ST001211 Metabolomic Markers of Methotrexate Response, In Vitro
List of human metabolic pathways and metabolites (REACTOME)

Pathway name (# of metabolites detected in study)Reactome pathway
5-Phosphoribose 1-diphosphate biosynthesis (1) REACT_850
Abacavir metabolism (6) REACT_121388
ABCA transporters in lipid homeostasis (1) REACT_111158
ABH2 mediated Reversal of Alkylation Damage (1) REACT_526
ABH3 mediated Reversal of Alkylation Damage (1) REACT_1662
Abnormal metabolism in phenylketonuria (7) REACT_121117
Acetylation (2) REACT_6732
Acetylcholine Neurotransmitter Release Cycle (1) REACT_15309
Activation of AMPA receptors (1) REACT_18338
Activation of Ca-permeable Kainate Receptor (1) REACT_21346
Activation of gene expression by SREBF (SREBP) (3) REACT_147904
Activation of Na-permeable Kainate Receptors (1) REACT_21343
Activation of PPARGC1A (PGC-1alpha) by phosphorylation (1) REACT_200686
Activation of the phototransduction cascade (1) REACT_163932
Adenosine P1 receptors (1) REACT_18288
Adenylate cyclase activating pathway (1) REACT_15312
Aflatoxin activation and detoxification (3) REACT_228214
Agmatine biosynthesis (3) REACT_14800
alpha-linolenic acid (ALA) metabolism (5) REACT_121147
Alpha-oxidation of phytanate (4) REACT_17003
Amino acid synthesis and interconversion (transamination) (10) REACT_238
Amino acid transport across the plasma membrane (24) REACT_13796
AMPK inhibits chREBP transcriptional activation activity (1) REACT_1988
Androgen biosynthesis (1) REACT_11059
Antigen Presentation: Folding, assembly and peptide loading of class I MHC (20) REACT_75795
Antigen processing: Ubiquitination & Proteasome degradation (22) REACT_75842
Arachidonate production from DAG (1) REACT_19308
Arachidonic acid metabolism (1) REACT_147851
Aromatic amines can be N-hydroxylated or N-dealkylated by CYP1A2 (2) REACT_13721
Astrocytic Glutamate-Glutamine Uptake And Metabolism (2) REACT_13639
A tetrasaccharide linker sequence is required for GAG synthesis (2) REACT_121408
Beta oxidation of butanoyl-CoA to acetyl-CoA (2) REACT_419
Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA (2) REACT_1708
Beta oxidation of hexanoyl-CoA to butanoyl-CoA (2) REACT_1887
Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA (2) REACT_735
Beta oxidation of myristoyl-CoA to lauroyl-CoA (2) REACT_2108
Beta oxidation of octanoyl-CoA to hexanoyl-CoA (2) REACT_1697
Beta oxidation of palmitoyl-CoA to myristoyl-CoA (2) REACT_2025
Beta-oxidation of pristanoyl-CoA (2) REACT_17017
Beta-oxidation of very long chain fatty acids (2) REACT_17062
Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB (2) REACT_416
Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein (1) REACT_22433
Biotin transport and metabolism (4) REACT_11153
BMAL1:CLOCK,NPAS2 activates circadian gene expression (3) REACT_111118
Branched-chain amino acid catabolism (7) REACT_197
Ca2+ pathway (1) REACT_172761
Cam-PDE 1 activation (1) REACT_15408
Carnitine synthesis (5) REACT_2125
Catecholamine biosynthesis (3) REACT_15551
Cell redox homeostasis (2) REACT_121394
Cell surface interactions at the vascular wall (1) REACT_12051
cGMP effects (1) REACT_23767
Cholesterol biosynthesis (4) REACT_9405
Chondroitin sulfate biosynthesis (1) REACT_120989
Chylomicron-mediated lipid transport (1) REACT_6841
Circadian Clock (3) REACT_24941
Citric acid cycle (TCA cycle) (6) REACT_1785
Class A/1 (Rhodopsin-like receptors) (3) REACT_14828
Class C/3 (Metabotropic glutamate/pheromone receptors) (6) REACT_18319
Cleavage of the damaged purine (1) REACT_1729
Cleavage of the damaged pyrimidine (1) REACT_2156
Cobalamin (Cbl, vitamin B12) transport and metabolism (5) REACT_163862
Coenzyme A biosynthesis (3) REACT_11218
Collagen biosynthesis and modifying enzymes (2) REACT_121139
