AtMetExpress overview (Arabidopsis thaliana)

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1, 3XyloseGlycerol 2-phosphatePhosphoenolpyruvic acid3-Phosphoglyceric acidGlucoseFructoseNicotianamineGlyceric acidFlavonoid biosynthesisGlutamic acidFructose-6-phosphateOxaloacetic acidPyruvic acidFatty acid synthesisAcetyl-CoASucroseGlucose-6-phosphateGlycerol 3-phosphateCampesterolFructose 1,6-bisphosphateThreoninePhytolAlanineLeucineRaffinoseGlycineLactic acidDehydroascorbic acidAscorbic acidHomocysteineMyo-inositol 1-phosphateGABABeta-SitosterolCysteineGalactinolRhamnoseDihydrouracilIsorhamnetinMyoinositolNicotinic acidThreonic acidMaltoseHomoserineMannoseCystineSuccinyl-CoASerineGalacturonic acidArabinoseRiboseTrehaloseLysineAspartic acidBeta-AlanineValineUracilIsoleucineAsparagineCitric acidIsocitric acidcis-Aconitic acid2-Oxo-glutaric acidSuccinic acidFumaric acidMalic acidMethionineS-AdenosylmethionineArginineGlutamineHistidineProlineOrnithineHydroxylaminePutrescineSpermidineEthanolamineF12Shikimic acidQuinic acidPhenylalanineF2TryptophanTyrosineF5F6F3F4TryptamineIndoleGSLTriethanolamineBenzoic acidCaffeic acidAlpha-TocopherolTyramineA1A22A5A6A3A4A7A8A11A9A10F7F8F14F15F19F25F23F20F24F27F28F29F30F32QuercetinKaempferolCyanidinGluconic acidGlutathioneglycerate 3-phosphateC14:0C16:0C18:0C18:2C18:3C24:0CholesterolStigmasterolGlutaric acidSalicylic acid3-MTP3-MSOP4-MSOB4-MTB5-MTP5-MSOP6-MTH6-MSOH7-MTH7-MSOH8-MTO8-MSOOPADAGMGDGDGDGSQDGPCPEPGPIlysoPCTAGTCA cycleLong chain organic acidsSugar metabolismGlycolysisAromatic amino acid metabolismAmino acid metabolismGlucosinolate biosynthesis


Description

Since early 2000, a number of metabolome analyses have been demonstrated using combined hyphenated chromatographic and mass spectral methods as well as nuclear-magnetic-resonance. Although metabolite profiling experiments are becoming routine in many research groups, making the studies remains expensive and laborious. While the metabolomics community is working towards the setup of sharing metabolome data, mining publicly available information and demonstrating the richness of integration of multiple metabolome datasets remain largely unexploited. The aims of this project are (1) to establish a new web-based platform for metabolome meta-analysis and (2) to use these sets of combined metabolite levels to explore the diversity of complex metabolic networks in the model plant, Arabidopsis thaliana. We constructed our database, called AtMetExpress (http://prime.psc.riken.jp/AtMetExpress/), to store the metabolome information.

Quality Tags

Ontology Terms

 

Bibliography

  1. Sumner LW, Lei Z, Nikolau BJ, Saito K; ''Modern plant metabolomics: advanced natural product gene discoveries, improved technologies, and future prospects.''; Nat Prod Rep, 2015 PubMed Europe PMC
  2. Saito K, Yonekura-Sakakibara K, Nakabayashi R, Higashi Y, Yamazaki M, Tohge T, Fernie AR; ''The flavonoid biosynthetic pathway in Arabidopsis: structural and genetic diversity.''; Plant Physiol Biochem, 2013 PubMed Europe PMC
  3. Fukushima A, Kusano M; ''Recent progress in the development of metabolome databases for plant systems biology.''; Front Plant Sci, 2013 PubMed Europe PMC

