Co-expression analysis

Gene ID At3g21230
Gene name 4CL5 (4-coumarate:CoA ligase 5)
Module size 8 genes
NF 0.30
%ile 37.6



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
0.2115.81.00At3g212308216774CL5 (4-coumarate:CoA ligase 5)The gene encodes a 4-coumarate coenzyme A ligase being able to use sinapate as substrate. The catalytic efficiency was in the following (descending) order: p-coumaric acid, caffeic acid, 5-OH-ferulic acid, ferulic acid and sinapic acid. At4CL5 was unable to use cinnamic acid as substrate. Knockout of At4CL5 (4cl5) revealed no effect on syringyl lignin content indicating that the activity observed does probably not occur in vivo.O.I.H.G.S.X.
0.5065.30.64At2g34930818058disease resistance family proteinF:protein binding;P:signal transduction, defense response to fungus, defense response;C:cell wall;PMOBFAVO.I.H.G.S.X.
0.4659.80.62At2g27690817315CYP94C1Encodes a CYP94C1. Has highest omega-hydroxylase activity with 9,10-epoxystearic acid, while also metabolized lauric acid (C12:0) and C18 unsaturated fatty acids. Gene expression is induced in response to wounding and jasmonic acid treatment.O.I.H.G.S.X.
0.3643.60.63At2g38240818403oxidoreductase, 2OG-Fe(II) oxygenase family proteinF:oxidoreductase activity;P:response to salt stress;C:unknown;POBFMO.I.H.G.S.X.
0.3643.60.65At5g53750835456-F:molecular_function unknown;P:response to wounding;C:cellular_component unknown;PO.I.H.G.S.X.
0.3032.10.64At1g17420838314LOX3LipoxygenaseO.I.H.G.S.X.
0.2319.30.67At4g23200828419protein kinase family proteinF:protein serine/threonine kinase activity, protein tyrosine kinase activity, protein kinase activity, ATP binding;P:protein amino acid phosphorylation;C:vacuole;MPOBFVAO.I.H.G.S.X.
0.146.80.69At1g02400839508GA2OX6 (GIBBERELLIN 2-OXIDASE 6)Encodes a gibberellin 2-oxidase.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
233.6100.0GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
131.099.9GSM284388Arabidopsis GMPE1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
79.599.9GSM284389Arabidopsis GMPE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
70.399.9GSM13779Dexamethasone plus cycloheximideGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
64.999.8E-MEXP-807-raw-cel-1173273252
63.899.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
63.299.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
62.999.8GSM13784Cycloheximide - replicateGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
62.599.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
59.999.8GSM13783Dexamethasone plus cycloheximide - replicateGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
58.599.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
58.399.8GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
55.599.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
51.099.8GSM13780CycloheximideGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
45.199.8GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
43.099.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
40.499.8E-MEXP-807-raw-cel-1173273144
37.399.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.099.7GSM266667Arabidopsis, root cells, columella root cap, -Fe, replicate 2GSE10501Expression analysis of root cell-types after iron deficiency (-Fe) treatmentLink to GEO
33.899.7GSM266668Arabidopsis, root cells, columella root cap, -Fe, replicate 3GSE10501Expression analysis of root cell-types after iron deficiency (-Fe) treatmentLink to GEO
32.799.7GSM131322AtGen_6-3422_Saltstress-Roots-6.0h_Rep2GSE5623AtGenExpress: Stress Treatments (Salt stress)Link to GEO
31.599.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.199.7E-MEXP-739-raw-cel-1099467339
29.599.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
29.099.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
26.499.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
26.099.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
25.499.6GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
24.599.6GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
24.499.6GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
23.499.6GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
22.899.6GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
22.899.6GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
22.799.6E-MEXP-828-raw-cel-1156922342
21.899.6GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
21.199.6GSM131607ATGE_42_CGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
20.999.6GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
20.799.6GSM131608ATGE_42_DGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
20.499.6E-MEXP-739-raw-cel-1099467384
20.099.6GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
19.899.6GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
19.699.6GSM266666Arabidopsis, root cells, columella root cap, -Fe, replicate 1GSE10501Expression analysis of root cell-types after iron deficiency (-Fe) treatmentLink to GEO
16.599.5GSM131611ATGE_43_CGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
16.199.5GSM131606ATGE_42_BGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
15.599.5GSM284386Arabidopsis GSUS3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
14.899.4GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
14.899.4E-MEXP-739-raw-cel-1099467393
14.499.4E-MEXP-739-raw-cel-1099467321
13.799.4GSM131317AtGen_6-3321_Saltstress-Roots-3.0h_Rep1GSE5623AtGenExpress: Stress Treatments (Salt stress)Link to GEO
13.399.4GSM131610ATGE_43_BGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
12.999.3GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
12.699.3GSM128661Underwood_1-14_Cor-5x10e7-10h_Rep2_ATH1GSE5520Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interactionLink to GEO
12.599.3GSM131609ATGE_43_AGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
12.399.3GSM184894Arabidopsis, root cells, columella root cap, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
12.199.3GSM131318AtGen_6-3322_Saltstress-Roots-3.0h_Rep2GSE5623AtGenExpress: Stress Treatments (Salt stress)Link to GEO
11.199.2GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
10.899.2GSM133766Lindsey_1-18_torpedo-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
10.699.2E-MEXP-739-raw-cel-1099467375
10.199.2GSM142846MG001_ATH1_A27-Torres-9N1GSE6176Impact of Type III effectors on plant defense responsesLink to GEO
9.199.1GSM106915opr3_JA_22 hrs_Rep1GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
9.099.1GSM176879AWP_Control_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
8.999.0GSM131603ATGE_41_AGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
8.799.0GSM133029BC482-1GSE5684AtGenExpress: Pathogen Series: Response to Botrytis cinerea infectionLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1541GO:0045487The chemical reactions and pathways resulting in the breakdown of gibberellin. Gibberellins are a class of highly modified terpenes that function as plant growth regulators.Link to AmiGO
0.1051GO:0009699The chemical reactions and pathways resulting in the formation of aromatic derivatives of trans-cinnamic acid.Link to AmiGO
0.0951GO:0040007The increase in size or mass of an entire organism, a part of an organism or a cell.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.061100130Ubiquinone and other terpenoid-quinone biosynthesisLink to KEGG PATHWAY
0.054100592alpha-Linolenic acid metabolismLink to KEGG PATHWAY
0.018100940Phenylpropanoid 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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