN-NAKABAYASHI2AGSE5700AtGenExpress: Effect of ABA during seed imbibitionLink to GEO
12.699.3GSM134302Penfield_1-4_endosperm-ABA_Rep1_ATH1GSE5751The early post-germinative embryo and endosperm transcriptomes in ArabidopsisLink to GEO
12.699.3GSM134313Penfield_1-15_embryo-ABA_Rep3_ATH1GSE5751The early post-germinative embryo and endosperm transcriptomes in ArabidopsisLink to GEO
12.599.3GSM134457St.Clair_1-82_294_Mt-0_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1GSE5758Expression Level Polymorphism Project (ELP) - Mt-0Link to GEO
12.499.3GSM173626ARF10 rep1GSE7227microRNA160 resistant AUXIN RESPONSE FACTOR10 (mARF10) germinating seedsLink to GEO
12.499.3GSM134459St.Clair_1-84_379_Mt-0_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1GSE5758Expression Level Polymorphism Project (ELP) - Mt-0Link to GEO
12.299.3E-MEXP-1607-raw-cel-1620685818
11.799.3GSM133309RIKEN-NAKABAYASHI4BGSE5700AtGenExpress: Effect of ABA during seed imbibitionLink to GEO
11.599.3GSM252677Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 13 hrs Taking 70 mm of Stump (4dpg) rep3GSE9996Organ regeneration in plants is independent of stem cell niche activityLink to GEO
11.499.3GSM184842Arabidopsis, root, longitudinal zone 2, standard conditions, NaCl, replicate 2GSE7639Expression analysis of root developmental zones after treatment with saltLink to GEO
11.399.3GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
11.399.3GSM299324Wild Type Germinating Seeds With Solvent Treatment Only Set 4 of 6GSE11852Effect of uniconazole on wt and pkl mutant germinating seedsLink to GEO
11.199.2GSM184552Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
10.999.2E-MEXP-1607-raw-cel-1620685834
10.999.2GSM134405St.Clair_1-102_350_Tsu-1_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1GSE5755Expression Level Polymorphism Project (ELP) - Tsu-1Link to GEO
10.599.2GSM265420Arabidopsis, root, longitudinal zone 2, standard conditions, rep 1GSE10497Expression analysis of root developmental zones after iron deficiency (-Fe) treatmentLink to GEO
10.399.2GSM133978Birnbaum_1-8_StageII-1_Rep1_ATH1GSE5749A gene expression map of the Arabidopsis rootLink to GEO
10.399.2GSM131105Broadley_1-3_A3-Bo-P2-phosphate-starved_Rep2_ATH1GSE5614Changes in Gene Expression in Brassica oleracea Shoots during Phosphate Starvation (Cross-species study)Link to GEO
10.399.2GSM299325Wild Type Germinating Seeds With Solvent Treatment Only Set 5 of 6GSE11852Effect of uniconazole on wt and pkl mutant germinating seedsLink to GEO
10.299.2GSM13783Dexamethasone plus cycloheximide - replicateGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
10.299.2GSM299322Wild Type Germinating Seeds With Solvent Treatment Only Set 2 of 6GSE11852Effect of uniconazole on wt and pkl mutant germinating seedsLink to GEO
10.299.2GSM173624Col-0 rep3GSE7227microRNA160 resistant AUXIN RESPONSE FACTOR10 (mARF10) germinating seedsLink to GEO
10.099.2E-MEXP-1607-raw-cel-1620685826
9.899.1GSM133962Fukuda_1-7_6A_Rep1_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
9.899.1GSM299326Wild Type Germinating Seeds With Solvent Treatment Only Set 6 of 6GSE11852Effect of uniconazole on wt and pkl mutant germinating seedsLink to GEO
9.799.1GSM133321RIKEN-LI6AGSE5701AtGenExpress: Basic hormone treatment of seedsLink to GEO
9.699.1GSM134441St.Clair_1-66_380_Kin-0_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1GSE5757Expression Level Polymorphism Project (ELP) - Kin-0Link to GEO
9.599.1GSM252672Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 5 hrs Taking 70 mm of Stump (4dpg) rep2GSE9996Organ regeneration in plants is independent of stem cell niche activityLink to GEO
9.599.1GSM133963Fukuda_1-8_6B_Rep2_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
9.599.1GSM173621Col-0 rep1GSE7227microRNA160 resistant AUXIN RESPONSE FACTOR10 (mARF10) germinating seedsLink to GEO
9.299.1GSM173649mARF10 rep2GSE7227microRNA160 resistant AUXIN RESPONSE FACTOR10 (mARF10) germinating seedsLink to GEO
9.099.1GSM299323Wild Type Germinating Seeds With Solvent Treatment Only Set 3 of 6GSE11852Effect of uniconazole on wt and pkl mutant germinating seedsLink to GEO
8.799.0GSM184909Arabidopsis, root cells, epidermis and lateral root cap, 140 mM NaCl, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
8.699.0GSM184833Arabidopsis, root, longitudinal zone 2, standard conditions, replicate 3GSE7639Expression analysis of root developmental zones after treatment with saltLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.2501GO:0010480The process aimed at the progression of a microsporocyte cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. A microsporocyte is a diploid (2n) cell that undergoes meiosis and forms four haploid (1n) microspores; also called microspore mother cell and, in seed plants, pollen mother cell.Link to AmiGO
0.2001GO:0048229The process whose specific outcome is the progression of the gametophyte over time, from its formation to the mature structure. The gametophyte is the gamete-producing individual or phase in the life cycle having alternation of generations. An example of this process is found in Arabidopsis thaliana.Link to AmiGO
0.1541GO:0048437The process whose specific outcome is the progression of the floral organ over time, from its formation to the mature structure.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG

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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