HumanCyc Pathways Dataset

Description sets of proteins participating in pathways
Measurement association by literature curation
Association protein-pathway associations from curated pathways
Category structural or functional annotations
Resource HumanCyc
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Last Updated
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  1. 932 genes
  2. 286 pathways
  3. 1839 gene-pathway associations

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pathway Gene Sets

286 sets of proteins participating in pathways from the HumanCyc Pathways dataset.

Gene Set Description
α-tocopherol degradation
β-alanine degradation The chemical reactions and pathways resulting in the breakdown of beta-alanine (3-aminopropanoic acid), an achiral amino acid and an isomer of alanine. It occurs free (e.g. in brain) and in combination (e.g. in pantothenate) but it is not a constituent of proteins.
γ-glutamyl cycle
γ-linolenate biosynthesis
(S)-reticuline biosynthesis The chemical reactions and pathways resulting in the formation of (S)-reticuline.
1,25-dihydroxyvitamin D3 biosynthesis
1D-myo-inositol hexakisphosphate biosynthesis II (mammalian)
1D-myo-inositol hexakisphosphate biosynthesis V (from Ins(1,3,4)P3)
2'-deoxy-α-D-ribose 1-phosphate degradation
2-amino-3-carboxymuconate semialdehyde degradation to glutaryl-CoA
2-oxobutanoate degradation
3-phosphoinositide biosynthesis
3-phosphoinositide degradation
4-aminobutyrate degradation
4-hydroxy-2-nonenal detoxification
4-hydroxybenzoate biosynthesis
4-hydroxyproline degradation The chemical reactions and pathways resulting in the breakdown of 4-hydroxyproline, C5H9NO3, a derivative of the amino acid proline.
5-aminoimidazole ribonucleotide biosynthesis
7-(3-amino-3-carboxypropyl)-wyosine biosynthesis
acetate conversion to acetyl-CoA
acetyl-CoA biosynthesis from citrate
acyl carrier protein metabolism
acyl-CoA hydrolysis
adenine and adenosine salvage I
adenine and adenosine salvage II
adenine and adenosine salvage III
adenosine deoxyribonucleotides de novo biosynthesis
adenosine nucleotides degradation
adenosine ribonucleotides de novo biosynthesis
alanine biosynthesis/degradation
allopregnanolone biosynthesis
anandamide degradation
androgen biosynthesis The chemical reactions and pathways resulting in the formation of androgens, C19 steroid hormones that can stimulate the development of male sexual characteristics.
ascorbate recycling (cytosolic)
asparagine biosynthesis The chemical reactions and pathways resulting in the formation of asparagine, 2-amino-3-carbamoylpropanoic acid.
asparagine degradation The chemical reactions and pathways resulting in the breakdown of asparagine, 2-amino-3-carbamoylpropanoic acid.
aspartate biosynthesis The chemical reactions and pathways resulting in the formation of aspartate, the anion derived from aspartic acid, 2-aminobutanedioic acid.
aspirin triggered resolvin D biosynthesis
aspirin triggered resolvin E biosynthesis
aspirin-triggered lipoxin biosynthesis
bile acid biosynthesis, neutral pathway
BMP Signalling Pathway A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
C20 prostanoid biosynthesis
cardiolipin biosynthesis
carnosine biosynthesis The chemical reactions and pathways resulting in the formation of the dipeptide beta-alanyl-L-histidine (carnosine).
catecholamine biosynthesis The chemical reactions and pathways resulting in the formation of any of a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine.
CDP-diacylglycerol biosynthesis The chemical reactions and pathways resulting in the formation of CDP-diacylglycerol, CDP-1,2-diacylglycerol, a substance composed of diacylglycerol in glycosidic linkage with cytidine diphosphate.
ceramide de novo biosynthesis
cholesterol biosynthesis I
cholesterol biosynthesis II (via 24,25-dihydrolanosterol)
cholesterol biosynthesis III (via desmosterol)
choline degradation The chemical reactions and pathways resulting in the breakdown of choline (2-hydroxyethyltrimethylammonium), an amino alcohol that occurs widely in living organisms as a constituent of certain types of phospholipids and in the neurotransmitter acetylcholine.
chondroitin sulfate degradation (metazoa)
citrulline-nitric oxide cycle
CMP phosphorylation The process of introducing a phosphate group into CMP, cytidine monophosphate, to produce CDP. Addition of two phosphate groups produces CTP.
