Selenium micronutrient network (WP15)

Homo sapiens

The selenium-centred micronutrient biological network. The most relevant biochemical processes related to selenium in the context of metabolism, oxidation and inflammation are represented. Also, the compartmental separation (intracellular vs. plasma) is presented, identifying the selenium centred plasma metabolome. A selenoprotein database exists at: http://www.selenodb.org. Proteins on this pathway have targeted assays available via the [https://assays.cancer.gov/available_assays?wp_id=WP15 CPTAC Assay Portal]

Authors

Egoyenechea , Alex Pico , Thomas Kelder , Ben Van Ommen , Chris Evelo , Martijn Van Iersel , Jildau Bouwman , Kristina Hanspers , Damariz Rivero , Andra Waagmeester , Egon Willighagen , Martina Summer-Kutmon , Marianthi Kalafati , Denise Slenter , Eric Weitz , Marvin Martens , and Susan Coort

Activity

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Organisms

Homo sapiens

Communities

Micronutrients

Annotations

Pathway Ontology

classic metabolic pathway selenoamino acid metabolic pathway

Participants

Label Type Compact URI Comment
Lipoxin A4 Metabolite hmdb:HMDB0004385
PGD2 Metabolite hmdb:HMDB0001403 Prostaglandin D2
Arachidonic acid Metabolite hmdb:HMDB0001043
PGE1 Metabolite hmdb:HMDB0001442 Prostaglandin E1
Thromboxane B2 Metabolite hmdb:HMDB0003252
Lipoxin B4 Metabolite hmdb:HMDB0005082
Thromboxane A2 Metabolite hmdb:HMDB0001452
Linoleic acid Metabolite hmdb:HMDB0000673
a-Tocopherol Metabolite hmdb:HMDB0001893
F2-Isoprostane Metabolite wikidata:Q33659470
DHA Metabolite hmdb:HMDB0002183 Docosahexaenoic acid
8-Isoprostaglandin F2a Metabolite hmdb:HMDB0005083
PGI2 Metabolite hmdb:HMDB0001335 Prostaglandin I2
PGE2 Metabolite hmdb:HMDB0001220 Prostaglandin E2
MDA Metabolite hmdb:HMDB0006112 Malondialdehyde
PGF2a Metabolite hmdb:HMDB0001139 Prostaglandin F2a
ALA Metabolite hmdb:HMDB0001388 Alpha-Linolenic acid
EPA Metabolite hmdb:HMDB0001999 Eicosapentaenoic acid
DGLA Metabolite hmdb:HMDB0002925 Dihomo-gamma-linolenic acid
8,11,14-Eicosatrienoic acid
DPA Metabolite hmdb:HMDB0001976 Docosapentaenoic acid
PGH3 Metabolite hmdb:HMDB0013040 Prostaglandin H3
PGG2 Metabolite hmdb:HMDB0003235 Prostaglandin G2
PGH2 Metabolite hmdb:HMDB0001381 Prostaglandin H2
PGE3 Metabolite hmdb:HMDB0002664 Prostaglandin E3
Kynurenine Metabolite hmdb:HMDB0000684
Iodine Metabolite wikidata:Q1103
R-Triiodothyronine (rT3) Metabolite chebi:28774 Reverse triiodothyronine
Triiodothyronine (T3) Metabolite chebi:18258
15-HETE Metabolite hmdb:HMDB0003876 15S-hydroxy-5Z,8Z,11Z,13E-eicosatetraenoic acid
Thyroxine (T4) Metabolite chebi:30660
5-HPETE Metabolite hmdb:HMDB0001193 5(S)-Hydroperoxyeicosatetraenoic acid
5,6-Epoxytetraene Metabolite kegg.compound:C14815
5-HETE Metabolite hmdb:HMDB0011134 5-hydroxyeicosatetraenoic acid
NADP+ Metabolite hmdb:HMDB0000217 Nicotinamide adenine dinucleotide phosphate-Oxidized
Uric acid Metabolite hmdb:HMDB0000289
Cysteine Metabolite hmdb:HMDB0000574
H2O2 Metabolite hmdb:HMDB0003125 Hydrogen peroxide
Copper Metabolite hmdb:HMDB0000657
Vitamin B12 Metabolite hmdb:HMDB0002174
5,10-Methylene-THF Metabolite hmdb:HMDB0001533 5,10-Methylenetetrahydrofolate
Tryptophan Metabolite hmdb:HMDB0000929
5-methyl-THF Metabolite hmdb:HMDB0001396 5-methyltetrahydrofolate
H2O Metabolite hmdb:HMDB0002111 Glutathione disulfide