History

View all...
CompareRevisionActionTimeUserComment
105906view11:40, 16 August 2019MkutmonHMDB identifier normalization
105229view08:04, 23 July 2019EgonwReplaced a (no longer) existing HMDB identifier.
102131view07:19, 2 December 2018EgonwFixed the data source, was KNApSAcK not KEGG, for five compounds.
89229view07:57, 24 August 2016Afukushimaadded KNApSAcK-IDs for isorhamnetin derivatives
89228view07:54, 24 August 2016Afukushimaadded KNApSAcK-IDs for quercetin derivatives
89227view07:50, 24 August 2016Afukushimaadded KNApSAcK-IDs for kaempferol derivatives
89226view07:43, 24 August 2016Afukushimaadded KNApSAcK-IDs for anthocyanins
89135view21:51, 22 August 2016AriuttaOntology Term : 'classic metabolic pathway' added !
84720view07:29, 16 March 2016AfukushimaSpecify description
84719view07:23, 16 March 2016AfukushimaModified description
84718view07:16, 16 March 2016Afukushimaadded literature
84717view07:08, 16 March 2016AfukushimaReverted to version '05:06, 16 March 2016' by Afukushima
84716view05:09, 16 March 2016AfukushimaReverted to version '03:42, 15 March 2016' by Afukushima
84715view05:06, 16 March 2016Afukushimaadded litt of F1
84714view05:04, 16 March 2016Afukushimaadded literature of A1
84675view03:42, 15 March 2016AfukushimaNew pathway