CMP-N-acetylneuraminate biosynthesis I (eukaryotes)
coenzyme A biosynthesis The chemical reactions and pathways resulting in the formation of coenzyme A, 3'-phosphoadenosine-(5')diphospho(4')pantatheine, an acyl carrier in many acylation and acyl-transfer reactions in which the intermediate is a thiol ester.
creatine biosynthesis The chemical reactions and pathways resulting in the formation of creatine, N-[amino(imino)methyl]-N-methylglycine. Creatine is formed by a process beginning with amidino group transfer from L-arginine to glycine to form guanidinoacetate, followed by methyl group transfer from S-adenosyl-L-methionine to guanidinoacetate; it is then is phosphorylated to form a pool that stores high energy phosphate for the replenishment of ATP during periods of high, or fluctuating energy demand. In animals, most creatine is transported to and used in muscle.
creatine-phosphate biosynthesis
cysteine biosynthesis The chemical reactions and pathways resulting in the formation of cysteine, 2-amino-3-mercaptopropanoic acid.
cysteine biosynthesis/homocysteine degradation (trans-sulfuration)
D-galactose degradation V (Leloir pathway)
D-glucuronate degradation The chemical reactions and pathways resulting in the breakdown of D-glucuronate, the D-enantiomer of glucuronate.
D-mannose degradation
D-myo-inositol (1,3,4)-trisphosphate biosynthesis
D-myo-inositol (1,4,5)-trisphosphate biosynthesis
D-myo-inositol (1,4,5)-trisphosphate degradation
D-myo-inositol (1,4,5,6)-tetrakisphosphate biosynthesis
D-myo-inositol (3,4,5,6)-tetrakisphosphate biosynthesis
D-myo-inositol-5-phosphate metabolism
dermatan sulfate biosynthesis (late stages)
dermatan sulfate degradation (metazoa)
diphthamide biosynthesis
dolichol and dolichyl phosphate biosynthesis
dolichyl-diphosphooligosaccharide biosynthesis
dopamine degradation The chemical reactions and pathways resulting in the breakdown of dopamine, a catecholamine neurotransmitter and a metabolic precursor of noradrenaline and adrenaline.
dTMP de novo biosynthesis (mitochondrial)
eicosapentaenoate biosynthesis
epoxysqualene biosynthesis
ethanol degradation II
ethanol degradation IV
eumelanin biosynthesis
fatty acid α-oxidation A metabolic pathway by which 3-methyl branched fatty acids are degraded. These compounds are not degraded by the normal peroxisomal beta-oxidation pathway, because the 3-methyl blocks the dehydrogenation of the hydroxyl group by hydroxyacyl-CoA dehydrogenase. The 3-methyl branched fatty acid is converted in several steps to pristenic acid, which can then feed into the beta-oxidative pathway.
fatty acid α-oxidation III
fatty acid β-oxidation A fatty acid oxidation process that results in the complete oxidation of a long-chain fatty acid. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and occurs by successive cycles of reactions during each of which the fatty acid is shortened by a two-carbon fragment removed as acetyl coenzyme A; the cycle continues until only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).
fatty acid β-oxidation (peroxisome)
fatty acid β-oxidation (unsaturated, odd number) A fatty acid beta-oxidation pathway by which fatty acids having cis-double bonds on odd-numbered carbons are degraded. In this pathway, a cis-3-enoyl-CoA is generated by the core beta-oxidation pathway, and then converted to a trans-2-enoyl-CoA, which can return to the core beta-oxidation pathway for complete degradation. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and ends when only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).
fatty acid activation
fatty acid biosynthesis initiation
flavin biosynthesis
folate polyglutamylation
folate transformations
formaldehyde oxidation
fructose 2,6-bisphosphate synthesis/dephosphorylation
GABA shunt The chemical reactions and pathways resulting in the formation of succinate from glutamate. Also known as GABA (gamma-aminobutyrate) shunt since it channels glutamate into the TCA cycle bypassing two steps of that cycle. There are three enzymes involved in the GABA shunt: glutamate decarboxylase (GAD), GABA aminotransferase (GABA-TA), and succinate semialdehyde dehydrogenase (SSADH). These three enzymes acting in concert to convert glutamate into succinate. The GABA shunt is predominantly associated with neurotransmission in the mammalian brain. It is also present in nonneuronal cells, in plants, in unicellular eukaryotes, and in prokaryotes.
