List of human metabolic pathways and metabolites (REACTOME)

Pathway name (# of metabolites detected in study)Reactome pathway
5-Phosphoribose 1-diphosphate biosynthesis REACT_850
Abacavir metabolism REACT_121388
Abacavir transmembrane transport REACT_120801
ABCA transporters in lipid homeostasis REACT_111158
ABC-family proteins mediated transport REACT_15480
Acetylcholine Neurotransmitter Release Cycle REACT_15309
Acetylcholine regulates insulin secretion REACT_18405
Activated point mutants of FGFR2 REACT_120863
activated TAK1 mediates p38 MAPK activation REACT_21399
Activation of ATR in response to replication stress REACT_6769
Activation of BAD and translocation to mitochondria REACT_549
Activation of CaMK IV REACT_20652
Activation of caspases through apoptosome-mediated cleavage REACT_607
Activation of IRF3/IRF7 mediated by TBK1/IKK epsilon REACT_25148
Activation of NF-kappaB in B cells REACT_118656
Activation of NIMA Kinases NEK9, NEK6, NEK7 REACT_160122
Activation of PKB REACT_790
Activation of PPARGC1A (PGC-1alpha) by phosphorylation REACT_200686
Activation of RAS in B cells REACT_118778
Activation of the AP-1 family of transcription factors REACT_21326
Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S REACT_1258
Activation of the pre-replicative complex REACT_1095
Adenylate cyclase activating pathway REACT_15312
Adherens junctions interactions REACT_19195
ADP signalling through P2Y purinoceptor 1 REACT_19140
AKT-mediated inactivation of FOXO1A REACT_13655
AKT phosphorylates targets in the cytosol REACT_12564
AKT phosphorylates targets in the nucleus REACT_12442
alpha-linolenic acid (ALA) metabolism REACT_121147
Alpha-oxidation of phytanate REACT_17003
Amino acid synthesis and interconversion (transamination) REACT_238
AMPK inhibits chREBP transcriptional activation activity REACT_1988
Antigen activates B Cell Receptor (BCR) leading to generation of second messengers REACT_118700
Antigen Presentation: Folding, assembly and peptide loading of class I MHC REACT_75795
Antigen processing: Ubiquitination & Proteasome degradation REACT_75842
ARMS-mediated activation REACT_12002
Astrocytic Glutamate-Glutamine Uptake And Metabolism REACT_13639
Asymmetric localization of PCP proteins REACT_172638
ATM mediated phosphorylation of repair proteins REACT_1924
ATM mediated response to DNA double-strand break REACT_204
ATP sensitive Potassium channels REACT_75775
Autodegradation of the E3 ubiquitin ligase COP1 REACT_20549
Beta-catenin phosphorylation cascade REACT_11065
betaKlotho-mediated ligand binding REACT_111046
Biotin transport and metabolism REACT_11153
Branched-chain amino acid catabolism REACT_197
Butyrate Response Factor 1 (BRF1) destabilizes mRNA REACT_24915
Ca2+ pathway REACT_172761
Calmodulin induced events REACT_9000
CaMK IV-mediated phosphorylation of CREB REACT_15502
CD28 co-stimulation REACT_19183
CD28 dependent PI3K/Akt signaling REACT_19358
CD28 dependent Vav1 pathway REACT_19238
CDK-mediated phosphorylation and removal of Cdc6 REACT_1221
CDO in myogenesis REACT_21402
Cell-extracellular matrix interactions REACT_20649
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex REACT_407
Cholesterol biosynthesis REACT_9405
Citric acid cycle (TCA cycle) REACT_1785
Clearance of Nuclear Envelope Membranes from Chromatin REACT_160251
Cobalamin (Cbl, vitamin B12) transport and metabolism REACT_163862
Coenzyme A biosynthesis REACT_11218
Condensation of Prometaphase Chromosomes REACT_150260
Condensation of Prophase Chromosomes REACT_172744
