ST000711 Microbial ecology of nontuberculous mycobacteria (NTM) in cystic fibrosis (CF) sputum
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 (4) REACT_121388
ABCA transporters in lipid homeostasis (1) REACT_111158
Abnormal metabolism in phenylketonuria (7) REACT_121117
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
Aflatoxin activation and detoxification (3) REACT_228214
Agmatine biosynthesis (1) REACT_14800
alpha-linolenic acid (ALA) metabolism (3) REACT_121147
Alpha-oxidation of phytanate (2) REACT_17003
Amino acid synthesis and interconversion (transamination) (7) REACT_238
Amino acid transport across the plasma membrane (15) 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 (14) REACT_75795
Antigen processing: Ubiquitination & Proteasome degradation (15) 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 (1) REACT_13721
Astrocytic Glutamate-Glutamine Uptake And Metabolism (1) REACT_13639
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 (1) 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 (2) REACT_11153
BMAL1:CLOCK,NPAS2 activates circadian gene expression (3) REACT_111118
Branched-chain amino acid catabolism (5) REACT_197
Cam-PDE 1 activation (1) REACT_15408
Carnitine synthesis (2) REACT_2125
Catecholamine biosynthesis (1) REACT_15551
Cell redox homeostasis (2) REACT_121394
Cell surface interactions at the vascular wall (1) REACT_12051
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) (5) 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 (3) REACT_163862
Coenzyme A biosynthesis (1) REACT_11218
Conjugation of benzoate with glycine (3) REACT_6933
Conjugation of phenylacetate with glutamine (1) REACT_6800
Conjugation of salicylate with glycine (3) REACT_6812
COX reactions (1) REACT_1396
Creatine metabolism (3) REACT_813
CREB phosphorylation through the activation of CaMKII (2) REACT_20642
Cross-presentation of soluble exogenous antigens (endosomes) (14) REACT_111056
CYP2E1 reactions (1) REACT_13797
Cysteine formation from homocysteine (1) REACT_115589
Cytosolic iron-sulfur cluster assembly (1) REACT_160176
Cytosolic sulfonation of small molecules (4) REACT_6913
Cytosolic tRNA aminoacylation (15) REACT_15306
DARPP-32 events (1) REACT_15334
Deadenylation of mRNA (1) REACT_20514
Defective CHSY1 causes TPBS (1) REACT_267682
Defective MTR causes methylmalonic aciduria and homocystinuria type cblG (1) REACT_169149
Defective MTRR causes methylmalonic aciduria and homocystinuria type cblE (1) REACT_169439
degradation of AXIN (1) REACT_200766
Degradation of cysteine and homocysteine (4) REACT_115654
Degradation of GABA (2) REACT_23964
Detoxification of Reactive Oxygen Species (2) REACT_172715
Digestion of dietary carbohydrate (1) REACT_9472
Digestion of dietary lipid (6) REACT_9518
Downregulation of SMAD2/3:SMAD4 transcriptional activity (1) REACT_121111
Eicosanoids (1) REACT_13645
Electron transport from NADPH to Ferredoxin (1) REACT_150128
Endogenous sterols (4) REACT_13812
Endosomal/Vacuolar pathway (14) REACT_111168
eNOS activation (4) REACT_12477
Enzymatic degradation of dopamine by COMT (1) REACT_15548
Enzymatic degradation of Dopamine by monoamine oxidase (1) REACT_15511
EPHB-mediated forward signaling (2) REACT_228085
ER-Phagosome pathway (14) REACT_111178
Ethanol oxidation (2) REACT_34
Factors involved in megakaryocyte development and platelet production (1) REACT_24970
Fatty acids (3) REACT_13814
Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion (3) REACT_19193
Fatty acid, triacylglycerol, and ketone body metabolism (1) REACT_22279
Fatty Acyl-CoA Biosynthesis (4) REACT_1319
FCERI mediated NF-kB activation (1) REACT_163994
FMO oxidises nucleophiles (1) REACT_13653
Formation of the active cofactor, UDP-glucuronate (1) REACT_6737
Free fatty acid receptors (7) REACT_21268
