Pathway Human Homo sapiens

Biological oxidations

R-HSA-211859 in Reactome release 97: under Metabolism, with 217 genes placed in it by the mapping files and 3 child pathways in the hierarchy.

The same number in the other species

Reactome writes the mouse and rat events it infers from a human pathway under the human number with the species token. A door opens only where that species' own list in this release holds the id: R-MMU-211859 (mouse), R-RNO-211859 (rat). Whether the event was inferred from this one is what the record says.

The record
The genes
Parents and children

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This page reads the pathway's record from its source while you read the rest; with scripts off the card stays at its loading line. Reload with scripts on to see it, or open the source's own page from the link in the card.

01The record

Reactome's own record of this pathway

What this tells you

The pathway list, the hierarchy and the genes on this page are read from the files Reactome publishes for Reactome release 97, built into this site on 2026-09-09: the pathway list, the hierarchy relationship file and the two gene mapping files. The record card is the one live read, Reactome's own record of this pathway.

Reactome's download page describes the mapping files: Mapping files link the source database identifier to the lowest level pathway diagram or subset of the pathway, all levels of the pathway hierarchy or database identifier to all reactions. [R13] The gene list here is the all-levels mapping of NCBI Gene ids, filled from the all-levels mapping of Ensembl ids where the NCBI file has no row for a gene; each row names which file it came from by the shape of its source id. Each row carries the evidence codes the file writes for it, as written and unranked, and both where the file writes both; no page of Reactome's documentation the survey read defines the codes, so this page does not expand them. A gene id the identity files do not name is kept as the source's own id with no door rather than turned into a symbol.

On citing what a search finds, Reactome says: It should be remembered that while we strive to contain the most current and accurate data, Reactome should not be used in citations where other primary sources of information are available. [R12] The record card prints the literature Reactome attaches to a curated pathway for that reason. The data are public domain: All data in the Reactome database and files derived from that data are licensed under the Creative Commons Public Domain Dedication (CC0). User may copy, modify, and distribute these data, even for commercial purposes, without asking for permission. Attribution is encouraged but not required. [R10] The pathway illustrations are licensed apart, under CC BY 4.0, and none is shown here.

A gene on this list is one Reactome places in this pathway in this release, and that is all the row says: it does not say the gene is expressed in a tissue or associated with a disease, which are the other two explorers' questions, read from other sources. Reactome's papers of record are [R01] [R02].

[R01] Ragueneau E, Gong C, Sinquin P, Sevilla C, Beavers D, Grentner A, et al. (2026). The Reactome Knowledgebase 2026. Nucleic Acids Research 54:D673-D681. PMID 41251150, doi 10.1093/nar/gkaf1223.
[R02] Milacic M, Beavers D, Conley P, Gong C, Gillespie M, Griss J, et al. (2024). The Reactome Pathway Knowledgebase 2024. Nucleic Acids Research 52:D672-D678. PMID 37941124, doi 10.1093/nar/gkad1025.
[R10] Reactome, reactome.org. License Agreement. https://reactome.org/license, read 2026-09-09.
[R12] Reactome, reactome.org. Citing us. https://reactome.org/cite, read 2026-09-09.
[R13] Reactome, reactome.org. Download. https://reactome.org/download-data, read 2026-09-09.

Stable id: R-HSA-211859.4
Class: Pathway
Species: Homo sapiens (human)
Inferred: no: a curated human pathway
Disease pathway: no
Released: 2008-06-30
Last updated: 2023-09-13
Events inside: 3, counted from the record

All organisms are constantly exposed to foreign chemicals every day. These can be man-made (drugs, industrial chemicals) or natural (alkaloids, toxins from plants and animals). Uptake is usually via ingestion but inhalation and transdermal routes are also common.

The very nature of many chemicals that make them suitable for uptake by these routes, in other words their lipophilicty (favours fat solubility) is also the main reason organisms have developed mechanisms that convert them to hydrophilic (favours water solubility) compounds which are readily excreted via bile and urine. Otherwise, lipophilic chemicals would accumulate in the body and overwhelm defense mechanisms. This process is called biotransformation and is catalyzed by enzymes mainly in the liver of higher organisms but a number of other organs have considerable ability to process xenobiotica such as kidneys, gut and lungs. As well as xenobiotics, many endogenous compounds are commonly eliminated by this process.

