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 (, to store the metabolome information.


Atsushi Fukushima , Anders Riutta , Egon Willighagen , and Martina Summer-Kutmon


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Arabidopsis thaliana



Pathway Ontology

classic 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
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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


  1. 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
  2. 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
  3. 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