Co-expression analysis

Gene ID At5g48100
Gene name TT10 (TRANSPARENT TESTA 10)
Module size 8 genes
NF 0.58
%ile 79.3



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
0.3439.81.00At5g48100834862TT10 (TRANSPARENT TESTA 10)Encodes a protein that is similar to laccase-like polyphenol oxidases. Involved in lignin and flavonoids biosynthesis. It has four conserved copper binding domains. Expressed in developing testa, where it colocalizes with the flavonoid end products proanthocyanidins and flavonols. Mutant plants exhibited a delay in developmentally determined browning of the testa, characterized by the pale brown color of seed coat. The tt10 mutant seeds accumulate more epicatechin monomers and more soluble proanthocyanidins than wild-type seeds. Flavonol composition was also affected in tt10 seeds, which exhibited a higher ratio of quercetin rhamnoside monomers versus dimers than wild-type seeds.O.I.H.G.S.X.
0.7184.20.66At2g23550816887MES6 (METHYL ESTERASE 6)Encodes a protein predicted to act as a carboxylesterase. It has similarity to the SABP2 methyl salicylate esterase from tobacco but no enzymatic activity has been identified for this protein.O.I.H.G.S.X.
0.6781.60.71At1g23200838928pectinesterase family proteinF:enzyme inhibitor activity, pectinesterase activity;P:cell wall modification;C:endomembrane system, cell wall, plant-type cell wall;PBFAOMO.I.H.G.S.X.
0.6781.60.66At4g11180826720disease resistance-responsive family protein / dirigent family proteinF:molecular_function unknown;P:lignan biosynthetic process, defense response;C:endomembrane system;PO.I.H.G.S.X.
0.6781.60.76At5g50750835147RGP4 (REVERSIBLY GLYCOSYLATED POLYPEPTIDE 4)reversibly glycosylated polypeptide RGP-4 (RGP4)O.I.H.G.S.X.
0.6781.60.72At5g59845836106gibberellin-regulated family proteinF:molecular_function unknown;P:response to gibberellin stimulus;C:endomembrane system;PO.I.H.G.S.X.
0.6478.90.67At1g205008386384-coumarate-CoA ligaseF:4-coumarate-CoA ligase activity;P:phenylpropanoid metabolic process, metabolic process;C:unknown;BOMFPAVO.I.H.G.S.X.
0.6378.10.68At2g23580816890MES4 (METHYL ESTERASE 4)Encodes a protein shown to have carboxylesterase activity and methyl salicylate esterase activity in vitro. This protein does not act on methyl IAA, methyl JA, MeGA4, or MEGA9 in vitro.O.I.H.G.S.X.

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Link to AtGenExpress Visualization Tool



Specific experiments for the module

Std2 GX %ile GSM ID Assay name GSE ID Experiment title Link to GEO
152.499.9GSM184905Arabidopsis, root cells, protophloem, standard conditions, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
144.499.9GSM184906Arabidopsis, root cells, protophloem, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
140.499.9GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
127.899.9GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
127.099.9GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
107.199.9GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
106.399.9GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
101.599.9GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
96.299.9GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
94.599.9GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
93.899.9GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
91.999.9GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
90.999.9GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
88.999.9GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
83.899.9GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
80.399.9GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
78.299.9GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
75.899.9GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
75.799.9GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
72.499.9GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
71.499.9GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
68.899.9GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
68.699.9GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
56.399.8GSM184923Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
54.099.8GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
52.299.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
47.599.8GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
36.299.7GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
25.399.6GSM284394Arabidopsis GCE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
24.799.6GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
23.099.6GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
20.799.6GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
18.799.5GSM184635Arabidopsis, root cells, 140 mM NaCl, replicate 2GSE7636Expression analysis of the effect of protoplasting and FACS sorting in rootsLink to GEO
18.199.5GSM184916Arabidopsis, root cells, endodermis and quiescent center, 140 mM NaCl, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
18.199.5GSM284393Arabidopsis GCE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
16.699.5GSM284389Arabidopsis GMPE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
14.699.4GSM184917Arabidopsis, root cells, endodermis and quiescent center, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
14.399.4GSM226550Slice8JWGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
14.399.4GSM184922Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
14.399.4GSM184900Arabidopsis, root cells, endodermis and quiescent center, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
13.499.4GSM265414Arabidopsis, root cells, -Fe, replicate 1GSE10496Expression analysis of the effect of protoplasting and FACS sorting in roots exposed to iron deficiency (-Fe)Link to GEO
12.899.3GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
12.099.3GSM226548Slice6JWGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
10.999.2GSM133759Lindsey_1-9_heart-stage-cotyledon_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
10.799.2E-ATMX-31-raw-cel-1516947916
10.099.2GSM311291Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 1GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
9.899.1GSM265415Arabidopsis, root cells, -Fe, replicate 2GSE10496Expression analysis of the effect of protoplasting and FACS sorting in roots exposed to iron deficiency (-Fe)Link to GEO
9.699.1GSM284392Arabidopsis GCE1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
8.999.0E-ATMX-31-raw-cel-1516947882
8.899.0GSM265416Arabidopsis, root cells, -Fe, replicate 3GSE10496Expression analysis of the effect of protoplasting and FACS sorting in roots exposed to iron deficiency (-Fe)Link to GEO
8.699.0GSM184908Arabidopsis, root cells, epidermis and lateral root cap, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1541GO:0007047A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.Link to AmiGO
0.1541GO:0009696The chemical reactions and pathways involving of salicylic acid (2-hydroxybenzoic acid), a derivative of benzoic acid.Link to AmiGO
0.1001GO: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

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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