Condensation of Prophase Chromosomes (3) REACT_172744
Conjugation of benzoate with glycine (5) REACT_6933
Conjugation of phenylacetate with glutamine (4) REACT_6800
Conjugation of salicylate with glycine (3) REACT_6812
Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase (1) REACT_6867
COX reactions (1) REACT_1396
Creatine metabolism (7) REACT_813
CREB phosphorylation through the activation of Adenylate Cyclase (1) REACT_20625
CREB phosphorylation through the activation of CaMKII (2) REACT_20642
Cross-presentation of soluble exogenous antigens (endosomes) (20) REACT_111056
CYP2E1 reactions (1) REACT_13797
Cysteine formation from homocysteine (3) REACT_115589
Cytosolic iron-sulfur cluster assembly (1) REACT_160176
Cytosolic sulfonation of small molecules (3) REACT_6913
Cytosolic tRNA aminoacylation (22) REACT_15306
DARPP-32 events (1) REACT_15334
Deadenylation of mRNA (1) REACT_20514
Defective B3GAT3 causes JDSSDHD (1) REACT_267659
Defective B4GALT1 causes B4GALT1-CDG (CDG-2d) (1) REACT_267635
Defective B4GALT7 causes EDS, progeroid type (1) REACT_267711
Defective CHSY1 causes TPBS (1) REACT_267682
Defective EXT1 causes exostoses 1, TRPS2 and CHDS (1) REACT_267674
Defective EXT2 causes exostoses 2 (1) REACT_267654
Defective HLCS causes multiple carboxylase deficiency (1) REACT_169312
Defective MTR causes methylmalonic aciduria and homocystinuria type cblG (1) REACT_169149
Defective MTRR causes methylmalonic aciduria and homocystinuria type cblE (2) REACT_169439
degradation of AXIN (2) REACT_200766
Degradation of cysteine and homocysteine (5) REACT_115654
Degradation of GABA (3) REACT_23964
Detoxification of Reactive Oxygen Species (2) REACT_172715
Digestion of dietary carbohydrate (2) REACT_9472
Digestion of dietary lipid (3) REACT_9518
DNA methylation (2) REACT_267652
Downregulation of SMAD2/3:SMAD4 transcriptional activity (2) REACT_121111
Downstream TCR signaling (1) REACT_12555
Electron transport from NADPH to Ferredoxin (1) REACT_150128
Endogenous sterols (3) REACT_13812
Endosomal/Vacuolar pathway (20) REACT_111168
eNOS activation (4) REACT_12477
Enzymatic degradation of dopamine by COMT (3) REACT_15548
Enzymatic degradation of Dopamine by monoamine oxidase (2) REACT_15511
EPHB-mediated forward signaling (2) REACT_228085
ER-Phagosome pathway (20) REACT_111178
ER Quality Control Compartment (ERQC) (1) REACT_25091
Ethanol oxidation (3) REACT_34
Factors involved in megakaryocyte development and platelet production (1) REACT_24970
Fatty acids (1) REACT_13814
Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion (3) REACT_19193
Fatty acid, triacylglycerol, and ketone body metabolism (2) REACT_22279
Fatty Acyl-CoA Biosynthesis (3) REACT_1319
FCERI mediated NF-kB activation (2) REACT_163994
FMO oxidises nucleophiles (2) REACT_13653
Formation of the active cofactor, UDP-glucuronate (3) REACT_6737
formation of the beta-catenin:TCF transactivating complex (2) REACT_200753
Free fatty acid receptors (7) REACT_21268
Fructose catabolism (1) REACT_1571
GABA synthesis (1) REACT_24020
Galactose catabolism (2) REACT_532
G alpha (i) signalling events (9) REACT_19231
G alpha (q) signalling events (8) REACT_18283
G alpha (s) signalling events (4) REACT_19327
G alpha (z) signalling events (1) REACT_19333
Glucagon-like Peptide-1 (GLP1) regulates insulin secretion (1) REACT_18274
Glucocorticoid biosynthesis (2) REACT_11036
Gluconeogenesis (8) REACT_1520
Glucuronidation (2) REACT_6784
Glutamate Neurotransmitter Release Cycle (2) REACT_12591
Glutathione conjugation (1) REACT_6926
Glutathione synthesis and recycling (22) REACT_6960
Glycogen breakdown (glycogenolysis) (1) REACT_1008
Glycogen synthesis (2) REACT_169208
Glycolysis (4) REACT_1383
