Co-expression analysis

Gene ID At1g51680
Gene name 4CL1 (4-COUMARATE:COA LIGASE 1)
Module size 5 genes
NF 0.40
%ile 55.9



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
0.2930.31.00At1g516808415934CL1 (4-COUMARATE:COA LIGASE 1)encodes an isoform of 4-coumarate:CoA ligase (4CL), which is involved in the last step of the general phenylpropanoid pathway. In addition to 4-coumarate, it also converts ferulate. The catalytic efficiency was in the following (descending) order: p-coumaric acid, ferulic acid, caffeic acid and 5-OH-ferulic acid. At4CL1 was unable to use sinapic acid as substrate.O.I.H.G.S.X.
0.5773.80.79At3g19450821479ATCAD4Encodes a catalytically active cinnamyl alcohol dehydrogenase which uses p-coumaryl aldehyde as a preferred substrate. It can also use caffeyl, coniferyl and d-hydroxyconiferyl aldehydes as substrates.O.I.H.G.S.X.
0.4659.80.85At3g53260824493PAL2Encodes phenylalanine lyase.O.I.H.G.S.X.
0.4050.80.80At1g28680839768transferase family proteinF:transferase activity, transferring acyl groups other than amino-acyl groups, transferase activity;P:biological_process unknown;C:cellular_component unknown;PFO.I.H.G.S.X.
0.3846.70.84At2g40890818686CYP98A3 (cytochrome P450, family 98, subfamily A, polypeptide 3)encodes coumarate 3-hydroxylase (C3H), a P450-dependent monooxygenase. Involved in lignin biosynthesis and flavonoid biosynthesis. Also affects the biosynthesis of coumarins such as scopoletin and scopolin as a branching-out-pathway from the phenylpropanoid acid level.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
52.299.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
46.999.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
45.099.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
42.899.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
42.699.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
42.599.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
42.499.8GSM270814Arabidopsis cell culture, 4 h_control_rep1GSE10719Response of Arabidopsis cell culture to phytoprostane A1Link to GEO
41.899.8GSM270853Arabidopsis cell culture, 4 h_control_rep2GSE10719Response of Arabidopsis cell culture to phytoprostane A1Link to GEO
41.699.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.299.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.599.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.499.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.799.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.699.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.399.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.599.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.299.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.199.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
26.799.7GSM270865Arabidopsis cell culture, 4 h_control_rep3GSE10719Response of Arabidopsis cell culture to phytoprostane A1Link to GEO
25.699.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
23.999.6GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
23.899.6GSM157330Coates_1-2_ara1OX_Rep1_ATH1GSE6826Identification of candidate Arabidillo target genes in ArabidopsisLink to GEO
23.899.6GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
21.799.6GSM157331Coates_1-3_Col-3_Rep1_ATH1GSE6826Identification of candidate Arabidillo target genes in ArabidopsisLink to GEO
20.399.6GSM265423Arabidopsis, root, longitudinal zone 3, standard conditions, rep 2GSE10497Expression analysis of root developmental zones after iron deficiency (-Fe) treatmentLink to GEO
20.299.6GSM131588ATGE_35_AGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
18.999.5GSM131589ATGE_35_BGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
18.499.5GSM265431Arabidopsis, root, longitudinal zone 3, -Fe conditions, rep 2GSE10497Expression analysis of root developmental zones after iron deficiency (-Fe) treatmentLink to GEO
17.699.5GSM131590ATGE_35_CGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
17.099.5GSM157339Coates_1-11_Col-3_Rep3_ATH1GSE6826Identification of candidate Arabidillo target genes in ArabidopsisLink to GEO
16.099.5GSM157335Coates_1-7_Col-3_Rep2_ATH1GSE6826Identification of candidate Arabidillo target genes in ArabidopsisLink to GEO
16.099.5GSM157333Coates_1-5_Col-0_Rep2_ATH1GSE6826Identification of candidate Arabidillo target genes in ArabidopsisLink to GEO
15.699.5GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
14.799.4GSM270868Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep2GSE10719Response of Arabidopsis cell culture to phytoprostane A1Link to GEO
14.199.4GSM157334Coates_1-6_ara1OX_Rep2_ATH1GSE6826Identification of candidate Arabidillo target genes in ArabidopsisLink to GEO
13.899.4GSM270870Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep3GSE10719Response of Arabidopsis cell culture to phytoprostane A1Link to GEO
13.499.4GSM157329Coates_1-1_Col-0_Rep1_ATH1GSE6826Identification of candidate Arabidillo target genes in ArabidopsisLink to GEO
12.799.3GSM270866Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep1GSE10719Response of Arabidopsis cell culture to phytoprostane A1Link to GEO
12.799.3GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
12.799.3GSM226538L8SBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
12.599.3GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
12.499.3GSM157332Coates_1-4_ara1/2mut_Rep1_ATH1GSE6826Identification of candidate Arabidillo target genes in ArabidopsisLink to GEO
12.199.3GSM184552Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
12.099.3GSM67086Arabidopsis_Stigma02GSE3056Arabidopsis Pollination StudyLink to GEO
11.599.3GSM131562ATGE_93_BGSE5631AtGenExpress: Developmental series (roots)Link to GEO
10.499.2GSM131567ATGE_95_AGSE5631AtGenExpress: Developmental series (roots)Link to GEO
10.299.2GSM157336Coates_1-8_ara1/2mut_Rep2_ATH1GSE6826Identification of candidate Arabidillo target genes in ArabidopsisLink to GEO
10.299.2GSM142754MJ001_ATH1_A5-jones-WT-Rep3GSE6165The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.Link to GEO
10.099.2GSM157340Coates_1-12_ara1/2mut_Rep3_ATH1GSE6826Identification of candidate Arabidillo target genes in ArabidopsisLink to GEO
9.799.1GSM131568ATGE_95_BGSE5631AtGenExpress: Developmental series (roots)Link to GEO
9.099.1GSM133766Lindsey_1-18_torpedo-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
9.099.1GSM157337Coates_1-9_Col-0_Rep3_ATH1GSE6826Identification of candidate Arabidillo target genes in ArabidopsisLink to GEO
8.899.0GSM131563ATGE_93_CGSE5631AtGenExpress: Developmental series (roots)Link to GEO
8.799.0GSM67087Arabidopsis_Stigma03GSE3056Arabidopsis Pollination StudyLink to GEO
8.799.0GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
8.699.0GSM131569ATGE_95_CGSE5631AtGenExpress: Developmental series (roots)Link to GEO
8.699.0GSM157338Coates_1-10_ara1OX_Rep3_ATH1GSE6826Identification of candidate Arabidillo target genes in ArabidopsisLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.2501GO:0009805The chemical reactions and pathways resulting in the formation of coumarins, a class of compounds derived from the phenylacrylic skeleton of cinnamic acids.Link to AmiGO
0.2502GO:0009699The chemical reactions and pathways resulting in the formation of aromatic derivatives of trans-cinnamic acid.Link to AmiGO
0.1181GO:0009698The chemical reactions and pathways involving aromatic derivatives of trans-cinnamic acid.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.095100941Flavonoid biosynthesisLink to KEGG PATHWAY
0.087100960Tropane, piperidine and pyridine alkaloid biosynthesisLink to KEGG PATHWAY
0.075400940Phenylpropanoid 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



Back to the CoP portal site

Back to the KAGIANA project homepage