Conjugation of benzoate with glycine REACT_6933
Conjugation of phenylacetate with glutamine REACT_6800
Conjugation of salicylate with glycine REACT_6812
Constitutive PI3K/AKT Signaling in Cancer REACT_147727
Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants REACT_160254
Constitutive Signaling by NOTCH1 PEST Domain Mutants REACT_160243
Creatine metabolism REACT_813
CREB phosphorylation REACT_12524
CREB phosphorylation through the activation of Adenylate Cyclase REACT_20625
CREB phosphorylation through the activation of CaMKII REACT_20642
CREB phosphorylation through the activation of CaMKK REACT_20661
CREB phosphorylation through the activation of Ras REACT_20568
CRMPs in Sema3A signaling REACT_19199
c-src mediated regulation of Cx43 function and closure of gap junctions REACT_11043
CTLA4 inhibitory signaling REACT_19405
Cyclin A/B1 associated events during G2/M transition REACT_1857
Cyclin A:Cdk2-associated events at S phase entry REACT_9029
Cyclin B2 mediated events REACT_2101
Cyclin D associated events in G1 REACT_821
Cyclin E associated events during G1/S transition REACT_1574
Cytosolic tRNA aminoacylation REACT_15306
DAG and IP3 signaling REACT_111064
DAP12 signaling REACT_147814
DARPP-32 events REACT_15334
DCC mediated attractive signaling REACT_22351
deactivation of the beta-catenin transactivating complex REACT_200731
Defective HLCS causes multiple carboxylase deficiency REACT_169312
Defective MMAB causes methylmalonic aciduria type cblB REACT_169318
Defective PAPSS2 causes SEMD-PA REACT_267645
Degradation of beta-catenin by the destruction complex REACT_11063
Degradation of GLI1 by the proteasome REACT_267605
Degradation of GLI2 by the proteasome REACT_206597
Depolymerisation of the Nuclear Lamina REACT_200828
Detoxification of Reactive Oxygen Species REACT_172715
disassembly of the destruction complex and recruitment of AXIN to the membrane REACT_200610
Disinhibition of SNARE formation REACT_1178
DNA Damage/Telomere Stress Induced Senescence REACT_169185
Dopamine Neurotransmitter Release Cycle REACT_15293
Downregulation of ERBB2:ERBB3 signaling REACT_115662
Downstream signal transduction REACT_17025
Downstream TCR signaling REACT_12555
DSCAM interactions REACT_25299
Effects of PIP2 hydrolysis REACT_2202
EGFR downregulation REACT_12484
EGFR interacts with phospholipase C-gamma REACT_12478
Elevation of cytosolic Ca2+ levels REACT_162
Endosomal Sorting Complex Required For Transport (ESCRT) REACT_27258
eNOS activation REACT_12477
EPHA-mediated growth cone collapse REACT_228063
EPHB-mediated forward signaling REACT_228085
EPH-ephrin mediated repulsion of cells REACT_228189
EPH-Ephrin signaling REACT_228170
Ephrin signaling REACT_228226
ERK1 activation REACT_1391
ERK2 activation REACT_1183
ERK/MAPK targets REACT_12599
ER-Phagosome pathway REACT_111178
Ethanol oxidation REACT_34
Factors involved in megakaryocyte development and platelet production REACT_24970
Fatty Acyl-CoA Biosynthesis REACT_1319
Fc epsilon receptor (FCERI) signaling REACT_163936
FCERI mediated Ca+2 mobilization REACT_163834
FCERI mediated MAPK activation REACT_163701
FCERI mediated NF-kB activation REACT_163994
FCGR activation REACT_160274
FGFR1b ligand binding and activation REACT_9400
FGFR1c and Klotho ligand binding and activation REACT_9484
FGFR1c ligand binding and activation REACT_9515
FGFR2b ligand binding and activation REACT_9416
FGFR2c ligand binding and activation REACT_9413
FGFR3b ligand binding and activation REACT_9508
FGFR3c ligand binding and activation REACT_9510