GABA synthesis (1) REACT_24020
Galactose catabolism (1) REACT_532
G alpha (i) signalling events (4) REACT_19231
G alpha (q) signalling events (9) REACT_18283
G alpha (s) signalling events (4) REACT_19327
Glucocorticoid biosynthesis (3) REACT_11036
Gluconeogenesis (8) REACT_1520
Glucuronidation (2) REACT_6784
Glutamate Neurotransmitter Release Cycle (1) REACT_12591
Glutathione conjugation (1) REACT_6926
Glutathione synthesis and recycling (16) REACT_6960
Glycogen breakdown (glycogenolysis) (1) REACT_1008
Glycogen synthesis (1) REACT_169208
Glycolysis (4) REACT_1383
Glycosphingolipid metabolism (1) REACT_116105
Glyoxylate metabolism (3) REACT_16925
HDL-mediated lipid transport (1) REACT_13621
Hedgehog ligand biogenesis (1) REACT_228111
Heme biosynthesis (2) REACT_9465
Heme degradation (1) REACT_22297
Histidine catabolism (4) REACT_1249
Hormone-sensitive lipase (HSL)-mediated triacylglycerol hydrolysis (1) REACT_494
HS-GAG biosynthesis (1) REACT_121248
HS-GAG degradation (1) REACT_120752
Hydrolysis of LPC (1) REACT_120977
Hydroxycarboxylic acid-binding receptors (1) REACT_163785
Hypusine synthesis from eIF5A-lysine (2) REACT_12469
Inactivation, recovery and regulation of the phototransduction cascade (1) REACT_163919
Interconversion of 2-oxoglutarate and 2-hydroxyglutarate (1) REACT_25367
Interconversion of polyamines (2) REACT_14805
Iron uptake and transport (1) REACT_25060
ISG15 antiviral mechanism (1) REACT_115831
Keratan sulfate biosynthesis (1) REACT_121120
LDL-mediated lipid transport (1) REACT_6934
Leukotriene receptors (1) REACT_18302
Ligand-gated ion channel transport (1) REACT_25387
Linoleic acid (LA) metabolism (3) REACT_121100
Lysine catabolism (4) REACT_1298
Metabolism of folate and pterines (3) REACT_11167
Metabolism of nucleotides (2) REACT_1698
Metabolism of polyamines (3) REACT_14820
Metabolism of serotonin (2) REACT_15532
Methionine salvage pathway (2) REACT_75881
Methylation (3) REACT_6946
Mineralocorticoid biosynthesis (1) REACT_11047
Miscellaneous substrates (1) REACT_13425
Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) (1) REACT_228019
Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) (1) REACT_228145
mitochondrial fatty acid beta-oxidation of unsaturated fatty acids (2) REACT_160
Mitochondrial tRNA aminoacylation (15) REACT_15302
Molybdenum cofactor biosynthesis (2) REACT_25073
mRNA decay by 3' to 5' exoribonuclease (2) REACT_20619
mRNA decay by 5' to 3' exoribonuclease (2) REACT_20518
Na+/Cl- dependent neurotransmitter transporters (13) REACT_20506
Neurotransmitter Clearance In The Synaptic Cleft (1) REACT_13583
Nicotinamide salvaging (1) REACT_11213
Nicotinate metabolism (3) REACT_11088
Nitric oxide stimulates guanylate cyclase (2) REACT_23862
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 transporters (2) REACT_19372
Organic cation transport (2) REACT_22357
Orphan transporters (11) REACT_267716
PAOs oxidise polyamines to amines (2) REACT_505
PDE3B signalling (1) REACT_1451
Phagosomal maturation (early endosomal stage) (4) REACT_121256
Phenylalanine and tyrosine catabolism (5) REACT_1786
Phosphate bond hydrolysis by NUDT proteins (2) REACT_150237
phospho-PLA2 pathway (1) REACT_15466
Plasmalogen biosynthesis (2) REACT_1407
Platelet sensitization by LDL (1) REACT_23879
PPARA activates gene expression (4) REACT_116145
Pregnenolone biosynthesis (1) REACT_11038
Presynaptic function of Kainate receptors (1) REACT_21254
Proline catabolism (4) REACT_1002
Prostanoid ligand receptors (1) REACT_18425
Proton-coupled neutral amino acid transporters (2) REACT_19348
Proton/oligonucleotide cotransporters (14) REACT_19328
Purine catabolism (9) REACT_2086
Purine ribonucleoside monophosphate biosynthesis (7) REACT_1776
Purine salvage (6) REACT_1923
Pyrimidine biosynthesis (3) REACT_21376