GDP-glucose biosynthesis II
GDP-L-fucose biosynthesis I (from GDP-D-mannose)
GDP-L-fucose biosynthesis II (from L-fucose)
GDP-mannose biosynthesis The chemical reactions and pathways resulting in the formation of GDP-mannose, a substance composed of mannose in glycosidic linkage with guanosine diphosphate.
geranylgeranyldiphosphate biosynthesis The chemical reactions and pathways resulting in the formation of geranylgeranyl diphosphate.
gluconeogenesis The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
glutamate biosynthesis/degradation
glutamate dependent acid resistance
glutamate removal from folates
glutamine biosynthesis The chemical reactions and pathways resulting in the formation of glutamine, 2-amino-4-carbamoylbutanoic acid.
glutamine degradation/glutamate biosynthesis
glutaryl-CoA degradation
glutathione biosynthesis The chemical reactions and pathways resulting in the formation of glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins.
glutathione redox reactions I
glutathione-mediated detoxification
glycerol degradation The chemical reactions and pathways resulting in the breakdown of glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
glycerol-3-phosphate shuttle
glycine betaine degradation The chemical reactions and pathways resulting in the breakdown of glycine betaine, N-trimethylglycine.
glycine biosynthesis The chemical reactions and pathways resulting in the formation of glycine, aminoethanoic acid.
glycine cleavage
glycine/serine biosynthesis
glycogenolysis The chemical reactions and pathways resulting in the breakdown of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues.
glycolysis The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
guanine and guanosine salvage
guanosine deoxyribonucleotides de novo biosynthesis
guanosine nucleotides de novo biosynthesis
guanosine nucleotides degradation
guanosine ribonucleotides de novo biosynthesis
heme biosynthesis The chemical reactions and pathways resulting in the formation of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, from less complex precursors.
heme biosynthesis from uroporphyrinogen-III I
heme degradation The chemical reactions and pathways resulting in the breakdown of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
histamine biosynthesis The chemical reactions and pathways resulting in the formation of histamine, a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans.
histamine degradation The chemical reactions and pathways resulting in the breakdown of histamine, a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans.
histidine degradation The chemical reactions and pathways resulting in the breakdown of histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.
homocarnosine biosynthesis
hydrogen sulfide biosynthesis (trans-sulfuration)
hypusine biosynthesis The modification of peptidyl-lysine to form hypusine, peptidyl-N6-(4-amino-2-hydroxybutyl)-L-lysine.
inosine-5'-phosphate biosynthesis
inositol pyrophosphates biosynthesis
iron-sulfur cluster biosynthesis
ketogenesis
ketolysis
L-carnitine biosynthesis
L-cysteine degradation I
L-cysteine degradation II
L-dopa degradation
L-dopachrome biosynthesis
L-glutamine tRNA biosynthesis
L-kynurenine degradation The chemical reactions and pathways resulting in the breakdown of L-kynurenine, the L-enantiomer of the amino acid kynurenine (3-(2-aminobenzoyl)-alanine).
L-serine degradation The chemical reactions and pathways resulting in the breakdown of L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
lactate fermentation (reoxidation of cytosolic NADH)
lactose degradation III
lanosterol biosynthesis
leukotriene biosynthesis The chemical reactions and pathways resulting in the formation of leukotriene, a pharmacologically active substance derived from a polyunsaturated fatty acid, such as arachidonic acid.
lipoxin biosynthesis The chemical reactions and pathways resulting in the formation of a lipoxin. A lipoxin is a non-classic eicosanoid and signalling molecule that has four conjugated double bonds and is derived from arachidonic acid.
lysine degradation I (saccharopine pathway)
lysine degradation II (pipecolate pathway)
malate-aspartate shuttle The process of transferring reducing equivalents from the cytosol into the mitochondria; NADH is used to synthesise malate in the cytosol; this compound is then transported into the mitochondria where it is converted to oxaloacetate using NADH, the oxaloacetate reacts with gluamate to form aspartate, and the aspartate then returns to the cytosol to complete the cycle.