This mechanism is of ancient origin and a major factor for its development in animals is plants. Most animals are plant eaters and thus are subject to a huge variety of chemical compounds which plants produce to stop themselves being eaten. This complex set of enzymes have several features which make them ideal for biotransformation;

(1) metabolites of the parent chemical are usually made more water soluble so it favours rapid excretion via bile and urine

(2) the enzymes possess broad and overlapping specificity to be able to deal with newly exposed chemicals

(3) metabolites of the parent generally don't have adverse biological effects.

In the real world however, all these criteria have exceptions. Many chemicals are transformed into reactive metabolites. In pharmacology, the metabolites of some parent drugs exert the desired pharmacological effect but in the case of polycyclic aromatic hydrocarbons (PAHs), which can undergo epoxidation, it results in the formation of an electrophile which can attack proteins and DNA.

Metabolism of xenobiotica occurs in several steps called Phase 1 (functionalization) and Phase 2 (conjugation). To improve water solubility, a functional group is added to or exposed on the chemical in one or more steps (Phase 1) to which hydrophilic conjugating species can be added (Phase 2). Functional groups can either be electrophilic (epoxides, carbonyl groups) or nucleophilic (hydroxyls, amino and sulfhydryl groups, carboxylic groups) (see picture).

Once chemicals undergo functionalization, the electrophilic or nucleophilic species can be detrimental to biological systems. Electrophiles can react with electron-rich macromolecules such as proteins, DNA and RNA by covalent interaction whilst nucleophiles have the potential to interact with biological receptors. That's why conjugation is so important as it mops up these potentially reactive species.

Many chemicals, when exposed to certain metabolizing enzymes can induce those enzymes, a process called enzyme induction. The effect of this is that these chemicals accelerate their own biotransformation and excretion. The reverse is also true where some chemicals cause enzyme inhibition. Some other factors that alter enzyme levels are sex, age and genetic predisposition. Between species, there can be considerable differences in biotransformation ability which is a problem faced by drug researchers interpreting toxicological results to humans.

Literature Reactome attaches

Toxicology1999, p. 83-107

Reactome's record lists 14 orthologous events, R-RNO-211859 (Rattus norvegicus), R-MMU-211859 (Mus musculus) among the species this site serves, and 12 in species this site opens no page for.

Reactome ContentService, this pathway's record · Reactome v97 · read 2026-10-01 ET · Reactome pathway browser"Biological oxidations". Reactome, release 97, https://reactome.org/PathwayBrowser/#/R-HSA-211859 with StableID: R-HSA-211859.4 (accessed 2026-10-01 ET). Reactome version 97 (CC0).

Reading this pathway's record from Reactome (the pathway record).Still reading. A first read of a pathway can take a while; this page waits up to 35 seconds for it, and its scripts then bring in the panel, or a line saying what did not arrive.

02The genes

Genes Reactome places in this human pathway

The mapping files place 217 genes in this human pathway; showing 101 to 200, in pages of 100, sorted by symbol for reading. The order carries no ranking.