External references

DataNodes

View all...
NameTypeDatabase referenceComment
2-Oxo-glutaric acidMetaboliteHMDB0000208 (HMDB)
3-MSOPMetaboliteC08405 (KEGG Compound)
3-MTPMetaboliteC08412 (KEGG Compound)
3-Phosphoglyceric acidMetaboliteHMDB0000807 (HMDB)
4-MSOBMetaboliteC08410 (KEGG Compound)
4-MTBMetaboliteC08409 (KEGG Compound)
5-MSOPMetaboliteC08400 (KEGG Compound)
5-MTPMetaboliteC08401 (KEGG Compound)
6-MSOHMetaboliteC00007348 (KNApSAcK)
6-MTHMetaboliteC00007844 (KNApSAcK)
7-MSOHMetaboliteC00007352 (KNApSAcK)
7-MTHMetaboliteC00007353 (KNApSAcK)
8-MSOOMetaboliteC00007355 (KNApSAcK)
8-MTOMetaboliteC00007356 (KNApSAcK)
A10MetaboliteC00007661 (KNApSAcK)
A11MetaboliteC00007570 (KNApSAcK)
A1MetaboliteC20493 (KEGG Compound)
  • Cyanidin 3-sambubioside-5-glucoside
  • Type your comment here
A2MetaboliteC00007655 (KNApSAcK)
A3MetaboliteC00006836 (KNApSAcK)
A4MetaboliteC00007656 (KNApSAcK)
A5MetaboliteC00007657 (KNApSAcK)
A6MetaboliteC00007658 (KNApSAcK)
A7MetaboliteC00007660 (KNApSAcK)
A8MetaboliteC00007659 (KNApSAcK)
A9MetaboliteC00006838 (KNApSAcK)
Acetyl-CoAMetaboliteHMDB0001206 (HMDB)
AlanineMetaboliteHMDB0000161 (HMDB)
Alpha-TocopherolMetaboliteHMDB0001893 (HMDB)
Amino acid metabolismPathway
ArabinoseMetaboliteHMDB0029942 (HMDB)
ArginineMetaboliteHMDB0000517 (HMDB)
Aromatic amino acid metabolismPathway
Ascorbic acidMetaboliteHMDB0000044 (HMDB)
AsparagineMetaboliteHMDB0000168 (HMDB)
Aspartic acidMetaboliteHMDB0000191 (HMDB)
Benzoic acidMetaboliteHMDB0001870 (HMDB)
Beta-AlanineMetaboliteHMDB0000056 (HMDB)
Beta-SitosterolMetaboliteHMDB0000852 (HMDB)
C14:0MetaboliteHMDB0000806 (HMDB)
C16:0MetaboliteHMDB0000220 (HMDB)
C18:0MetaboliteHMDB0000827 (HMDB)
C18:2MetaboliteHMDB0000673 (HMDB)
C18:3MetaboliteHMDB0001388 (HMDB)
C24:0MetaboliteHMDB0002003 (HMDB)
Caffeic acidMetaboliteHMDB0001964 (HMDB)
CampesterolMetaboliteHMDB0002869 (HMDB)
CholesterolMetaboliteHMDB0000067 (HMDB)
Citric acidMetaboliteHMDB0000094 (HMDB)
CyanidinMetaboliteCHEBI:27843 (ChEBI)
CysteineMetaboliteHMDB0000574 (HMDB)
CystineMetaboliteHMDB0000192 (HMDB)
DAGMetaboliteC00165 (KEGG Compound)
DGDGMetabolite28495919 (Chemspider)
Dehydroascorbic acidMetaboliteHMDB0001264 (HMDB)
DihydrouracilMetaboliteHMDB0000076 (HMDB)
EthanolamineMetaboliteHMDB0000149 (HMDB)
F14MetaboliteC00005557 (KNApSAcK)
F15MetaboliteC00005558 (KNApSAcK)
F19MetaboliteC00005174 (KNApSAcK)
F1MetaboliteC16981 (KEGG Compound)
F20MetaboliteC00005188 (KNApSAcK)
F23MetaboliteC00005368 (KNApSAcK)
F24MetaboliteC01750 (KEGG Compound)
F25Metabolite
  • FL5FACGS0030
  • Type your comment here
F27MetaboliteC00005526 (KNApSAcK)
F28MetaboliteC00005525 (KNApSAcK)
F29MetaboliteC00005551 (KNApSAcK)
F2MetaboliteC00005184 (KNApSAcK)
F30MetaboliteC00005559 (KNApSAcK)
F32Metabolite
  • Isorhamnetin 3-neohesperidoside-7-rhamnoside
  • Type your comment here
F3MetaboliteC00005237 (KNApSAcK)
F4MetaboliteC00005234 (KNApSAcK)
F5MetaboliteC00005432 (KNApSAcK)
F6MetaboliteC00005428 (KNApSAcK)
F7MetaboliteC19796 (KEGG Compound)
F8MetaboliteC00005470 (KNApSAcK)
Fatty acid synthesisPathway
Flavonoid biosynthesisPathway
Fructose 1,6-bisphosphateMetaboliteHMDB0001058 (HMDB)
Fructose-6-phosphateMetaboliteHMDB0000124 (HMDB)
FructoseMetaboliteHMDB0000660 (HMDB)
Fumaric acidMetaboliteHMDB0000134 (HMDB)
GABAMetaboliteHMDB0000112 (HMDB)
