CoP: Co-expressed Biological Processes

Gene omics information

Query gene ID At2g38080

Gene name IRX12 (IRREGULAR XYLEM 12)

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
1.00 100.0 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. S.X. H.G.
0.97 97.6 At5g54690 835558 GAUT12 (GALACTURONOSYLTRANSFERASE 12) Encodes a protein with putative galacturonosyltransferase activity. Mutants defective in this gene displayed a notable reduction in xylose (>50%) in the cell walls from stems and roots and a reduction in cellulose (~25%). S.X. H.G.
0.95 97.0 At5g15630 831417 IRX6 Encodes a member of the COBRA family, similar to phytochelatin synthetase. Involved in secondary cell wall biosynthesis. Mutants make smaller plants with reduced levels of cellulose and cell wall sugars. S.X. H.G.
0.95 97.0 At5g44030 834426 CESA4 (CELLULOSE SYNTHASE A4) Encodes a cellulose synthase involved in secondary cell wall biosynthesis. Confers resistance towards bacterial and fungal pathogens, independent of salicylic acid, ethylene and jasmonate signaling. S.X. H.G.
0.95 97.0 At5g67210 836856 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POB S.X. H.G.
0.93 96.4 At3g18660 821397 PGSIP1 (PLANT GLYCOGENIN-LIKE STARCH INITIATION PROTEIN 1) Plants expressing an RNAi construct specifically targeting PGSIP1 was shown to have a dramatically reduced amount of starch. S.X. H.G.
0.91 95.6 At3g16920 820947 chitinase F:chitinase activity;P:cell wall macromolecule catabolic process;C:unknown;PBMOF S.X. H.G.
0.91 95.6 At4g27435 828852 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P S.X. H.G.
0.91 95.6 At4g28500 828968 ANAC073 (ARABIDOPSIS NAC DOMAIN CONTAINING PROTEIN 73) F:transcription factor activity, transcription activator activity;P:multicellular organismal development, regulation of secondary cell wall thickening;C:nucleus;PO S.X. H.G.
0.90 95.1 At5g17420 831608 IRX3 (IRREGULAR XYLEM 3) Encodes a xylem-specific cellulose synthase that is phosphorylated on one or more serine residues (on either S185 or one of S180 or S181). 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
246.9 100.0 GSM133962 Fukuda_1-7_6A_Rep1_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
204.1 100.0 GSM131656 ATGE_27_B GSE5633 AtGenExpress: Developmental series (shoots and stems)
195.2 100.0 GSM131655 ATGE_27_A GSE5633 AtGenExpress: Developmental series (shoots and stems)
184.8 100.0 E-MEXP-265-raw-cel-414618491
183.3 100.0 GSM131657 ATGE_27_C GSE5633 AtGenExpress: Developmental series (shoots and stems)
167.0 100.0 GSM133754 Turner_A-8-Turne-WT-Base2_SLD GSE5729 Role of COV in vascular patterning
161.4 99.9 E-MEXP-265-raw-cel-414618796
160.2 99.9 E-MEXP-265-raw-cel-414618585
157.4 99.9 E-MEXP-265-raw-cel-414618693
155.5 99.9 E-MEXP-265-raw-cel-414618394
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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
0.27 7e-23 109 At5g01190 831697 LAC10 (laccase 10) putative laccase, a member of laccase family of genes (17 members in Arabidopsis). C.G. S.X.
0.17 1e-18 95 At5g58910 836008 LAC16 (laccase 16) putative laccase, a member of laccase family of genes (17 members in Arabidopsis). C.G. S.X.
0.11 1e-12 75 At5g03260 831887 LAC11 (laccase 11) putative laccase, a member of laccase family of genes (17 members in Arabidopsis). C.G. S.X.
0.03 4e-12 73 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. C.G. S.X.
0.08 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.
0.05 6e-5 50 At2g30210 817571 LAC3 (laccase 3) putative laccase, a member of laccase family of genes (17 members in Arabidopsis). C.G. S.X.
0.09 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.
0.04 1e-2 42 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 At3g26240 822226 DC1 domain-containing protein F:unknown;P:intracellular signaling cascade;C:cellular_component unknown;PMBOF 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
0.10 6e-15 83 Glycine max GmaAffx.51444.2.S1_at BQ612052 - - 2e-35 At5g60020 LAC17 (laccase 17) C.G. S.X.
0.03 1e-4 48 Hordeum vulgare Contig18447_at Contig18447 - - 2e-1 At4g29670 thioredoxin family protein C.G. S.X.
0.09 1e-4 50 Oryza sativa Os01g0842400 AK068901.1 - Laccase (EC 1.10.3.2) 7e-5 At2g38080 IRX12 (IRREGULAR XYLEM 12) C.G. S.X.
0.11 9e-17 89 Populus trichocarpa PtpAffx.164036.1.S1_at Y13769.1 - - 3e-22 At5g01190 LAC10 (laccase 10) C.G. S.X.
0.07 9e-1 36 Triticum aestivum Ta.4455.2.S1_x_at BJ255523 - - 3e-1 At2g38080 IRX12 (IRREGULAR XYLEM 12) C.G. S.X.
0.13 3e-25 115 Vitis vinifera 1607667_at CF212686 hypothetical protein LOC100240808 - 3e-32 At5g01190 LAC10 (laccase 10) C.G. S.X.
0.02 6e+0 32 Zea mays Zm.2785.1.A1_at CF004244 major Facilitator superfamily protein - 2e-11 At4g27720 - 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:0009834 The chemical reactions and pathways resulting in the formation of inextensible cellulose and pectin-containing cell walls that are formed between the plasma membrane and primary cell wall after cell expansion is complete. An example of this is found in Arabidopsis thaliana.
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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
00103 Catechol, protocatechuate, 1,4-Dichlorobenzeneand pentachlorophenol degradation pathway

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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