Genes Reactome places in this human pathway, page 2 of 3
Gene	Authority id	Mapping file id	Evidence codes
GeneCYP7B1	AuthorityHGNC:2652	Mapping file id9420 NCBI file	EvidenceTAS
GeneCYP8B1	AuthorityHGNC:2653	Mapping file id1582 NCBI file	EvidenceTAS
GeneDPEP1	AuthorityHGNC:3002	Mapping file id1800 NCBI file	EvidenceTAS
GeneDPEP2	AuthorityHGNC:23028	Mapping file id64174 NCBI file	EvidenceTAS
GeneEPHX1	AuthorityHGNC:3401	Mapping file id2052 NCBI file	EvidenceTAS
GeneESD	AuthorityHGNC:3465	Mapping file id2098 NCBI file	EvidenceTAS
GeneFDX1	AuthorityHGNC:3638	Mapping file id2230 NCBI file	EvidenceTAS
GeneFDX2	AuthorityHGNC:30546	Mapping file id112812 NCBI file	EvidenceTAS
GeneFDXR	AuthorityHGNC:3642	Mapping file id2232 NCBI file	EvidenceTAS
GeneFMO1	AuthorityHGNC:3769	Mapping file id2326 NCBI file	EvidenceTAS
GeneFMO2	AuthorityHGNC:3770	Mapping file id2327 NCBI file	EvidenceTAS
GeneFMO3	AuthorityHGNC:3771	Mapping file id2328 NCBI file	EvidenceTAS
GeneGCLC	AuthorityHGNC:4311	Mapping file id2729 NCBI file	EvidenceTAS
GeneGCLM	AuthorityHGNC:4312	Mapping file id2730 NCBI file	EvidenceTAS
GeneGGCT	AuthorityHGNC:21705	Mapping file id79017 NCBI file	EvidenceTAS
GeneGGT1	AuthorityHGNC:4250	Mapping file id2678 NCBI file	EvidenceTAS
GeneGGT5	AuthorityHGNC:4260	Mapping file id2687 NCBI file	EvidenceTAS
GeneGGT6	AuthorityHGNC:26891	Mapping file id124975 NCBI file	EvidenceTAS
GeneGGT7	AuthorityHGNC:4259	Mapping file id2686 NCBI file	EvidenceTAS
GeneGLYAT	AuthorityHGNC:13734	Mapping file id10249 NCBI file	EvidenceTAS
GeneGLYATL1	AuthorityHGNC:30519	Mapping file id92292 NCBI file	EvidenceTAS
GeneGLYATL2	AuthorityHGNC:24178	Mapping file id219970 NCBI file	EvidenceTAS
GeneGLYATL3	AuthorityHGNC:21349	Mapping file id389396 NCBI file	EvidenceTAS
GeneGSS	AuthorityHGNC:4624	Mapping file id2937 NCBI file	EvidenceTAS
GeneGSTA1	AuthorityHGNC:4626	Mapping file id2938 NCBI file	EvidenceTAS
GeneGSTA2	AuthorityHGNC:4627	Mapping file id2939 NCBI file	EvidenceTAS
GeneGSTA3	AuthorityHGNC:4628	Mapping file id2940 NCBI file	EvidenceTAS
GeneGSTA4	AuthorityHGNC:4629	Mapping file id2941 NCBI file	EvidenceTAS
GeneGSTA5	AuthorityHGNC:19662	Mapping file id221357 NCBI file	EvidenceTAS
GeneGSTK1	AuthorityHGNC:16906	Mapping file id373156 NCBI file	EvidenceTAS
GeneGSTM1	AuthorityHGNC:4632	Mapping file id2944 NCBI file	EvidenceTAS
GeneGSTM2	AuthorityHGNC:4634	Mapping file id2946 NCBI file	EvidenceTAS
GeneGSTM3	AuthorityHGNC:4635	Mapping file id2947 NCBI file	EvidenceTAS
GeneGSTM4	AuthorityHGNC:4636	Mapping file id2948 NCBI file	EvidenceTAS
GeneGSTM5	AuthorityHGNC:4637	Mapping file id2949 NCBI file	EvidenceTAS
GeneGSTO1	AuthorityHGNC:13312	Mapping file id9446 NCBI file	EvidenceTAS
GeneGSTO2	AuthorityHGNC:23064	Mapping file id119391 NCBI file	EvidenceTAS
GeneGSTP1	AuthorityHGNC:4638	Mapping file id2950 NCBI file	EvidenceTAS
GeneGSTT1	AuthorityHGNC:4641	Mapping file id2952 NCBI file	EvidenceTAS
GeneGSTT2	AuthorityHGNC:4642	Mapping file id2953 NCBI file	EvidenceTAS
GeneGSTT2B	AuthorityHGNC:33437	Mapping file id653689 NCBI file	EvidenceTAS
GeneGSTZ1	AuthorityHGNC:4643	Mapping file id2954 NCBI file	EvidenceTAS
GeneHEMK2	AuthorityHGNC:16021	Mapping file id29104 NCBI file	EvidenceTAS
GeneHPGDS	AuthorityHGNC:17890	Mapping file id27306 NCBI file	EvidenceTAS
GeneHSP90AB1	AuthorityHGNC:5258	Mapping file id3326 NCBI file	EvidenceTAS
GeneMAOA	AuthorityHGNC:6833	Mapping file id4128 NCBI file	EvidenceTAS
GeneMAOB	AuthorityHGNC:6834	Mapping file id4129 NCBI file	EvidenceTAS
GeneMAT1A	AuthorityHGNC:6903	Mapping file id4143 NCBI file	EvidenceTAS
GeneMAT2A	AuthorityHGNC:6904	Mapping file id4144 NCBI file	EvidenceTAS
GeneMAT2B	AuthorityHGNC:6905	Mapping file id27430 NCBI file	EvidenceTAS