Glycosphingolipid metabolism (2) REACT_116105
Glyoxylate metabolism (3) REACT_16925
HDL-mediated lipid transport (1) REACT_13621
HDMs demethylate histones (1) REACT_228178
Hedgehog ligand biogenesis (1) REACT_228111
Hedgehog 'off' state (1) REACT_267634
Heme biosynthesis (3) REACT_9465
Heme degradation (2) REACT_22297
Histidine catabolism (4) REACT_1249
HIV Transcription Initiation (1) REACT_6332
Hormone-sensitive lipase (HSL)-mediated triacylglycerol hydrolysis (1) REACT_494
HS-GAG biosynthesis (2) REACT_121248
HS-GAG degradation (1) REACT_120752
Hydrolysis of LPC (2) REACT_120977
Hydrolysis of LPE (2) REACT_120785
Hydroxycarboxylic acid-binding receptors (3) REACT_163785
Hypusine synthesis from eIF5A-lysine (2) REACT_12469
Import of palmitoyl-CoA into the mitochondrial matrix (2) REACT_11082
Inactivation, recovery and regulation of the phototransduction cascade (2) REACT_163919
Inositol transporters (1) REACT_19188
Interconversion of 2-oxoglutarate and 2-hydroxyglutarate (2) REACT_25367
Interconversion of polyamines (3) REACT_14805
Iron uptake and transport (1) REACT_25060
ISG15 antiviral mechanism (2) REACT_115831
Keratan sulfate biosynthesis (3) REACT_121120
LDL-mediated lipid transport (1) REACT_6934
Ligand-gated ion channel transport (2) REACT_25387
Linoleic acid (LA) metabolism (4) REACT_121100
Lysine catabolism (4) REACT_1298
Meiotic recombination (2) REACT_27271
Metabolism of folate and pterines (3) REACT_11167
Metabolism of nucleotides (2) REACT_1698
Metabolism of polyamines (5) REACT_14820
Metabolism of serotonin (3) REACT_15532
Methionine salvage pathway (3) REACT_75881
Methylation (7) REACT_6946
Mineralocorticoid biosynthesis (2) REACT_11047
Minus-strand DNA synthesis (1) REACT_9055
Miscellaneous substrates (2) REACT_13425
Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) (2) REACT_228019
Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) (2) REACT_228145
mitochondrial fatty acid beta-oxidation of unsaturated fatty acids (2) REACT_160
Mitochondrial iron-sulfur cluster biogenesis (2) REACT_150353
Mitochondrial tRNA aminoacylation (22) REACT_15302
Molybdenum cofactor biosynthesis (6) REACT_25073
mRNA Capping (3) REACT_1470
mRNA decay by 3' to 5' exoribonuclease (4) REACT_20619
mRNA decay by 5' to 3' exoribonuclease (4) REACT_20518
Na+/Cl- dependent neurotransmitter transporters (22) REACT_20506
Na+-dependent glucose transporters (1) REACT_19165
Neurotransmitter Clearance In The Synaptic Cleft (1) REACT_13583
NGF-independant TRKA activation (1) REACT_11046
N-Glycan antennae elongation (1) REACT_25085
Nicotinamide salvaging (4) REACT_11213
Nicotinate metabolism (5) REACT_11088
Nitric oxide stimulates guanylate cyclase (3) REACT_23862
NoRC negatively regulates rRNA expression (2) REACT_200856
Norepinephrine Neurotransmitter Release Cycle (1) REACT_15418
NOSIP mediated eNOS trafficking (1) REACT_12510
NOSTRIN mediated eNOS trafficking (1) REACT_12541
O-linked glycosylation of mucins (1) REACT_115606
Organic anion transport (1) REACT_22310
Organic anion transporters (3) REACT_19372
Organic cation transport (6) REACT_22357
Orphan transporters (5) REACT_267716
Oxidative Stress Induced Senescence (3) REACT_169436
Oxygen-dependent asparagine hydroxylation of Hypoxia-inducible Factor Alpha (1) REACT_121226
Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha (1) REACT_120916
PAOs oxidise polyamines to amines (3) REACT_505
Passive transport by Aquaporins (1) REACT_23826
PD-1 signaling (1) REACT_19324
PDE3B signalling (1) REACT_1451
Phagosomal maturation (early endosomal stage) (4) REACT_121256
Phenylalanine and tyrosine catabolism (6) REACT_1786
Phosphate bond hydrolysis by NUDT proteins (3) REACT_150237
phospho-PLA2 pathway (1) REACT_15466
PKA activation (1) REACT_15530