Niacinamide Metabolite hmdb:HMDB0001406
Heme Metabolite hmdb:HMDB0003178
NADPH Metabolite hmdb:HMDB0000221 Nicotinamide adenine dinucleotide phosphate-Reduced
Lipoic acid Metabolite hmdb:HMDB0001451
Manganese Metabolite hmdb:HMDB0001333
FAD Metabolite hmdb:HMDB0001248 Flavin adenine dinucleotide
Methionine sulfoxide Metabolite hmdb:HMDB0002005
Dehydroascorbic acid Metabolite chebi:17242
Leukotriene A4 Metabolite hmdb:HMDB0001337
THF Metabolite hmdb:HMDB0001846 Tetrahydrofolic acid
Hydroxykynurenine Metabolite hmdb:HMDB0000732
Folic acid Metabolite hmdb:HMDB0000121
Selenium Metabolite hmdb:HMDB0001349
GSH Metabolite hmdb:HMDB0000125 Glutathione
Calcium Metabolite hmdb:HMDB0000464
Methionine Metabolite hmdb:HMDB0000696
FMN Metabolite hmdb:HMDB0001520 Flavin Mononucleotide
Selenocysteine Metabolite hmdb:HMDB0003288
Selenide Metabolite chebi:15076
Selenophosphate Metabolite chebi:16144
Leukotriene C4 Metabolite hmdb:HMDB0001198
Ascorbic acid Metabolite chebi:29073
Homocysteine Metabolite hmdb:HMDB0000742
ROS Metabolite chebi:26523 reactive oxygen species
http://en.wikipedia.org/wiki/Reactive_Oxygen_Species
RNS Metabolite chebi:62764 reactive nitrogen species
http://en.wikipedia.org/wiki/Reactive_nitrogen_species
Pyridoxal 5'-phosphate Metabolite hmdb:HMDB0001491
Serine Metabolite hmdb:HMDB0000187
Iron Metabolite wikidata:Q26840996
Hypoxanthine Metabolite hmdb:HMDB0000157
VLDL Metabolite chebi:39027 very-low-density lipoprotein
LDL Metabolite chebi:39026 low-density lipoprotein
Cholesterol Metabolite hmdb:HMDB0000067
HDL Metabolite chebi:39025 high-density lipoprotein
VLDL-TAG Metabolite chebi:47776 very-low-density lipoprotein-triglyceride
Triglyceride transport
HDL-C Metabolite chebi:47775 high-density lipoprotein cholesterol
Cholesterol transport
TAG Metabolite chebi:17855 Triglyceride
Triacylglycerol
HDL-C Metabolite chebi:47775 high-density lipoprotein cholesterol
oxLDL Metabolite chebi:60151 oxidized low-density lipoprotein
HDL/APOA1 Metabolite chebi:39025 high-density lipoprotein
ApoA-I is present on the majority of HDL particles and constitutes aprox 70% of the apolipoprotein content of HDL particles
HDL/SAA Metabolite chebi:39025 high-density lipoprotein
SAA circulates in plasma as a constituent of high density lipoproteins (HDL).
VLDL/APOB Metabolite chebi:39027 very-low-density lipoprotein
The VLDL is produced in the liver, contains one molecule of apoB100
O2 Metabolite hmdb:HMDB0001377
8-OHdG Metabolite hmdb:HMDB0003333 8-Hydroxy-deoxyguanosine
ADP Metabolite hmdb:HMDB0001341 Adenosine diphosphate
Leukotriene D4 Metabolite hmdb:HMDB0003080
Chlorine Metabolite hmdb:HMDB0000492
Cystathionine Metabolite hmdb:HMDB0000099
Dihydrolipoate Metabolite hmdb:HMDB0012210
ATP Metabolite hmdb:HMDB0000538 Adenosine triphosphate
Zinc Metabolite hmdb:HMDB0015532
GSSG Metabolite hmdb:HMDB0000656 Glutathione disulfide
Niacin Metabolite hmdb:HMDB0001488
Leukotriene B4 Metabolite hmdb:HMDB0001085
Quinolinic Acid Metabolite hmdb:HMDB0000232
PMP Metabolite hmdb:HMDB0001555 Pyridoxamine 5'-phosphate
NO Metabolite hmdb:HMDB0003378 Nitric oxide
O3 Metabolite chebi:25812 ozone
HNO2 Metabolite chebi:25567 Nitrous acid
NO2 Metabolite chebi:33101 Nitrogen dioxide
HOCl Metabolite hmdb:HMDB0001050 Hypochlorite
Fibrin Metabolite wikidata:Q27205
Riboflavin Metabolite hmdb:HMDB0000244