GeneMGST1	AuthorityHGNC:7061	Mapping file id4257 NCBI file	EvidenceTAS
GeneMGST2	AuthorityHGNC:7063	Mapping file id4258 NCBI file	EvidenceTAS
GeneMGST3	AuthorityHGNC:7064	Mapping file id4259 NCBI file	EvidenceTAS
GeneMTARC1	AuthorityHGNC:26189	Mapping file id64757 NCBI file	EvidenceTAS
GeneMTARC2	AuthorityHGNC:26064	Mapping file id54996 NCBI file	EvidenceTAS
GeneMTR	AuthorityHGNC:7468	Mapping file id4548 NCBI file	EvidenceTAS
GeneMTRR	AuthorityHGNC:7473	Mapping file id4552 NCBI file	EvidenceTAS
GeneNAT1	AuthorityHGNC:7645	Mapping file id9 NCBI file	EvidenceTAS
GeneNAT2	AuthorityHGNC:7646	Mapping file id10 NCBI file	EvidenceTAS
GeneNCOA1	AuthorityHGNC:7668	Mapping file id8648 NCBI file	EvidenceTAS
GeneNCOA2	AuthorityHGNC:7669	Mapping file id10499 NCBI file	EvidenceTAS
GeneNNMT	AuthorityHGNC:7861	Mapping file id4837 NCBI file	EvidenceTAS
GeneNQO2	AuthorityHGNC:7856	Mapping file id4835 NCBI file	EvidenceTAS
GeneNR1H4	AuthorityHGNC:7967	Mapping file id9971 NCBI file	EvidenceTAS
GeneOPLAH	AuthorityHGNC:8149	Mapping file id26873 NCBI file	EvidenceTAS
GenePAOX	AuthorityHGNC:20837	Mapping file id196743 NCBI file	EvidenceTAS
GenePODXL2	AuthorityHGNC:17936	Mapping file id50512 NCBI file	EvidenceTAS
GenePOMC	AuthorityHGNC:9201	Mapping file id5443 NCBI file	EvidenceTAS
GenePOR	AuthorityHGNC:9208	Mapping file id5447 NCBI file	EvidenceTAS
GenePTGES3	AuthorityHGNC:16049	Mapping file id10728 NCBI file	EvidenceTAS
GenePTGIS	AuthorityHGNC:9603	Mapping file id5740 NCBI file	EvidenceTAS
GenePTGS1	AuthorityHGNC:9604	Mapping file id5742 NCBI file	EvidenceTAS
GeneRXRA	AuthorityHGNC:10477	Mapping file id6256 NCBI file	EvidenceTAS
GeneSLC35D1	AuthorityHGNC:20800	Mapping file id23169 NCBI file	EvidenceTAS
GeneSLC35D2	AuthorityHGNC:20799	Mapping file id11046 NCBI file	EvidenceIEA
GeneSMOX	AuthorityHGNC:15862	Mapping file id54498 NCBI file	EvidenceTAS
GeneSULT1A1	AuthorityHGNC:11453	Mapping file id6817 NCBI file	EvidenceTAS
GeneSULT1A2	AuthorityHGNC:11454	Mapping file id6799 NCBI file	EvidenceTAS
GeneSULT1A3	AuthorityHGNC:11455	Mapping file id6818 NCBI file	EvidenceTAS
GeneSULT1A4	AuthorityHGNC:30004	Mapping file id445329 NCBI file	EvidenceTAS
GeneSULT1B1	AuthorityHGNC:17845	Mapping file id27284 NCBI file	EvidenceTAS
GeneSULT1C2	AuthorityHGNC:11456	Mapping file id6819 NCBI file	EvidenceTAS
GeneSULT1C4	AuthorityHGNC:11457	Mapping file id27233 NCBI file	EvidenceTAS
GeneSULT1E1	AuthorityHGNC:11377	Mapping file id6783 NCBI file	EvidenceTAS
GeneSULT2A1	AuthorityHGNC:11458	Mapping file id6822 NCBI file	EvidenceTAS
GeneSULT2B1	AuthorityHGNC:11459	Mapping file id6820 NCBI file	EvidenceTAS
GeneSULT4A1	AuthorityHGNC:14903	Mapping file id25830 NCBI file	EvidenceTAS
GeneSULT6B1	AuthorityHGNC:33433	Mapping file id391365 NCBI file	EvidenceTAS
GeneTBXAS1	AuthorityHGNC:11609	Mapping file id6916 NCBI file	EvidenceTAS
GeneTPMT	AuthorityHGNC:12014	Mapping file id7172 NCBI file	EvidenceTAS
GeneTPST1	AuthorityHGNC:12020	Mapping file id8460 NCBI file	EvidenceTAS
GeneTPST2	AuthorityHGNC:12021	Mapping file id8459 NCBI file	EvidenceTAS
GeneTRMT112	AuthorityHGNC:26940	Mapping file id51504 NCBI file	EvidenceTAS
GeneUGDH	AuthorityHGNC:12525	Mapping file id7358 NCBI file	EvidenceTAS
GeneUGP2	AuthorityHGNC:12527	Mapping file id7360 NCBI file	EvidenceTAS
GeneUGT1A1	AuthorityHGNC:12530	Mapping file id54658 NCBI file	EvidenceTAS
GeneUGT1A10	AuthorityHGNC:12531	Mapping file id54575 NCBI file	EvidenceTAS
GeneUGT1A3	AuthorityHGNC:12535	Mapping file id54659 NCBI file	EvidenceTAS
GeneUGT1A4	AuthorityHGNC:12536	Mapping file id54657 NCBI file	EvidenceTAS
GeneUGT1A5	AuthorityHGNC:12537	Mapping file id54579 NCBI file	EvidenceTAS

