AtMetExpress overview (WP3622)
Arabidopsis thaliana
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.
Authors
Atsushi Fukushima , Anders Riutta , Egon Willighagen , Martina Summer-Kutmon , and Eric WeitzActivity
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Organisms
Arabidopsis thalianaCommunities
Annotations
Pathway Ontology
fatty acid biosynthetic pathway citric acid cycle pathway glycolysis pathway flavonoid biosynthetic pathway classic metabolic pathway amino acid metabolic pathway| Label | Type | Compact URI | Comment |
|---|---|---|---|
| Lactic acid | Metabolite | hmdb:HMDB0000190 | |
| Glycerol 3-phosphate | Metabolite | hmdb:HMDB0000126 | |
| GABA | Metabolite | hmdb:HMDB0000112 | |
| Cystine | Metabolite | hmdb:HMDB0000192 | |
| Dihydrouracil | Metabolite | hmdb:HMDB0000076 | |
| Pyruvic acid | Metabolite | hmdb:HMDB0000243 | |
| Leucine | Metabolite | hmdb:HMDB0000687 | |
| Galactinol | Metabolite | hmdb:HMDB0005826 | |
| Glucose | Metabolite | hmdb:HMDB0000122 | |
| Xylose | Metabolite | hmdb:HMDB0000098 | |
| Threonine | Metabolite | hmdb:HMDB0000167 | |
| Glutamic acid | Metabolite | hmdb:HMDB0000148 | |
| Nicotinic acid | Metabolite | hmdb:HMDB0001488 | |
| Threonic acid | Metabolite | hmdb:HMDB0000943 | |
| Mannose | Metabolite | hmdb:HMDB0000169 | |
| Fructose 1,6-bisphosphate | Metabolite | hmdb:HMDB0001058 | |
| Glyceric acid | Metabolite | hmdb:HMDB0000139 | |
| Serine | Metabolite | hmdb:HMDB0000187 | |
| Glucose-6-phosphate | Metabolite | hmdb:HMDB0001401 | |
| Myo-inositol 1-phosphate | Metabolite | hmdb:HMDB0000213 | |
| Campesterol | Metabolite | hmdb:HMDB0002869 | |
| Sucrose | Metabolite | kegg.compound:C00089 | |
| Ascorbic acid | Metabolite | hmdb:HMDB0000044 | |
| Homocysteine | Metabolite | hmdb:HMDB0000742 | |
| Glycine | Metabolite | hmdb:HMDB0000123 | |
| Glycerol 2-phosphate | Metabolite | kegg.compound:C02979 | |
| Fructose | Metabolite | hmdb:HMDB0000660 | |
| Homoserine | Metabolite | hmdb:HMDB0000719 | |
| Phytol | Metabolite | hmdb:HMDB0002019 | |
| Cysteine | Metabolite | hmdb:HMDB0000574 | |
| 3-Phosphoglyceric acid | Metabolite | hmdb:HMDB0000807 | |
| Beta-Sitosterol | Metabolite | hmdb:HMDB0000852 | |
| Alanine | Metabolite | hmdb:HMDB0000161 | |
| Rhamnose | Metabolite | hmdb:HMDB0000849 | |
| Maltose | Metabolite | hmdb:HMDB0000163 | |
| Phosphoenolpyruvic acid | Metabolite | hmdb:HMDB0000263 | |
| Succinyl-CoA | Metabolite | hmdb:HMDB0001022 | |
| Isorhamnetin | Metabolite | hmdb:HMDB0002655 | |
| Acetyl-CoA | Metabolite | hmdb:HMDB0001206 | |
| Dehydroascorbic acid | Metabolite | hmdb:HMDB0001264 | |
| Oxaloacetic acid | Metabolite | hmdb:HMDB0000223 | |
| Myoinositol | Metabolite | hmdb:HMDB0000211 | |
| Fructose-6-phosphate | Metabolite | hmdb:HMDB0000124 | |
| Raffinose | Metabolite | hmdb:HMDB0003213 | |
| Nicotianamine | Metabolite | kegg.compound:C05324 | |