Ascorbate Metabolite chebi:38290
O2-radical (aka Hyperoxid or superoxide) Metabolite hmdb:HMDB0002168 Superoxide
Xanthine Metabolite hmdb:HMDB0000292
Nitrotyrosine Metabolite hmdb:HMDB0001904
ONOO-/ONOOH Metabolite hmdb:HMDB0002179 Peroxynitrite
Leukotriene E4 Metabolite hmdb:HMDB0002200
Leukotriene F4 Metabolite hmdb:HMDB0006465
Glucose Metabolite hmdb:HMDB0000122
Fructosamine Metabolite hmdb:HMDB0002030
RELA GeneProduct ncbigene:5970 nuclear factor of kappa light polypeptide gene enhancer in B-cells 3, p65
NFKB1 GeneProduct ncbigene:4790 nuclear factor NF-kappa-B p50 subunit
NFKB2 GeneProduct ncbigene:4791 nuclear factor of kappa light polypeptide gene enhancer in B-cells 2
FGA Protein ensembl:ENSG00000171560
COX2 Protein ncbigene:5743 EC 1.14.99.1
Cyclooxygenase 2
COX-2 inducible
COX1 Protein ncbigene:5742 EC 1.14.99.1
Cyclooxygenase 1
COX-1 constitutive
MTR Protein ncbigene:4548 EC 2.1.1.13
5-methyltetrahydrofolate-homocysteine methyltransferase
TRXR1 Protein ncbigene:7296 EC 1.8.1.9
Selenoprotein-thioredoxin reductase 1
CBS Protein ncbigene:875 EC 4.2.1.22
cystathionine-beta-synthase
KMO Protein ncbigene:8564 EC 1.14.13.9
kynurenine 3-hydroxylase
MPO Protein ncbigene:4353 EC 1.11.1.7
Myeloperoxidase
Catalase Protein ncbigene:847 EC 1.11.1.6
Factor VII Protein ncbigene:2155 EC 3.4.21.21
coagulation factor VII (serum prothrombin conversion accelerator)
Thrombin Protein ncbigene:2147 EC 3.4.21.5
coagulation factor II (thrombin)
tPA Protein ncbigene:5327 EC 3.4.21.68
plasminogen activator, tissue
PAI-1 Protein ncbigene:5054 Serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1
PLG Protein ncbigene:5340 EC 3.4.21.7
Plasminogen
GGT1 Protein ncbigene:2678 EC 2.3.2.2
gamma-glutamyltransferase 1
GPX 4 Protein ncbigene:2879 EC 1.11.1.12
Selenoprotein-glutathione peroxidase 4
TRXR2 Protein ncbigene:10587 EC 1.8.1.9
Selenoprotein-thioredoxin reductase 2
Xantine oxidase Protein ncbigene:7498 EC 1.17.3.2
http://en.wikipedia.org/wiki/Xanthine_oxidase
PRDX5 Protein ncbigene:25824 EC 1.11.1.15
peroxiredoxin 5
ALOX5 Protein ncbigene:240 EC 1.13.11.34
arachidonate 5-lipoxygenase
ALOX15B Protein ncbigene:247 EC 1.13.11.33
arachidonate 15-lipoxygenase, type B
SelR Protein ncbigene:51734 EC 1.8.4.-
Selenoprotein-selenoprotein X
SOD3 Protein ncbigene:6649 EC 1.15.1.1
superoxide dismutase 3, extracellular
PRDX1 Protein ncbigene:5052 EC 1.11.1.15
peroxiredoxin 1
RFK Protein ncbigene:55312 EC 2.7.1.26
riboflavin kinase
GPX 3 Protein ncbigene:2878 EC 1.11.1.9
Selenoprotein-glutathione peroxidase 3
CTH Protein ncbigene:1491 EC 4.4.1.1
cystathionase
PNPO Protein ncbigene:55163 EC 1.4.3.5
pyridoxamine 5'-phosphate oxidase
SelK Protein ncbigene:58515 Selenoprotein-selenoprotein K
Sep15 Protein ncbigene:9403 Selenoprotein-15 kDa selenoprotein
GPX 6 Protein ncbigene:257202 EC 1.11.1.9
Selenoprotein-glutathione peroxidase 6
Nicotinamidase Protein eccode:3.5.1.19 Catalysis of the reaction: nicotinamide + H2O = nicotinate + NH3 GO:0008936
GPX 3 Protein ncbigene:2878 Selenoprotein-glutathione peroxidase 3
GPX 2 Protein ncbigene:2877 EC 1.11.1.9
Selenoprotein-glutathione peroxidase 2
SelP Protein ncbigene:6414 Selenoprotein-selenoprotein P
Trx-S2 Protein ncbigene:7295 oxidized thioredoxin
PRDX4 Protein ncbigene:10549 EC 1.11.1.15
peroxiredoxin 4
GPX 1 Protein ncbigene:2876 EC 1.11.1.9