PKA activation in glucagon signalling (1) REACT_1946
Plasmalogen biosynthesis (3) REACT_1407
Platelet degranulation (2) REACT_318
Platelet sensitization by LDL (1) REACT_23879
PPARA activates gene expression (3) REACT_116145
PRC2 methylates histones and DNA (2) REACT_200808
Pregnenolone biosynthesis (1) REACT_11038
Pre-NOTCH Processing in Golgi (2) REACT_118798
Presynaptic function of Kainate receptors (1) REACT_21254
Progressive trimming of alpha-1,2-linked mannose residues from Man9/8/7GlcNAc2 to produce Man5GlcNAc2 (1) REACT_25396
Proline catabolism (4) REACT_1002
Proton-coupled monocarboxylate transport (1) REACT_20515
Proton-coupled neutral amino acid transporters (3) REACT_19348
Proton/oligonucleotide cotransporters (20) REACT_19328
Purine catabolism (12) REACT_2086
Purine ribonucleoside monophosphate biosynthesis (9) REACT_1776
Purine salvage (11) REACT_1923
Pyrimidine biosynthesis (6) REACT_21376
Pyrimidine catabolism (11) REACT_1023
Pyrimidine salvage reactions (8) REACT_655
Pyruvate metabolism (3) REACT_2071
Rap1 signalling (1) REACT_23898
Ras activation uopn Ca2+ infux through NMDA receptor (2) REACT_20546
Reactions specific to the complex N-glycan synthesis pathway (1) REACT_25302
Recycling of bile acids and salts (5) REACT_11042
Regulation by TREX1 (1) REACT_163652
Regulation of AMPK activity via LKB1 (1) REACT_21285
Regulation of cholesterol biosynthesis by SREBP (SREBF) (1) REACT_147797
Regulation of Glucokinase by Glucokinase Regulatory Protein (1) REACT_6804
Regulation of HSF1-mediated heat shock response (2) REACT_200780
Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha) (3) REACT_19241
Regulation of pyruvate dehydrogenase (PDH) complex (2) REACT_12528
Regulation of Rheb GTPase activity by AMPK (1) REACT_21393
Removal of DNA patch containing abasic residue (1) REACT_2192
Removal of the Flap Intermediate (4) REACT_70
Removal of the Flap Intermediate from the C-strand (4) REACT_7999
Resolution of AP sites via the single-nucleotide replacement pathway (1) REACT_933
Respiratory electron transport (3) REACT_22393
Retinoid cycle disease events (2) REACT_160130
Retinoid metabolism and transport (4) REACT_24968
Reuptake of GABA (2) REACT_23910
REV-ERBA represses gene expression (3) REACT_118789
RMTs methylate histone arginines (2) REACT_228108
RNA Polymerase II HIV Promoter Escape (1) REACT_6253
RNA Polymerase II Promoter Escape (1) REACT_2089
RNA Polymerase II Transcription Initiation (1) REACT_1851
Role of phospholipids in phagocytosis (2) REACT_160158
RORA activates circadian gene expression (3) REACT_118659
Scavenging by Class A Receptors (5) REACT_163699
Scavenging by Class B Receptors (1) REACT_163679
Scavenging by Class F Receptors (1) REACT_163813
Scavenging by Class H Receptors (1) REACT_164002
Scavenging of heme from plasma (1) REACT_160163
Senescence-Associated Secretory Phenotype (SASP) (2) REACT_169168
Serine biosynthesis (4) REACT_115789
Serotonin and melatonin biosynthesis (5) REACT_15439
Serotonin clearance from the synaptic cleft (1) REACT_15391
Serotonin Neurotransmitter Release Cycle (1) REACT_15425
Serotonin receptors (1) REACT_17064
Sialic acid metabolism (2) REACT_200874
SIRT1 negatively regulates rRNA Expression (4) REACT_200827
snRNP Assembly (1) REACT_11066
Sodium-coupled sulphate, di- and tri-carboxylate transporters (2) REACT_20646
Sphingolipid de novo biosynthesis (4) REACT_115810
Stimuli-sensing channels (2) REACT_160189
STING mediated induction of host immune responses (1) REACT_147841
Sulfide oxidation to sulfate (3) REACT_116010
Sulfur amino acid metabolism (11) REACT_115639
SUMO is conjugated to E1 (UBA2:SAE1) (2) REACT_163812
Synthesis and interconversion of nucleotide di- and triphosphates (9) REACT_21330