| Galacturonic acid | Metabolite | hmdb:HMDB0002545 | |
| Arabinose | Metabolite | hmdb:HMDB0029942 | |
| Ribose | Metabolite | hmdb:HMDB0000283 | |
| Trehalose | Metabolite | hmdb:HMDB0000975 | |
| Lysine | Metabolite | hmdb:HMDB0000182 | |
| Aspartic acid | Metabolite | hmdb:HMDB0000191 | |
| Beta-Alanine | Metabolite | hmdb:HMDB0000056 | |
| Valine | Metabolite | hmdb:HMDB0000883 | |
| Uracil | Metabolite | hmdb:HMDB0000300 | |
| Isoleucine | Metabolite | hmdb:HMDB0000172 | |
| Asparagine | Metabolite | hmdb:HMDB0000168 | |
| Citric acid | Metabolite | hmdb:HMDB0000094 | |
| Isocitric acid | Metabolite | hmdb:HMDB0000193 | |
| cis-Aconitic acid | Metabolite | hmdb:HMDB0000072 | |
| 2-Oxo-glutaric acid | Metabolite | hmdb:HMDB0000208 | |
| Succinic acid | Metabolite | hmdb:HMDB0000254 | |
| Fumaric acid | Metabolite | hmdb:HMDB0000134 | |
| Malic acid | Metabolite | hmdb:HMDB0000744 | |
| Methionine | Metabolite | hmdb:HMDB0000696 | |
| S-Adenosylmethionine | Metabolite | hmdb:HMDB0001185 | |
| Arginine | Metabolite | hmdb:HMDB0000517 | |
| Glutamine | Metabolite | hmdb:HMDB0000641 | |
| Histidine | Metabolite | hmdb:HMDB0000177 | |
| Proline | Metabolite | hmdb:HMDB0000162 | |
| Ornithine | Metabolite | hmdb:HMDB0000214 | |
| Hydroxylamine | Metabolite | hmdb:HMDB0003338 | |
| Putrescine | Metabolite | hmdb:HMDB0001414 | |
| Spermidine | Metabolite | hmdb:HMDB0001257 | |
| Ethanolamine | Metabolite | hmdb:HMDB0000149 | |
| F1 | Metabolite | kegg.compound:C16981 | |
| Shikimic acid | Metabolite | hmdb:HMDB0003070 | |
| Quinic acid | Metabolite | hmdb:HMDB0003072 | |
| Phenylalanine | Metabolite | hmdb:HMDB0000159 | |
| F2 | Metabolite | knapsack:C00005184 | |
| Tryptophan | Metabolite | hmdb:HMDB0000929 | |
| Tyrosine | Metabolite | hmdb:HMDB0000158 | |
| F5 | Metabolite | knapsack:C00005432 | |
| F6 | Metabolite | knapsack:C00005428 | |
| F3 | Metabolite | knapsack:C00005237 | |
| F4 | Metabolite | knapsack:C00005234 | |
| Tryptamine | Metabolite | hmdb:HMDB0000303 | |
| Triethanolamine | Metabolite | hmdb:HMDB0032538 | |
| Benzoic acid | Metabolite | hmdb:HMDB0001870 | |
| Caffeic acid | Metabolite | hmdb:HMDB0001964 | |
| Alpha-Tocopherol | Metabolite | hmdb:HMDB0001893 | |
| Tyramine | Metabolite | hmdb:HMDB0000306 | |
| A1 | Metabolite | kegg.compound:C20493 | Cyanidin 3-sambubioside-5-glucoside |
| A2 | Metabolite | knapsack:C00007655 | |
| A5 | Metabolite | knapsack:C00007657 | |
| A6 | Metabolite | knapsack:C00007658 | |
| A3 | Metabolite | knapsack:C00006836 | |
| A4 | Metabolite | knapsack:C00007656 | |
| A7 | Metabolite | knapsack:C00007660 | |
| A8 | Metabolite | knapsack:C00007659 | |
| A11 | Metabolite | knapsack:C00007570 | |
| A9 | Metabolite | knapsack:C00006838 | |
| A10 | Metabolite | knapsack:C00007661 | |
| F7 | Metabolite | kegg.compound:C19796 | |
| F8 | Metabolite | knapsack:C00005470 | |
| F14 | Metabolite | knapsack:C00005557 | |