FGFR4 ligand binding and activation REACT_9452
Folding of actin by CCT/TriC REACT_17050
Formation of apoptosome REACT_89
Formation of ATP by chemiosmotic coupling REACT_6759
Formation of HIV-1 elongation complex containing HIV-1 Tat REACT_6346
Formation of tubulin folding intermediates by CCT/TriC REACT_16956
Frs2-mediated activation REACT_12076
FRS2-mediated cascade REACT_21247
Fructose catabolism REACT_1571
G0 and Early G1 REACT_111214
G2/M DNA damage checkpoint REACT_897
G2/M DNA replication checkpoint REACT_1846
G2 Phase REACT_1915
GAB1 signalosome REACT_12578
Galactose catabolism REACT_532
G alpha (i) signalling events REACT_19231
G alpha (q) signalling events REACT_18283
G alpha (s) signalling events REACT_19327
G alpha (z) signalling events REACT_19333
Gastrin-CREB signalling pathway via PKC and MAPK REACT_120966
G beta:gamma signalling through PI3Kgamma REACT_19290
Generation of second messenger molecules REACT_12623
GLI3 is processed to GLI3R by the proteasome REACT_231645
Glucagon-like Peptide-1 (GLP1) regulates insulin secretion REACT_18274
Gluconeogenesis REACT_1520
Glucose transport REACT_212
Glutathione synthesis and recycling REACT_6960
Glycogen breakdown (glycogenolysis) REACT_1008
Glycolysis REACT_1383
Glycosphingolipid metabolism REACT_116105
Golgi Associated Vesicle Biogenesis REACT_19400
Golgi Cisternae Pericentriolar Stack Reorganization REACT_1100
GPVI-mediated activation cascade REACT_1695
Growth hormone receptor signaling REACT_111133
HDL-mediated lipid transport REACT_13621
Hedgehog ligand biogenesis REACT_228111
Hedgehog 'off' state REACT_267634
Hh ligand biogenesis disease REACT_228209
Hormone-sensitive lipase (HSL)-mediated triacylglycerol hydrolysis REACT_494
HSF1-dependent transactivation REACT_200775
HuR stabilizes mRNA REACT_25218
Import of palmitoyl-CoA into the mitochondrial matrix REACT_11082
Inactivation, recovery and regulation of the phototransduction cascade REACT_163919
Inhibition of TSC complex formation by PKB REACT_6743
Integrin alphaIIb beta3 signaling REACT_15523
Interaction between L1 and Ankyrins REACT_22266
Interferon alpha/beta signaling REACT_25162
Interferon gamma signaling REACT_25078
Interleukin-1 signaling REACT_22442
Interleukin-2 signaling REACT_27283
Interleukin-3, 5 and GM-CSF signaling REACT_23837
Interleukin-6 signaling REACT_27307
Interleukin-7 signaling REACT_115529
Interleukin receptor SHC signaling REACT_23891
Ion transport by P-type ATPases REACT_25149
IRAK1 recruits IKK complex REACT_24918
IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation REACT_25354
IRAK2 mediated activation of TAK1 complex REACT_25380
IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation REACT_25018
IRE1alpha activates chaperones REACT_18368
IRF3 mediated activation of type 1 IFN REACT_118811
IRF3-mediated induction of type I IFN REACT_163993
Iron uptake and transport REACT_25060
IRS activation REACT_570
IRS-related events triggered by IGF1R REACT_150203
ISG15 antiviral mechanism REACT_115831
JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 REACT_21368
Kinesins REACT_25201
KSRP destabilizes mRNA REACT_25042
L1CAM interactions REACT_22205
Linoleic acid (LA) metabolism REACT_121100
Loss of Nlp from mitotic centrosomes REACT_15364
LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production REACT_163743
Lysosome Vesicle Biogenesis REACT_19287
MASTL Facilitates Mitotic Progression REACT_150182
Meiotic synapsis REACT_75792
Metabolism of folate and pterines REACT_11167
Methylation REACT_6946
MHC class II antigen presentation REACT_121399
Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) REACT_228019
Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) REACT_228145
Mitochondrial ABC transporters REACT_111108
Mitochondrial protein import REACT_118595
Mitochondrial tRNA aminoacylation REACT_15302
Molybdenum cofactor biosynthesis REACT_25073
mRNA 3'-end processing REACT_1849
MyD88 cascade initiated on plasma membrane REACT_27215
MyD88 dependent cascade initiated on endosome REACT_25222
MyD88:Mal cascade initiated on plasma membrane REACT_6788
NCAM1 interactions REACT_18312
NCAM signaling for neurite out-growth REACT_18334
Negative regulation of FGFR signaling REACT_111184
Negative regulators of RIG-I/MDA5 signaling REACT_25271
Nephrin interactions REACT_23832
Netrin-1 signaling REACT_22237
Netrin mediated repulsion signals REACT_22384
Neurofascin interactions REACT_22312
NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 REACT_25039
NF-kB is activated and signals survival REACT_13696
Nicotinate metabolism REACT_11088
NOD1/2 Signaling Pathway REACT_75776
Nonhomologous End-joining (NHEJ) REACT_1022
Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) REACT_75822
Norepinephrine Neurotransmitter Release Cycle REACT_15418
NOTCH1 Intracellular Domain Regulates Transcription REACT_118780
NRAGE signals death through JNK REACT_13638
NRIF signals cell death from the nucleus REACT_13643
Nuclear Pore Complex (NPC) Disassembly REACT_163931
Oncogene Induced Senescence REACT_169325
Orc1 removal from chromatin REACT_1156
Orphan transporters REACT_267716
Oxidative Stress Induced Senescence REACT_169436
p130Cas linkage to MAPK signaling for integrins REACT_15381
P2Y receptors REACT_18289
p38MAPK events REACT_12065
p53-Independent DNA Damage Response REACT_2160
p75NTR recruits signalling complexes REACT_13415
PCP/CE pathway REACT_172581
PD-1 signaling REACT_19324
PDE3B signalling REACT_1451
PECAM1 interactions REACT_12519
PERK regulates gene expression REACT_18277
Phospholipase C-mediated cascade REACT_21310
phospho-PLA2 pathway REACT_15466
Phosphorylation of CD3 and TCR zeta chains REACT_12582
Phosphorylation of Emi1 REACT_6875
Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes REACT_308
Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes REACT_6362
PI3K/AKT activation REACT_12464
PI-3K cascade REACT_21270
PI3K Cascade REACT_976
PI3K events in ERBB2 signaling REACT_116008
PI3K events in ERBB4 signaling REACT_115961
PIP3 activates AKT signaling REACT_75829
PKA activation REACT_15530
PKA activation in glucagon signalling REACT_1946
PKA-mediated phosphorylation of CREB REACT_15497
PKA-mediated phosphorylation of key metabolic factors REACT_1525
Platelet degranulation REACT_318
Platelet homeostasis REACT_23876
Platelet sensitization by LDL REACT_23879
PLCG1 events in ERBB2 signaling REACT_115720
Polo-like kinase mediated events REACT_1006
Polymerase switching REACT_1792
Polymerase switching on the C-strand of the telomere REACT_7987
Prolactin receptor signaling REACT_115697
Propionyl-CoA catabolism REACT_993
Purine ribonucleoside monophosphate biosynthesis REACT_1776
Purine salvage REACT_1923
Pyrimidine biosynthesis REACT_21376
Pyrimidine salvage reactions REACT_655
RAF activation REACT_2077
RAF phosphorylates MEK REACT_614
Rap1 signalling REACT_23898
Recruitment of NuMA to mitotic centrosomes REACT_15510
Recycling of bile acids and salts REACT_11042
Recycling pathway of L1 REACT_22365
Regulation of actin dynamics for phagocytic cup formation REACT_160086