MAP kinase cascade An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
melatonin degradation II
methionine degradation The chemical reactions and pathways resulting in the breakdown of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
methionine salvage
methylglyoxal degradation I
methylglyoxal degradation III
methylglyoxal degradation VI
methylthiopropionate biosynthesis
mevalonate pathway
mitochondrial L-carnitine shuttle
molybdenum cofactor biosynthesis
mRNA capping
mucin core 1 and core 2 O-glycosylation
myo-inositol de novo biosynthesis
N-acetylglucosamine degradation I
N-acetylglucosamine degradation II
NAD biosynthesis from 2-amino-3-carboxymuconate semialdehyde
NAD de novo biosynthesis
NAD phosphorylation and dephosphorylation
NAD salvage Any process that generates nicotinamide adenine dinucleotide (NAD) from derivatives of it, without de novo synthesis; salvage is usually from the degradation products nicotinic acid (Na) and nicotinamide (Nam).
NADH repair
noradrenaline and adrenaline degradation
oleate biosynthesis
ornithine de novo biosynthesis
oxidative ethanol degradation III
oxidized GTP and dGTP detoxification
pentose phosphate pathway The process in which glucose is oxidized, coupled to NADPH synthesis. Glucose 6-P is oxidized with the formation of carbon dioxide (CO2), ribulose 5-phosphate and reduced NADP; ribulose 5-P then enters a series of reactions interconverting sugar phosphates. The pentose phosphate pathway is a major source of reducing equivalents for biosynthesis reactions and is also important for the conversion of hexoses to pentoses.
pentose phosphate pathway (non-oxidative branch) The branch of the pentose-phosphate shunt which does not involve oxidation reactions. It comprises a series of sugar phosphate interconversions, starting with ribulose 5-P and producing fructose 6-P and glyceraldehyde 3-P.
pentose phosphate pathway (oxidative branch) The branch of the pentose-phosphate shunt which involves the oxidation of glucose 6-P and produces ribulose 5-P, reduced NADP+ and carbon dioxide (CO2).
phenylalanine degradation/tyrosine biosynthesis
phenylethylamine degradation I
phosphatidylcholine biosynthesis The chemical reactions and pathways resulting in the formation of phosphatidylcholines, any of a class of glycerophospholipids in which the phosphatidyl group is esterified to the hydroxyl group of choline.
phosphatidylethanolamine biosynthesis II
phosphatidylserine biosynthesis I
phospholipases
phytol degradation
progesterone biosynthesis The chemical reactions and pathways resulting in the formation of progesterone, a steroid hormone produced in the ovary which prepares and maintains the uterus for pregnancy. Also found in plants.
proline biosynthesis The chemical reactions and pathways resulting in the formation of proline (pyrrolidine-2-carboxylic acid), a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins.
proline degradation The chemical reactions and pathways resulting in the breakdown of proline (pyrrolidine-2-carboxylic acid), a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins.
propionyl-CoA degradation The chemical reactions and pathways resulting in the breakdown of propionyl-CoA.
protein citrullination The hydrolysis of peptidyl-arginine to form peptidyl-citrulline.
protein O-[N-acetyl]-glucosylation
PRPP biosynthesis
purine deoxyribonucleosides degradation
purine deoxyribonucleosides salvage
purine nucleotides de novo biosynthesis
purine nucleotides degradation
purine ribonucleosides degradation to ribose-1-phosphate
putrescine biosynthesis I
putrescine biosynthesis II
putrescine degradation III
pyridoxal 5'-phosphate salvage Any process that generates pyridoxal 5'-phosphate, the active form of vitamin B6, from derivatives of it without de novo synthesis.
pyrimidine deoxyribonucleosides degradation
pyrimidine deoxyribonucleosides salvage
pyrimidine deoxyribonucleotide phosphorylation
pyrimidine deoxyribonucleotides biosynthesis from CTP
pyrimidine deoxyribonucleotides de novo biosynthesis
pyrimidine ribonucleosides degradation
pyrimidine ribonucleosides salvage I
Rapoport-Luebering glycolytic shunt
resolvin D biosynthesis
retinoate biosynthesis I
retinoate biosynthesis II
retinol biosynthesis
S-adenosyl-L-methionine biosynthesis
S-methyl-5'-thioadenosine degradation
S-methyl-5-thio-α-D-ribose 1-phosphate degradation
selenocysteine biosynthesis The chemical reactions and pathways resulting in the formation of selenocysteine, an essential component of glutathione peroxidase and some other proteins.
serine and glycine biosynthesis
serine biosynthesis (phosphorylated route)
serotonin and melatonin biosynthesis
serotonin degradation The chemical reactions and pathways resulting in the breakdown of serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties.