| F15 | Metabolite | knapsack:C00005558 | |
| F19 | Metabolite | knapsack:C00005174 | |
| F23 | Metabolite | knapsack:C00005368 | |
| F20 | Metabolite | knapsack:C00005188 | |
| F24 | Metabolite | kegg.compound:C01750 | |
| F27 | Metabolite | knapsack:C00005526 | |
| F28 | Metabolite | knapsack:C00005525 | |
| F29 | Metabolite | knapsack:C00005551 | |
| F30 | Metabolite | knapsack:C00005559 | |
| Quercetin | Metabolite | hmdb:HMDB0005794 | |
| Kaempferol | Metabolite | hmdb:HMDB0005801 | |
| Cyanidin | Metabolite | chebi:27843 | |
| Gluconic acid | Metabolite | hmdb:HMDB0000625 | |
| Glutathione | Metabolite | hmdb:HMDB0000125 | |
| glycerate 3-phosphate | Metabolite | hmdb:HMDB0000807 | |
| C14:0 | Metabolite | hmdb:HMDB0000806 | |
| C16:0 | Metabolite | hmdb:HMDB0000220 | |
| C18:0 | Metabolite | hmdb:HMDB0000827 | |
| C18:2 | Metabolite | hmdb:HMDB0000673 | |
| C18:3 | Metabolite | hmdb:HMDB0001388 | |
| C24:0 | Metabolite | hmdb:HMDB0002003 | |
| Cholesterol | Metabolite | hmdb:HMDB0000067 | |
| Stigmasterol | Metabolite | hmdb:HMDB0000937 | |
| Glutaric acid | Metabolite | hmdb:HMDB0000661 | |
| Salicylic acid | Metabolite | hmdb:HMDB0001895 | |
| 3-MTP | Metabolite | kegg.compound:C08412 | |
| 3-MSOP | Metabolite | kegg.compound:C08405 | |
| 4-MSOB | Metabolite | kegg.compound:C08410 | |
| 4-MTB | Metabolite | kegg.compound:C08409 | |
| 5-MTP | Metabolite | kegg.compound:C08401 | |
| 5-MSOP | Metabolite | kegg.compound:C08400 | |
| 6-MTH | Metabolite | knapsack:C00007844 | |
| 6-MSOH | Metabolite | knapsack:C00007348 | |
| 7-MTH | Metabolite | knapsack:C00007353 | |
| 7-MSOH | Metabolite | knapsack:C00007352 | |
| 8-MTO | Metabolite | knapsack:C00007356 | |
| 8-MSOO | Metabolite | knapsack:C00007355 | |
| PA | Metabolite | kegg.compound:C00416 | |
| DAG | Metabolite | kegg.compound:C00165 | |
| MGDG | Metabolite | chemspider:4696840 | |
| DGDG | Metabolite | chemspider:28495919 | |
| SQDG | Metabolite | chemspider:140119 | |
| PC | Metabolite | chemspider:4946694 | |
| PE | Metabolite | chemspider:7825685 | |
| PG | Metabolite | chemspider:8593139 | |
| PI | Metabolite | chemspider:20058759 | |
| lysoPC | Metabolite | chemspider:24766528 | |
| TAG | Metabolite | chemspider:4575640 |
References
- The flavonoid biosynthetic pathway in Arabidopsis: structural and genetic diversity. Saito K, Yonekura-Sakakibara K, Nakabayashi R, Higashi Y, Yamazaki M, Tohge T, et al. Plant Physiol Biochem. 2013 Nov;72:21–34. PubMed Europe PMC Scholia
- Recent progress in the development of metabolome databases for plant systems biology. Fukushima A, Kusano M. Front Plant Sci. 2013 Apr 4;4:73. PubMed Europe PMC Scholia
- Modern plant metabolomics: advanced natural product gene discoveries, improved technologies, and future prospects. Sumner LW, Lei Z, Nikolau BJ, Saito K. Nat Prod Rep. 2015 Feb;32(2):212–29. PubMed Europe PMC Scholia