Synthesis of 12-eicosatetraenoic acid derivatives (2) REACT_150201
Synthesis of 15-eicosatetraenoic acid derivatives (3) REACT_150422
Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE) (1) REACT_150134
Synthesis of 5-eicosatetraenoic acids (2) REACT_150209
Synthesis of bile acids and bile salts (1) REACT_11054
Synthesis of bile acids and bile salts via 24-hydroxycholesterol (4) REACT_11053
Synthesis of bile acids and bile salts via 27-hydroxycholesterol (2) REACT_11048
Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol (8) REACT_11041
Synthesis of CL (1) REACT_120920
Synthesis of Dolichyl-phosphate (1) REACT_22230
Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) (1) REACT_150417
Synthesis of GDP-mannose (1) REACT_22423
Synthesis of Hepoxilins (HX) and Trioxilins (TrX) (1) REACT_150292
Synthesis of IP2, IP, and Ins in the cytosol (4) REACT_150352
Synthesis of Ketone Bodies (1) REACT_1464
Synthesis of Leukotrienes (LT) and Eoxins (EX) (4) REACT_150420
Synthesis of Lipoxins (LX) (1) REACT_150320
Synthesis of PA (3) REACT_120906
Synthesis of PC (5) REACT_121238
Synthesis of PE (5) REACT_120919
Synthesis of PG (4) REACT_121280
Synthesis of PI (3) REACT_121000
Synthesis of Prostaglandins (PG) and Thromboxanes (TX) (4) REACT_150149
Synthesis of PS (3) REACT_120823
Synthesis of UDP-N-acetyl-glucosamine (3) REACT_22394
Synthesis of very long-chain fatty acyl-CoAs (4) REACT_380
Synthesis, secretion, and deacylation of Ghrelin (1) REACT_19189
Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) (7) REACT_24019
Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) (3) REACT_23824
Termination of O-glycan biosynthesis (1) REACT_115835
TET1,2,3 and TDG demethylate DNA (1) REACT_200682
Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation (2) REACT_111176
The activation of arylsulfatases (1) REACT_121036
The canonical retinoid cycle in rods (twilight vision) (4) REACT_160156
The retinoid cycle in cones (daylight vision) (1) REACT_160083
Thyroxine biosynthesis (2) REACT_15292
Tolerance by Mtb to nitric oxide produced by macrophages (1) REACT_120983
Trafficking of dietary sterols (1) REACT_13781
Transcriptional activation of mitochondrial biogenesis (3) REACT_200608
Transcriptional regulation of white adipocyte differentiation (3) REACT_27161
Translocation of GLUT4 to the plasma membrane (1) REACT_147867
Transport and synthesis of PAPS (1) REACT_6840
Transport of fatty acids (5) REACT_23892
Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds (3) REACT_19305
Transport of inorganic cations/anions and amino acids/oligopeptides (3) REACT_19397
Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane (11) REACT_1206
Transport of nucleotide sugars (5) REACT_22151
Transport of organic anions (1) REACT_23988
Transport of vitamins, nucleosides, and related molecules (1) REACT_22285
Triglyceride Biosynthesis (2) REACT_1190
Tryptophan catabolism (6) REACT_916
Ubiquinol biosynthesis (4) REACT_160111
Unblocking of NMDA receptor, glutamate binding and activation (2) REACT_20594
Uptake and function of anthrax toxins (1) REACT_228255
Urea cycle (9) REACT_847
Utilization of Ketone Bodies (2) REACT_59
Vasopressin regulates renal water homeostasis via Aquaporins (1) REACT_24023
VEGFA-VEGFR2 Pathway (1) REACT_228166
VEGFR2 mediated cell proliferation (1) REACT_228024
VEGFR2 mediated vascular permeability (3) REACT_228016
Vitamin B1 (thiamin) metabolism (1) REACT_11117
Vitamin B2 (riboflavin) metabolism (3) REACT_11070
Vitamin C (ascorbate) metabolism (3) REACT_11202
Vitamins (1) REACT_13450
Vitamins B6 activation to pyridoxal phosphate (4) REACT_25012
YAP1- and WWTR1 (TAZ)-stimulated gene expression (3) REACT_118713
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