GalactinolMetaboliteHMDB0005826 (HMDB)
Galacturonic acidMetaboliteHMDB0002545 (HMDB)
Gluconic acidMetaboliteHMDB0000625 (HMDB)
Glucose-6-phosphateMetaboliteHMDB0001401 (HMDB)
GlucoseMetaboliteHMDB0000122 (HMDB)
Glucosinolate biosynthesisPathway
Glutamic acidMetaboliteHMDB0000148 (HMDB)
GlutamineMetaboliteHMDB0000641 (HMDB)
Glutaric acidMetaboliteHMDB0000661 (HMDB)
GlutathioneMetaboliteHMDB0000125 (HMDB)
Glyceric acidMetaboliteHMDB0000139 (HMDB)
Glycerol 2-phosphateMetaboliteC02979 (KEGG Compound)
Glycerol 3-phosphateMetaboliteHMDB0000126 (HMDB)
GlycineMetaboliteHMDB0000123 (HMDB)
GlycolysisPathway
HistidineMetaboliteHMDB0000177 (HMDB)
HomocysteineMetaboliteHMDB0000742 (HMDB)
HomoserineMetaboliteHMDB0000719 (HMDB)
HydroxylamineMetaboliteHMDB0003338 (HMDB)
IndoleGSLMetabolite
Isocitric acidMetaboliteHMDB0000193 (HMDB)
IsoleucineMetaboliteHMDB0000172 (HMDB)
IsorhamnetinMetaboliteHMDB0002655 (HMDB)
KaempferolMetaboliteHMDB0005801 (HMDB)
Lactic acidMetaboliteHMDB0000190 (HMDB)
LeucineMetaboliteHMDB0000687 (HMDB)
Long chain organic acidsPathway
LysineMetaboliteHMDB0000182 (HMDB)
MGDGMetabolite4696840 (Chemspider)
Malic acidMetaboliteHMDB0000744 (HMDB)
MaltoseMetaboliteHMDB0000163 (HMDB)
MannoseMetaboliteHMDB0000169 (HMDB)
MethionineMetaboliteHMDB0000696 (HMDB)
Myo-inositol 1-phosphateMetaboliteHMDB0000213 (HMDB)
MyoinositolMetaboliteHMDB0000211 (HMDB)
NicotianamineMetaboliteC05324 (KEGG Compound)
Nicotinic acidMetaboliteHMDB0001488 (HMDB)
OrnithineMetaboliteHMDB0000214 (HMDB)
Oxaloacetic acidMetaboliteHMDB0000223 (HMDB)
PAMetaboliteC00416 (KEGG Compound)
PCMetabolite4946694 (Chemspider)
PEMetabolite7825685 (Chemspider)
PGMetabolite8593139 (Chemspider)
PIMetabolite20058759 (Chemspider)
PhenylalanineMetaboliteHMDB0000159 (HMDB)
Phosphoenolpyruvic acidMetaboliteHMDB0000263 (HMDB)
PhytolMetaboliteHMDB0002019 (HMDB)
ProlineMetaboliteHMDB0000162 (HMDB)
PutrescineMetaboliteHMDB0001414 (HMDB)
Pyruvic acidMetaboliteHMDB0000243 (HMDB)
QuercetinMetaboliteHMDB0005794 (HMDB)
Quinic acidMetaboliteHMDB0003072 (HMDB)
RaffinoseMetaboliteHMDB0003213 (HMDB)
RhamnoseMetaboliteHMDB0000849 (HMDB)
RiboseMetaboliteHMDB0000283 (HMDB)
S-AdenosylmethionineMetaboliteHMDB0001185 (HMDB)
SQDGMetabolite140119 (Chemspider)
Salicylic acidMetaboliteHMDB0001895 (HMDB)
SerineMetaboliteHMDB0000187 (HMDB)
Shikimic acidMetaboliteHMDB0003070 (HMDB)
SpermidineMetaboliteHMDB0001257 (HMDB)
StigmasterolMetaboliteHMDB0000937 (HMDB)
Succinic acidMetaboliteHMDB0000254 (HMDB)
Succinyl-CoAMetaboliteHMDB0001022 (HMDB)
SucroseMetaboliteC00089 (KEGG Compound)
Sugar metabolismPathway
TAGMetabolite4575640 (Chemspider)
TCA cyclePathway
Threonic acidMetaboliteHMDB0000943 (HMDB)
ThreonineMetaboliteHMDB0000167 (HMDB)
TrehaloseMetaboliteHMDB0000975 (HMDB)
TriethanolamineMetaboliteHMDB0032538 (HMDB)
TryptamineMetaboliteHMDB0000303 (HMDB)
TryptophanMetaboliteHMDB0000929 (HMDB)
TyramineMetaboliteHMDB0000306 (HMDB)
TyrosineMetaboliteHMDB0000158 (HMDB)
UracilMetaboliteHMDB0000300 (HMDB)
ValineMetaboliteHMDB0000883 (HMDB)
XyloseMetaboliteHMDB0000098 (HMDB)
cis-Aconitic acidMetaboliteHMDB0000072 (HMDB)
glycerate 3-phosphateMetaboliteHMDB0000807 (HMDB)
lysoPCMetabolite24766528 (Chemspider)

Annotated Interactions

No annotated interactions

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