Selenoprotein-glutathione peroxidase 1
MTHFR Protein ncbigene:4524 EC 1.5.1.20
5,10-methylenetetrahydrofolate reductase
SelH Protein ncbigene:280636 Selenoprotein-selenoprotein H-chromosome 11 open reading frame 31
SPS2 Protein ncbigene:22928 EC2.7.9.3
Selenoprotein-selenophosphate synthetase 2
SelO Protein ncbigene:83642 Selenoprotein-selenoprotein O
Unknown function
SelN Protein ncbigene:57190 Selenoprotein-selenoprotein N, 1
DIO2 Protein ncbigene:1734 EC 1.97.1.10
Selenoprotein-deiodinase, iodothyronine, type II
SelT Protein ncbigene:51714 Selenoprotein-selenoprotein T
SelM Protein ncbigene:140606 Selenoprotein-selenoprotein M
DIO3 Protein ncbigene:1735 EC 1.97.1.11
Selenoprotein-deiodinase, iodothyronine type III
DIO1 Protein ncbigene:1733 EC 1.97.1.10
Selenoprotein-deiodinase, iodothyronine, type I
SelV Protein ncbigene:348303 Selenoprotein-selenoprotein V
Unknown function
SelI Protein ncbigene:85465 Selenoprotein-selenoprotein I
Unknown function
SelS Protein ncbigene:55829 Selenoprotein-selenoprotein S
SOD1 Protein ncbigene:6647 EC 1.15.1.1
superoxide dismutase 1, soluble
PRDX3 Protein ncbigene:10935 EC 1.11.1.15
peroxiredoxin 3
GSR Protein ncbigene:2936 EC 1.8.1.7
glutathione reductase
APOA1 Protein ncbigene:335 apolipoprotein A-I
APOB Protein ncbigene:338 apolipoprotein B
LDLR Protein ncbigene:3949 low density lipoprotein receptor
SAA4 Protein ncbigene:6291 serum amyloid A4, constitutive
SRB1 Protein ncbigene:949 scavenger receptor class B, member 1
ABCA1 Protein ncbigene:19 ATP-binding cassette, sub-family A (ABC1), member 1
APOA1-NO2Tyr Protein ncbigene:335 Nitrotyrosinated apolipoprotein A-I
ACT Protein ncbigene:12 alpha-1-antichymotrypsin
serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3
SAA2 Protein ncbigene:6289 serum amyloid A2
SAA1 Protein ncbigene:6288 serum amyloid A1
SAA3 Protein ncbigene:6290 serum amyloid A3 pseudogene
PRDX2 Protein ncbigene:7001 EC 1.11.1.15
peroxiredoxin 2
SOD2 Protein ncbigene:6648 EC 1.15.1.1
superoxide dismutase 2, mitochondrial
sICAM-1 Protein ncbigene:3383 soluble intercellular adhesion molecule 1
IL10 Protein ncbigene:3458 interferon, gamma
TNFa Protein ncbigene:7124 tumor necrosis factor (TNF superfamily, member 2)
IFNg Protein ncbigene:3458 interferon, gamma
ALB Protein ncbigene:213 albumin
INS Protein ncbigene:3630 Insulin
IL1B Protein ncbigene:3553 interleukin 1, beta
INSR Protein ncbigene:3643 Insulin receptor
HBB Protein ncbigene:3043 hemoglobin, beta
CRP Protein ncbigene:1401 C-reactive protein, pentraxin-related
Fibrin Protein wikidata:Q27205
CCL2 Protein ncbigene:6347 chemokine (C-C motif) ligand 2
FLAP Protein ncbigene:241 arachidonate 5-lipoxygenase-activating protein
IL6 Protein ncbigene:3569 interleukin 6 (interferon, beta 2)
HBA1 Protein ncbigene:3039 hemoglobin, alpha 1
SelW Protein ncbigene:6415 Selenoprotein-selenoprotein W
TRXR1 Protein ncbigene:7296 Selenoprotein-thioredoxin reductase 1
Kynureninase Protein ncbigene:8942 EC 3.7.1.3
Trx-(SH)2 Protein ncbigene:7295 reduced thioredoxin
TRXR3 Protein ncbigene:114112 EC 1.8.1.9
Selenoprotein-thioredoxin reductase 3
FLAD1 Protein ncbigene:80308 EC 2.7.7.2
FAD1 flavin adenine dinucleotide synthetase homolog (S. cerevisiae)
FGB Protein ensembl:ENSG00000171564
FGG Protein ensembl:ENSG00000171557

References

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