Regulation of AMPK activity via LKB1 REACT_21285
Regulation of APC/C activators between G1/S and early anaphase REACT_6837
Regulation of HSF1-mediated heat shock response REACT_200780
Regulation of insulin secretion REACT_18325
Regulation of KIT signaling REACT_111225
Regulation of PLK1 Activity at G2/M Transition REACT_160315
Regulation of pyruvate dehydrogenase (PDH) complex REACT_12528
Regulation of Rheb GTPase activity by AMPK REACT_21393
Regulation of signaling by CBL REACT_23787
Release of eIF4E REACT_6836
Resolution of Sister Chromatid Cohesion REACT_150425
Retinoid cycle disease events REACT_160130
Ribosomal scanning and start codon recognition REACT_931
RIG-I/MDA5 mediated induction of IFN-alpha/beta pathways REACT_25359
RIP-mediated NFkB activation via ZBP1 REACT_118563
RMTs methylate histone arginines REACT_228108
RNA Polymerase II Transcription Initiation And Promoter Clearance REACT_834
RNA Polymerase I Promoter Opening REACT_2232
Role of Abl in Robo-Slit signaling REACT_19230
Role of DCC in regulating apoptosis REACT_22128
Role of LAT2/NTAL/LAB on calcium mobilization REACT_163769
Role of phospholipids in phagocytosis REACT_160158
Role of second messengers in netrin-1 signaling REACT_22228
RSK activation REACT_20510
S33 mutants of beta-catenin aren't phosphorylated REACT_228159
S37 mutants of beta-catenin aren't phosphorylated REACT_228251
S45 mutants of beta-catenin aren't phosphorylated REACT_228137
S6K1-mediated signalling REACT_6754
S6K1 signalling REACT_6772
SCF(Skp2)-mediated degradation of p27/p21 REACT_9003
Sema3A PAK dependent Axon repulsion REACT_19236
SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion REACT_19279
Sema4D induced cell migration and growth-cone collapse REACT_19277
Sema4D mediated inhibition of cell attachment and migration REACT_19266
Senescence-Associated Secretory Phenotype (SASP) REACT_169168
Serotonin Neurotransmitter Release Cycle REACT_15425
SHC1 events in EGFR signaling REACT_12579
SHC1 events in ERBB2 signaling REACT_115993
SHC1 events in ERBB4 signaling REACT_116005
SHC activation REACT_1661
SHC-mediated cascade REACT_21374
SHC-related events triggered by IGF1R REACT_150139
Sialic acid metabolism REACT_200874
Signal attenuation REACT_508
Signaling by activated point mutants of FGFR1 REACT_121153
Signaling by activated point mutants of FGFR3 REACT_121337
Signaling by Activin REACT_150238
Signaling by BMP REACT_12034
Signaling by constitutively active EGFR REACT_115852
Signaling by EGFR REACT_9417
Signaling by ERBB2 REACT_115755
Signaling by ERBB4 REACT_115596
Signaling by FGFR REACT_9470
Signaling by FGFR1 amplification mutants REACT_120827
Signaling by FGFR1 fusion mutants REACT_121141
Signaling by FGFR2 amplification mutants REACT_121255
Signaling by FGFR4 mutants REACT_121286
Signaling by FGFR mutants REACT_121398
Signaling by Hippo REACT_118607
Signaling by Insulin receptor REACT_498
Signaling by Leptin REACT_169118
Signaling by NODAL REACT_111057
Signaling by PDGF REACT_16888
Signaling by SCF-KIT REACT_111040
Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) REACT_150359
Signalling to ERK5 REACT_12020
Signalling to STAT3 REACT_12049
Signal regulatory protein (SIRP) family interactions REACT_23916
Signal transduction by L1 REACT_22272
SMAD2/3 MH2 Domain Mutants in Cancer REACT_169165
SMAD2/3 Phosphorylation Motif Mutants in Cancer REACT_169103
SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription REACT_120734
Smooth Muscle Contraction REACT_20558
Sphingolipid de novo biosynthesis REACT_115810