Pyrimidine catabolism (4) REACT_1023
Pyrimidine salvage reactions (3) REACT_655
Pyruvate metabolism (2) REACT_2071
Ras activation uopn Ca2+ infux through NMDA receptor (2) REACT_20546
Recycling of bile acids and salts (9) REACT_11042
Regulation of AMPK activity via LKB1 (1) REACT_21285
Regulation of cholesterol biosynthesis by SREBP (SREBF) (1) REACT_147797
Regulation of HSF1-mediated heat shock response (1) REACT_200780
Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha) (3) REACT_19241
Regulation of pyruvate dehydrogenase (PDH) complex (1) REACT_12528
Regulation of Rheb GTPase activity by AMPK (1) REACT_21393
Removal of the Flap Intermediate (2) REACT_70
Removal of the Flap Intermediate from the C-strand (2) REACT_7999
Respiratory electron transport (3) REACT_22393
Retinoid cycle disease events (2) REACT_160130
Retinoid metabolism and transport (4) REACT_24968
REV-ERBA represses gene expression (3) REACT_118789
Role of phospholipids in phagocytosis (2) REACT_160158
RORA activates circadian gene expression (3) REACT_118659
Scavenging by Class A Receptors (2) 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
Serine biosynthesis (4) REACT_115789
Serotonin and melatonin biosynthesis (2) REACT_15439
SIRT1 negatively regulates rRNA Expression (1) REACT_200827
Sodium-coupled sulphate, di- and tri-carboxylate transporters (1) REACT_20646
Sphingolipid de novo biosynthesis (3) REACT_115810
Stimuli-sensing channels (1) REACT_160189
Sulfide oxidation to sulfate (3) REACT_116010
Sulfur amino acid metabolism (5) REACT_115639
SUMO is conjugated to E1 (UBA2:SAE1) (1) REACT_163812
Synthesis and interconversion of nucleotide di- and triphosphates (6) 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 (3) REACT_11054
Synthesis of bile acids and bile salts via 24-hydroxycholesterol (3) REACT_11053
Synthesis of bile acids and bile salts via 27-hydroxycholesterol (3) REACT_11048
Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol (12) REACT_11041
Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) (1) REACT_150417
Synthesis of Hepoxilins (HX) and Trioxilins (TrX) (1) REACT_150292
Synthesis of IP2, IP, and Ins in the cytosol (2) REACT_150352
Synthesis of Ketone Bodies (1) REACT_1464
Synthesis of Leukotrienes (LT) and Eoxins (EX) (5) REACT_150420
Synthesis of Lipoxins (LX) (1) REACT_150320
Synthesis of PA (2) REACT_120906
Synthesis of PC (1) REACT_121238
Synthesis of PE (1) REACT_120919
Synthesis of PG (1) REACT_121280
Synthesis of Prostaglandins (PG) and Thromboxanes (TX) (4) REACT_150149
Synthesis of PS (2) REACT_120823
Synthesis of UDP-N-acetyl-glucosamine (1) REACT_22394
Synthesis of very long-chain fatty acyl-CoAs (3) 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
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 (1) 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 of fatty acids (8) REACT_23892
Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds (1) 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 (4) REACT_1206
Transport of nucleotide sugars (2) REACT_22151
Transport of organic anions (5) REACT_23988
Triglyceride Biosynthesis (1) REACT_1190
Tryptophan catabolism (6) REACT_916
Ubiquinol biosynthesis (2) REACT_160111
Unblocking of NMDA receptor, glutamate binding and activation (2) REACT_20594
Urea cycle (6) REACT_847
Utilization of Ketone Bodies (1) REACT_59
VEGFA-VEGFR2 Pathway (1) REACT_228166
VEGFR2 mediated vascular permeability (3) REACT_228016
Vitamin B1 (thiamin) metabolism (1) REACT_11117
Vitamin B2 (riboflavin) metabolism (2) REACT_11070
Vitamin C (ascorbate) metabolism (3) REACT_11202
Vitamins B6 activation to pyridoxal phosphate (2) REACT_25012
YAP1- and WWTR1 (TAZ)-stimulated gene expression (3) REACT_118713
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