Evidence codes on this page: IEA, TAS, as the mapping file writes them; a row carrying two was written twice by the file, once under each. The mapping file id says which file placed the gene: an NCBI Gene id from NCBI2Reactome_All_Levels.txt, an Ensembl gene id from Ensembl2Reactome_All_Levels.txt. The two files can disagree about a code, so a row's codes are the one file's view. Measured by this site's build over this release on 2026-09-09: of the 138,908 human pathway-gene pairs both files place, 207 (0.149 per cent, over 47 genes) carry TAS in the Ensembl file where the NCBI rows carry IEA alone.

Reactome mapping files, the human rows for this pathway · Reactome release 97 · read 2026-09-09 · Reactome downloads"NCBI2Reactome_All_Levels.txt" and "Ensembl2Reactome_All_Levels.txt", Reactome, release 97, https://reactome.org/download-data/ (date of access 2026-09-09). Data CC0; attribution encouraged.

03The hierarchy

Parents and children in this release's hierarchy

Parents

MetabolismR-HSA-14307282,196 genes

Children

Reactome's hierarchy is a graph rather than a tree: a pathway can sit under more than one parent, and the gene counts are each pathway's own placements at every level under it, so a parent's count is not the sum of its children's.

Reactome, the human pathway list and hierarchy relationship file · Reactome release 97 · read 2026-09-09 · Reactome downloads"ReactomePathways.txt" and "ReactomePathwaysRelation.txt", Reactome, release 97, https://reactome.org/download-data/ (date of access 2026-09-09). Data CC0; attribution encouraged.