CoP: Co-expressed Biological Processes

Gene omics information

Query gene ID At3g25900

Gene name HMT-1

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 At3g25900 822186 HMT-1 F:homocysteine S-methyltransferase activity;P:methionine biosynthetic process;C:cellular_component unknown;BOMPFA S.X. H.G.
0.74 86.1 At2g46500 819260 phosphatidylinositol 3- and 4-kinase family protein / ubiquitin family protein F:inositol or phosphatidylinositol kinase activity, phosphotransferase activity, alcohol group as acceptor;P:protein modification process;C:cellular_component unknown;MPOFVB S.X. H.G.
0.73 85.5 At3g05990 819770 leucine-rich repeat family protein F:protein binding;P:signal transduction;C:endomembrane system;POBMFA S.X. H.G.
0.71 84.2 At3g48780 824039 SPT1 (SERINE PALMITOYLTRANSFERASE 1) Encodes one of the two LCB2 subunits (LCB2a and LCB2b) of serine palmitoyltransferase, an enzyme involved in sphingolipid biosynthesis. LCB2a and LCB2b are functional redundant. Double mutants are gametophytic lethal. S.X. H.G.
0.70 83.5 At1g67480 843069 kelch repeat-containing F-box family protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPBOVFA S.X. H.G.
0.69 82.9 At5g58380 835951 SIP1 (SOS3-INTERACTING PROTEIN 1) Encodes a CBL-interacting protein kinase with similarity to SOS protein kinase. S.X. H.G.
0.67 81.6 At4g22590 828355 trehalose-6-phosphate phosphatase, putative F:catalytic activity, trehalose-phosphatase activity;P:trehalose biosynthetic process, metabolic process;C:chloroplast;BPMOFA S.X. H.G.
0.67 81.6 At4g17790 827501 - F:unknown;P:biological_process unknown;C:unknown;BOMPFA S.X. H.G.
0.63 78.1 At4g20380 827786 zinc finger protein (LSD1) LSD1 monitors a superoxide-dependent signal and negatively regulates a plant cell death pathway. contains zinc-finger motifs. LSD1 negatively regulates a basal defense pathway that can act upstream or independently of both NIM1/NPR1 function and SA accumulation following avirulent or virulent pathogen challenge S.X. H.G.
0.61 76.7 At4g20870 827835 FAH2 (FATTY ACID HYDROXYLASE 2) encodes a fatty acid hydroxylase, required for the AtBI-1-mediated suppression of programmed cell death. 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
114.8 99.9 GSM142593 DB001_ATH1_A3-Brown-cal GSE6148 The trans-differentiation of cultured Arabidopsis cells
90.6 99.9 GSM184922 Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt
79.6 99.9 GSM142592 DB001_ATH1_A2-Brown-cal GSE6148 The trans-differentiation of cultured Arabidopsis cells
76.1 99.9 GSM239251 Columbia glabrous (C24) wild type pollen GSE9408 Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
69.9 99.9 GSM239253 CaMV::DME pollen GSE9408 Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
66.4 99.8 GSM142591 DB001_ATH1_A1-Brown-cal GSE6148 The trans-differentiation of cultured Arabidopsis cells
66.2 99.8 GSM266677 Arabidopsis, root cells, stele, -Fe, replicate 3 GSE10501 Expression analysis of root cell-types after iron deficiency (-Fe) treatment
64.0 99.8 GSM142594 DB001_ATH1_A4-Brown-cal GSE6148 The trans-differentiation of cultured Arabidopsis cells
61.3 99.8 GSM184921 Arabidopsis, root cells, stele, 140 mM NaCls, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
61.2 99.8 GSM142596 DB001_ATH1_A6-Brown-cal GSE6148 The trans-differentiation of cultured Arabidopsis cells
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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
0.04 8e-6 52 At3g63250 825500 HMT2 (HOMOCYSTEINE METHYLTRANSFERASE 2) Encodes a homocysteine methyltransferase (HMT). Among the three HMT coding genes in the genome, HMT2 is responsible for a significant proportion of HMT activity in the flower stalks and silique hulls. However, HMT2 does not significantly contribute to the total HMT activity in seeds. C.G. S.X.
0.01 3e-2 40 At5g42280 834233 DC1 domain-containing protein F:unknown;P:unknown;C:unknown;POM C.G. S.X.
0.01 1e-1 38 At2g28100 817355 ATFUC1 (alpha-L-fucosidase 1) Encodes a protein with α-fucosidase activity. The activity was assessed on 2'-fucosyl-lactitol. AtFUC1 was not able to act on XXFG substrates, at least when heterologously expressed in Pichia pastoris. The enzyme has been postulated to act on fucosylated substrates other than xyloglucan oligosaccharides. was shown (Pichia pastoris) to hydrolyze fucose in 3- and 4-linkage , hence was characterized as alpha-L-3,4-fucosidase C.G. S.X.
0.01 2e+0 34 At5g26250 832694 sugar transporter, putative F:carbohydrate transmembrane transporter activity, sugar:hydrogen symporter activity;P:transport, transmembrane transport;C:endomembrane system, integral to membrane, membrane;BFMPOA C.G. S.X.
0.01 2e+0 34 At5g11330 831004 monooxygenase family protein F:oxidoreductase activity, monooxygenase activity;P:metabolic process;C:endomembrane system;BFOPMA C.G. S.X.
0.02 2e+0 34 At3g55250 824691 unknown protein F:molecular_function unknown;P:biological_process unknown;C:mitochondrion, chloroplast, nucleus;P 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
0.27 2e-7 57 Glycine max GmaAffx.8081.1.S1_at BE657255 - - 6e-8 At3g25900 HMT-1 C.G. S.X.
0.02 9e-1 34 Hordeum vulgare Contig12465_at Contig12465 - - 3e-2 At3g63250 HMT2 (HOMOCYSTEINE METHYLTRANSFERASE 2) C.G. S.X.
0.08 2e-8 61 Oryza sativa Os12g0607000 AK065892.1 - Homocysteine S-methyltransferase 2 (EC 2.1.1.10)(S- methylmethionine:homocysteine methyltransferase 2)(SMM:Hcy S- methyltransferase 2) (ZmHMT-2) 5e-5 At3g22740 HMT3 C.G. S.X.
0.29 2e-32 141 Populus trichocarpa PtpAffx.17806.1.S1_at CV272450 homocysteine s-methyltransferase - 1e-32 At3g25900 HMT-1 C.G. S.X.
0.08 3e-8 59 Triticum aestivum Ta.6561.1.S1_at CD905008 - - 8e-1 At3g63250 HMT2 (HOMOCYSTEINE METHYLTRANSFERASE 2) C.G. S.X.
0.20 3e-15 81 Vitis vinifera 1622196_at CF511416 hypothetical protein LOC100247323 - 6e-15 At3g25900 HMT-1 C.G. S.X.
0.11 6e-8 57 Zea mays Zm.13424.1.A1_at AF297044.1 homocysteine S-methyltransferase-1 - 2e-7 At3g25900 HMT-1 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:0009086 The chemical reactions and pathways resulting in the formation of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
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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
00270 Cysteine and methionine metabolism
01100 Metabolic pathways
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