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 CoortActivity
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Cited In
- Selenotranscriptome Network in Non-alcoholic Fatty Liver Disease (2021).
- Copy Number Variants Captured by the Array Comparative Genomic Hybridization in a Cohort of Patients Affected with Hereditary Colorectal Cancer in Sri Lanka: The First CNV Analysis Study of the Hereditary Colorectal Cancer in the Sri Lankan Population (2021).
- Identification of biomarkers and pathways for the SARS-CoV-2 infections that make complexities in pulmonary arterial hypertension patients (2021).
- WikiPathways: connecting communities (2021).
- Network-based identification genetic effect of SARS-CoV-2 infections to Idiopathic pulmonary fibrosis (IPF) patients (2020).
- Nutrigenetics, Nutrigenomics, and Selenium (2011).
- The Micronutrient Genomics Project: a community-driven knowledge base for micronutrient research (2010).
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Organisms
Homo sapiensCommunities
MicronutrientsAnnotations
Pathway Ontology
classic metabolic pathway selenoamino acid metabolic pathwayLabel | 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 acid8,11,14-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 specieshttp://en.wikipedia.org/wiki/Reactive_Oxygen_Species |
RNS | Metabolite | chebi:62764 | reactive nitrogen specieshttp://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-triglycerideTriglyceride transport |
HDL-C | Metabolite | chebi:47775 | high-density lipoprotein cholesterolCholesterol transport |
TAG | Metabolite | chebi:17855 | TriglycerideTriacylglycerol |
HDL-C | Metabolite | chebi:47775 | high-density lipoprotein cholesterol |
oxLDL | Metabolite | chebi:60151 | oxidized low-density lipoprotein |
HDL/APOA1 | Metabolite | chebi:39025 | high-density lipoproteinApoA-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 lipoproteinSAA circulates in plasma as a constituent of high density lipoproteins (HDL). |
VLDL/APOB | Metabolite | chebi:39027 | very-low-density lipoproteinThe 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 1.14.99.1Cyclooxygenase 2COX-2 inducible |
COX1 | Protein | ncbigene:5742 | EC 1.14.99.1Cyclooxygenase 1COX-1 constitutive |
MTR | Protein | ncbigene:4548 | EC 2.1.1.135-methyltetrahydrofolate-homocysteine methyltransferase |
TRXR1 | Protein | ncbigene:7296 | EC 1.8.1.9Selenoprotein-thioredoxin reductase 1 |
CBS | Protein | ncbigene:875 | EC 4.2.1.22cystathionine-beta-synthase |
KMO | Protein | ncbigene:8564 | EC 1.14.13.9kynurenine 3-hydroxylase |
MPO | Protein | ncbigene:4353 | EC 1.11.1.7Myeloperoxidase |
Catalase | Protein | ncbigene:847 | EC 1.11.1.6 |
Factor VII | Protein | ncbigene:2155 | EC 3.4.21.21coagulation factor VII (serum prothrombin conversion accelerator) |
Thrombin | Protein | ncbigene:2147 | EC 3.4.21.5coagulation factor II (thrombin) |
tPA | Protein | ncbigene:5327 | EC 3.4.21.68plasminogen 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 3.4.21.7Plasminogen |
GGT1 | Protein | ncbigene:2678 | EC 2.3.2.2gamma-glutamyltransferase 1 |
GPX 4 | Protein | ncbigene:2879 | EC 1.11.1.12Selenoprotein-glutathione peroxidase 4 |
TRXR2 | Protein | ncbigene:10587 | EC 1.8.1.9Selenoprotein-thioredoxin reductase 2 |