Spry regulation of FGF signaling REACT_111080
Stabilization of p53 REACT_309
STAT6-mediated induction of chemokines REACT_163734
Stimulation of the cell death response by PAK-2p34 REACT_13532
Stimuli-sensing channels REACT_160189
STING mediated induction of host immune responses REACT_147841
Striated Muscle Contraction REACT_16969
Sulfur amino acid metabolism REACT_115639
SUMO is conjugated to E1 (UBA2:SAE1) REACT_163812
Synthesis and interconversion of nucleotide di- and triphosphates REACT_21330
Synthesis of bile acids and bile salts via 24-hydroxycholesterol REACT_11053
Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol REACT_11041
Synthesis of Dolichyl-phosphate REACT_22230
Synthesis of IP3 and IP4 in the cytosol REACT_150312
Synthesis of IPs in the nucleus REACT_150275
Synthesis of PC REACT_121238
Synthesis of PE REACT_120919
Synthesis of PIPs at the early endosome membrane REACT_120756
Synthesis of PIPs at the ER membrane REACT_121168
Synthesis of PIPs at the Golgi membrane REACT_120836
Synthesis of PIPs at the late endosome membrane REACT_120918
Synthesis of PIPs at the plasma membrane REACT_121025
Synthesis of pyrophosphates in the cytosol REACT_150188
Synthesis of very long-chain fatty acyl-CoAs REACT_380
t(4;14) translocations of FGFR3 REACT_121011
T41 mutants of beta-catenin aren't phosphorylated REACT_228261
TAK1 activates NFkB by phosphorylation and activation of IKKs complex REACT_21281
Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation REACT_111176
TGF-beta receptor signaling activates SMADs REACT_120850
TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) REACT_120726
TGFBR1 KD Mutants in Cancer REACT_169263
TGFBR2 Kinase Domain Mutants in Cancer REACT_169440
The canonical retinoid cycle in rods (twilight vision) REACT_160156
The NLRP1 inflammasome REACT_75927
The NLRP3 inflammasome REACT_75808
The proton buffering model REACT_6196
Tie2 Signaling REACT_12621
TRAF3-dependent IRF activation pathway REACT_25026
TRAF6 mediated induction of TAK1 complex REACT_25351
TRAF6 mediated IRF7 activation REACT_24938
TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling REACT_25120
TRAF6 mediated NF-kB activation REACT_24969
Trafficking and processing of endosomal TLR REACT_118632
Trafficking of AMPA receptors REACT_18307
Trafficking of dietary sterols REACT_13781
Trafficking of GluR2-containing AMPA receptors REACT_18422
Transcriptional activation of mitochondrial biogenesis REACT_200608
Transcription of the HIV genome REACT_6233
Transferrin endocytosis and recycling REACT_25283
Translocation of GLUT4 to the plasma membrane REACT_147867
Translocation of ZAP-70 to Immunological synapse REACT_12596
Transport and synthesis of PAPS REACT_6840
Triglyceride Biosynthesis REACT_1190
Tristetraprolin (TTP) destabilizes mRNA REACT_25064
TRKA activation by NGF REACT_11060
Ubiquitin-dependent degradation of Cyclin D1 REACT_4
Ubiquitin Mediated Degradation of Phosphorylated Cdc25A REACT_1614
Uptake and function of anthrax toxins REACT_228255
Urea cycle REACT_847
Vasopressin regulates renal water homeostasis via Aquaporins REACT_24023
VEGFA-VEGFR2 Pathway REACT_228166
VEGFR2 mediated cell proliferation REACT_228024
VEGFR2 mediated vascular permeability REACT_228016
Vitamin B1 (thiamin) metabolism REACT_11117
Vitamin B2 (riboflavin) metabolism REACT_11070
Vitamins B6 activation to pyridoxal phosphate REACT_25012
WNT5A-dependent internalization of FZD4 REACT_172599
WNT mediated activation of DVL REACT_200668
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