sorbitol degradation I
spermidine biosynthesis The chemical reactions and pathways resulting in the formation of spermidine, N-(3-aminopropyl)-1,4-diaminobutane.
spermine and spermidine degradation I
spermine biosynthesis The chemical reactions and pathways resulting in the formation of spermine, a polybasic amine found in human sperm, in ribosomes and in some viruses and involved in nucleic acid packaging.
sphingomyelin metabolism/ceramide salvage
sphingosine and sphingosine-1-phosphate metabolism
stearate biosynthesis
sucrose degradation The chemical reactions and pathways resulting in the breakdown of sucrose, the disaccharide fructofuranosyl-glucopyranoside.
sulfate activation for sulfonation
sulfite oxidation
superoxide radicals degradation
superpathway of cholesterol biosynthesis
superpathway of choline degradation to L-serine
superpathway of D-myo-inositol (1,4,5)-trisphosphate metabolism
superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate)
superpathway of inositol phosphate compounds
superpathway of methionine degradation
superpathway of purine nucleotide salvage
superpathway of pyrimidine deoxyribonucleoside salvage
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis
superpathway of pyrimidine ribonucleotides de novo biosynthesis
taurine biosynthesis The chemical reactions and pathways resulting in the formation of taurine (2-aminoethanesulfonic acid), a sulphur-containing amino acid derivative important in the metabolism of fats.
terminal O-glycans residues modification
tetrahydrobiopterin de novo biosynthesis
tetrahydrofolate salvage from 5,10-methenyltetrahydrofolate
tetrapyrrole biosynthesis The chemical reactions and pathways leading to the formation of tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next.
the visual cycle I (vertebrates)
thiamin salvage III
thio-molybdenum cofactor biosynthesis
thioredoxin pathway
thiosulfate disproportionation III (rhodanese)
threonine degradation The chemical reactions and pathways resulting in the breakdown of threonine (2-amino-3-hydroxybutyric acid), a polar, uncharged, essential amino acid found in peptide linkage in proteins.
thymine degradation The chemical reactions and pathways resulting in the breakdown of thymine, 5-methyluracil, one of the two major pyrimidine bases present (as thymidine) in DNA but not found in RNA other than (as ribothymidine) in transfer RNA, where it is a minor base.
thyroid hormone biosynthesis
thyroid hormone metabolism I (via deiodination)
thyroid hormone metabolism II (via conjugation and/or degradation)
thyronamine and iodothyronamine metabolism
trans, trans-farnesyl diphosphate biosynthesis
trehalose degradation The chemical reactions and pathways resulting in the breakdown of trehalose, a disaccharide isomeric with sucrose and obtained from certain lichens and fungi.
triacylglycerol biosynthesis The chemical reactions and pathways resulting in the formation of a triglyceride, any triester of glycerol.
triacylglycerol degradation
tRNA charging
tRNA splicing
tryptophan degradation The chemical reactions and pathways resulting in the breakdown of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid.
tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde
tryptophan degradation X (mammalian, via tryptamine)
tyrosine degradation The chemical reactions and pathways resulting in the breakdown of tyrosine, an aromatic amino acid, 2-amino-3-(4-hydroxyphenyl)propanoic acid.
ubiquinol-10 biosynthesis
UDP-D-xylose and UDP-D-glucuronate biosynthesis
UDP-N-acetyl-D-galactosamine biosynthesis I
UDP-N-acetyl-D-galactosamine biosynthesis II
UDP-N-acetyl-D-glucosamine biosynthesis II
UMP biosynthesis The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate.
uracil degradation The chemical reactions and pathways resulting in the breakdown of uracil, 2,4-dioxopyrimidine, one of the pyrimidine bases occurring in RNA, but not in DNA.
urate biosynthesis/inosine 5'-phosphate degradation
urea cycle The sequence of reactions by which arginine is synthesized from ornithine, then cleaved to yield urea and regenerate ornithine. The overall reaction equation is NH3 + CO2 + aspartate + 3 ATP + 2 H2O = urea + fumarate + 2 ADP + 2 phosphate + AMP + diphosphate.
UTP and CTP de novo biosynthesis
UTP and CTP dephosphorylation I
UTP and CTP dephosphorylation II
wybutosine biosynthesis
zymosterol biosynthesis The chemical reactions and pathways resulting in the formation of zymosterol, (5alpha-cholesta-8,24-dien-3beta-ol).