CoP: Co-expressed Biological Processes

Gene omics information

Query gene ID At5g48100

Gene name TT10 (TRANSPARENT TESTA 10)

Organism Arabidopsis thaliana

Co-expressed genes

As this page just shows up to 10 genes to the query, if you wish to have the complete list of co-expressed genes, click Gene/Probe ID.

VF %ile Gene/Probe ID Repr.ID Gene Name Functional Description S.X. H.G. Other DB
0.34 39.8 At5g48100 834862 TT10 (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. S.X. H.G.
0.71 84.2 At2g23550 816887 MES6 (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. S.X. H.G.
0.67 81.6 At1g23200 838928 pectinesterase family protein F:enzyme inhibitor activity, pectinesterase activity;P:cell wall modification;C:endomembrane system, cell wall, plant-type cell wall;PBFAOM S.X. H.G.
0.67 81.6 At4g11180 826720 disease resistance-responsive family protein / dirigent family protein F:molecular_function unknown;P:lignan biosynthetic process, defense response;C:endomembrane system;P S.X. H.G.
0.67 81.6 At5g50750 835147 RGP4 (REVERSIBLY GLYCOSYLATED POLYPEPTIDE 4) reversibly glycosylated polypeptide RGP-4 (RGP4) S.X. H.G.
0.67 81.6 At5g59845 836106 gibberellin-regulated family protein F:molecular_function unknown;P:response to gibberellin stimulus;C:endomembrane system;P S.X. H.G.
0.64 78.9 At1g20500 838638 4-coumarate-CoA ligase F:4-coumarate-CoA ligase activity;P:phenylpropanoid metabolic process, metabolic process;C:unknown;BOMFPAV S.X. H.G.
0.63 78.1 At2g23580 816890 MES4 (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. S.X. H.G.
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Specifically expressed experiments

As this page just shows up to 10 assays to the query, if you wish to have the complete list of assays that the query gene/probe was specifically expressed, click here.
Std2 GX %ile GSM ID Assay Name GSE ID Experiment Title
624.8 100.0 GSM311296 Laser capture microdissected (LCM) general seed coat at the linear-cotyledon stage, biological replicate 2 GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
424.3 100.0 GSM311295 Laser capture microdissected (LCM) general seed coat at the linear-cotyledon stage, biological replicate 1 GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
274.6 100.0 GSM311294 Laser capture microdissected (LCM) chalazal seed coat at the linear-cotyledon stage, biological replicate 2 GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
218.7 100.0 GSM10451 WT Mature Green Seed 1 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle
155.1 99.9 GSM10480 lec1-1 Cotyledon Stage Seed 2 GSE1051 Seed development in LEAFY COTYLEDON1 mutants
154.0 99.9 GSM10453 WT Mature Green Seed 2 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle
144.6 99.9 GSM131695 ATGE_79_B GSE5634 AtGenExpress: Developmental series (siliques and seeds)
144.1 99.9 GSM10448 WT Cotyledon Stage Seed 1 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle
141.3 99.9 GSM131696 ATGE_79_C GSE5634 AtGenExpress: Developmental series (siliques and seeds)
136.9 99.9 E-ATMX-1-raw-cel-1112746209
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Homologous genes

Paralogous genes

Click Gene ID to show a list of homologous genes.

HF Ev BS Gene ID Repr. ID Gene Name Functional description C.G. S.X. Other DB
0.03 4e-12 73 At2g38080 818386 IRX12 (IRREGULAR XYLEM 12) Encodes a protein with similarity to putative laccase, a member of laccase family (17 members in Arabidopsis). Might be involved in cell wall biosynthesis. Mutants have a mild irregular xylem phenotype. C.G. S.X.
0.07 2e-8 61 At5g05390 830421 LAC12 (laccase 12) putative laccase, a member of laccase family of genes (17 members in Arabidopsis). C.G. S.X.
0.02 2e-7 57 At5g03260 831887 LAC11 (laccase 11) putative laccase, a member of laccase family of genes (17 members in Arabidopsis). C.G. S.X.
0.02 9e-4 46 At5g09360 830795 LAC14 (laccase 14) putative laccase, a member of laccase family of genes (17 members in Arabidopsis). C.G. S.X.
0.01 9e-4 46 At5g60020 836124 LAC17 (laccase 17) putative laccase, a member of laccase family of genes (17 members in Arabidopsis). C.G. S.X.
0.02 9e-4 46 At5g58910 836008 LAC16 (laccase 16) putative laccase, a member of laccase family of genes (17 members in Arabidopsis). C.G. S.X.
0.02 1e-2 42 At5g01190 831697 LAC10 (laccase 10) putative laccase, a member of laccase family of genes (17 members in Arabidopsis). C.G. S.X.
0.01 5e-2 40 At2g40370 818630 LAC5 (laccase 5) putative laccase, a member of laccase family of genes (17 members in Arabidopsis). C.G. S.X.
0.01 2e-1 38 At3g09220 820078 LAC7 (laccase 7) putative laccase, a member of laccase family of genes (17 members in Arabidopsis). C.G. S.X.
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Orthologous genes

Click Gene ID to show a list of orthologous genes.

HF Ev BS Species Gene ID Repr. ID Gene Name Functional description Ev AGI code Arabidopsis gene name C.G. S.X. Other DB
0.05 1e-6 56 Glycine max GmaAffx.51444.2.S1_at BQ612052 - - 2e-35 At5g60020 LAC17 (laccase 17) C.G. S.X.
0.02 2e+0 34 Hordeum vulgare Contig18447_at Contig18447 - - 2e-1 At4g29670 thioredoxin family protein C.G. S.X.
0.02 7e-3 44 Oryza sativa Os12g0258700 BI813311 - Multicopper oxidase, type 1 domain containingprotein 1e-3 At5g05390 LAC12 (laccase 12) C.G. S.X.
0.07 5e-6 54 Populus trichocarpa PtpAffx.224482.1.S1_at pmrna43061 hypothetical protein - 4e-6 At5g48100 TT10 (TRANSPARENT TESTA 10) C.G. S.X.
0.02 9e-1 36 Triticum aestivum Ta.4455.1.A1_at BJ253690 - - 7e-6 At5g58910 LAC16 (laccase 16) C.G. S.X.
0.04 3e-7 56 Vitis vinifera 1607667_at CF212686 hypothetical protein LOC100240808 - 3e-32 At5g01190 LAC10 (laccase 10) C.G. S.X.
0.01 1e+0 34 Zea mays Zm.16750.1.A1_at CA401312 hypothetical protein LOC100191935 - 5e-1 At1g04445 zinc finger (C2H2 type) family protein C.G. S.X.
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Biological processes

Click GO ID to show a list of genes that are associated with the GO ID.

ECC GO ID Process Name
X GO:0046688 A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a copper ion stimulus.
X GO:0009809 The chemical reactions and pathways resulting in the formation of lignins, a class of polymers formed by the dehydrogenetive radical polymerization of various phenylpropanoid monomers.
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Metabolic pathways

Click KaPPA-View ID to show a list of genes that are assigned to the KaPPA-View ID.

KaPPA-View ID Link to Kappa-View Pathway Name

Click KEGG PATHWAY ID to show a list of genes that are assigned to the KEGG PATHWAY ID.

KEGG PATHWAY ID Link to KEGG PATHWAY Pathway Name
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