Xantine oxidase | Protein | ncbigene:7498 | EC 1.17.3.2http://en.wikipedia.org/wiki/Xanthine_oxidase |
PRDX5 | Protein | ncbigene:25824 | EC 1.11.1.15peroxiredoxin 5 |
ALOX5 | Protein | ncbigene:240 | EC 1.13.11.34arachidonate 5-lipoxygenase |
ALOX15B | Protein | ncbigene:247 | EC 1.13.11.33arachidonate 15-lipoxygenase, type B |
SelR | Protein | ncbigene:51734 | EC 1.8.4.-Selenoprotein-selenoprotein X |
SOD3 | Protein | ncbigene:6649 | EC 1.15.1.1superoxide dismutase 3, extracellular |
PRDX1 | Protein | ncbigene:5052 | EC 1.11.1.15peroxiredoxin 1 |
RFK | Protein | ncbigene:55312 | EC 2.7.1.26riboflavin kinase |
GPX 3 | Protein | ncbigene:2878 | EC 1.11.1.9Selenoprotein-glutathione peroxidase 3 |
CTH | Protein | ncbigene:1491 | EC 4.4.1.1cystathionase |
PNPO | Protein | ncbigene:55163 | EC 1.4.3.5pyridoxamine 5'-phosphate oxidase |
SelK | Protein | ncbigene:58515 | Selenoprotein-selenoprotein K |
Sep15 | Protein | ncbigene:9403 | Selenoprotein-15 kDa selenoprotein |
GPX 6 | Protein | ncbigene:257202 | EC 1.11.1.9Selenoprotein-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 1.11.1.9Selenoprotein-glutathione peroxidase 2 |
SelP | Protein | ncbigene:6414 | Selenoprotein-selenoprotein P |
Trx-S2 | Protein | ncbigene:7295 | oxidized thioredoxin |
PRDX4 | Protein | ncbigene:10549 | EC 1.11.1.15peroxiredoxin 4 |
GPX 1 | Protein | ncbigene:2876 | EC 1.11.1.9Selenoprotein-glutathione peroxidase 1 |
MTHFR | Protein | ncbigene:4524 | EC 1.5.1.205,10-methylenetetrahydrofolate reductase |
SelH | Protein | ncbigene:280636 | Selenoprotein-selenoprotein H-chromosome 11 open reading frame 31 |
SPS2 | Protein | ncbigene:22928 | EC2.7.9.3Selenoprotein-selenophosphate synthetase 2 |
SelO | Protein | ncbigene:83642 | Selenoprotein-selenoprotein OUnknown function |
SelN | Protein | ncbigene:57190 | Selenoprotein-selenoprotein N, 1 |
DIO2 | Protein | ncbigene:1734 | EC 1.97.1.10Selenoprotein-deiodinase, iodothyronine, type II |
SelT | Protein | ncbigene:51714 | Selenoprotein-selenoprotein T |
SelM | Protein | ncbigene:140606 | Selenoprotein-selenoprotein M |
DIO3 | Protein | ncbigene:1735 | EC 1.97.1.11Selenoprotein-deiodinase, iodothyronine type III |
DIO1 | Protein | ncbigene:1733 | EC 1.97.1.10Selenoprotein-deiodinase, iodothyronine, type I |
SelV | Protein | ncbigene:348303 | Selenoprotein-selenoprotein VUnknown function |
SelI | Protein | ncbigene:85465 | Selenoprotein-selenoprotein IUnknown function |
SelS | Protein | ncbigene:55829 | Selenoprotein-selenoprotein S |
SOD1 | Protein | ncbigene:6647 | EC 1.15.1.1superoxide dismutase 1, soluble |
PRDX3 | Protein | ncbigene:10935 | EC 1.11.1.15peroxiredoxin 3 |
GSR | Protein | ncbigene:2936 | EC 1.8.1.7glutathione 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-antichymotrypsinserpin 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 1.11.1.15peroxiredoxin 2 |
SOD2 | Protein | ncbigene:6648 | EC 1.15.1.1superoxide 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 1.8.1.9Selenoprotein-thioredoxin reductase 3 |
FLAD1 | Protein | ncbigene:80308 | EC 2.7.7.2FAD1 flavin adenine dinucleotide synthetase homolog (S. cerevisiae) |
FGB | Protein | ensembl:ENSG00000171564 | |
FGG | Protein | ensembl:ENSG00000171557 |
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