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 1 to 100, in pages of 100, sorted by symbol for reading. The order carries no ranking.

Genes Reactome places in this human pathway, page 1 of 3
Gene	Authority id	Mapping file id	Evidence codes
GeneAADAC	AuthorityHGNC:17	Mapping file id13 NCBI file	EvidenceTAS
GeneABHD10	AuthorityHGNC:25656	Mapping file id55347 NCBI file	EvidenceTAS
GeneABHD14B	AuthorityHGNC:28235	Mapping file id84836 NCBI file	EvidenceTAS
GeneACSM1	AuthorityHGNC:18049	Mapping file id116285 NCBI file	EvidenceTAS
GeneACSM2A	AuthorityHGNC:32017	Mapping file id123876 NCBI file	EvidenceTAS
GeneACSM2B	AuthorityHGNC:30931	Mapping file id348158 NCBI file	EvidenceTAS
GeneACSM4	AuthorityHGNC:32016	Mapping file id341392 NCBI file	EvidenceTAS
GeneACSM5	AuthorityHGNC:26060	Mapping file id54988 NCBI file	EvidenceTAS
GeneACSS1	AuthorityHGNC:16091	Mapping file id84532 NCBI file	EvidenceTAS
GeneACSS2	AuthorityHGNC:15814	Mapping file id55902 NCBI file	EvidenceTAS
GeneACY1	AuthorityHGNC:177	Mapping file id95 NCBI file	EvidenceTAS
GeneACY3	AuthorityHGNC:24104	Mapping file id91703 NCBI file	EvidenceTAS
GeneADH1A	AuthorityHGNC:249	Mapping file id124 NCBI file	EvidenceTAS
GeneADH1B	AuthorityHGNC:250	Mapping file id125 NCBI file	EvidenceTAS
GeneADH1C	AuthorityHGNC:251	Mapping file id126 NCBI file	EvidenceTAS
GeneADH4	AuthorityHGNC:252	Mapping file id127 NCBI file	EvidenceTAS
GeneADH5	AuthorityHGNC:253	Mapping file id128 NCBI file	EvidenceTAS
GeneADH6	AuthorityHGNC:255	Mapping file id130 NCBI file	EvidenceTAS
GeneADH7	AuthorityHGNC:256	Mapping file id131 NCBI file	EvidenceTAS
GeneAHCY	AuthorityHGNC:343	Mapping file id191 NCBI file	EvidenceTAS
GeneAHR	AuthorityHGNC:348	Mapping file id196 NCBI file	EvidenceTAS
GeneAHRR	AuthorityHGNC:346	Mapping file id57491 NCBI file	EvidenceTAS
GeneAIP	AuthorityHGNC:358	Mapping file id9049 NCBI file	EvidenceTAS
GeneAKR1A1	AuthorityHGNC:380	Mapping file id10327 NCBI file	EvidenceTAS
GeneAKR7A2	AuthorityHGNC:389	Mapping file id8574 NCBI file	EvidenceTAS
GeneAKR7A3	AuthorityHGNC:390	Mapping file id22977 NCBI file	EvidenceTAS
GeneAKR7L	AuthorityHGNC:24056	Mapping file id246181 NCBI file	EvidenceTAS
GeneALDH1A1	AuthorityHGNC:402	Mapping file id216 NCBI file	EvidenceTAS
GeneALDH1B1	AuthorityHGNC:407	Mapping file id219 NCBI file	EvidenceTAS
GeneALDH2	AuthorityHGNC:404	Mapping file id217 NCBI file	EvidenceTAS
GeneALDH3A1	AuthorityHGNC:405	Mapping file id218 NCBI file	EvidenceTAS
GeneAOC1	AuthorityHGNC:80	Mapping file id26 NCBI file	EvidenceTAS
GeneAOC2	AuthorityHGNC:549	Mapping file id314 NCBI file	EvidenceTAS
GeneAOC3	AuthorityHGNC:550	Mapping file id8639 NCBI file	EvidenceTAS
GeneARNT	AuthorityHGNC:700	Mapping file id405 NCBI file	EvidenceTAS
GeneARNT2	AuthorityHGNC:16876	Mapping file id9915 NCBI file	EvidenceTAS
GeneAS3MT	AuthorityHGNC:17452	Mapping file id57412 NCBI file	EvidenceTAS
GeneBPHL	AuthorityHGNC:1094	Mapping file id670 NCBI file	EvidenceTAS
GeneBPNT1	AuthorityHGNC:1096	Mapping file id10380 NCBI file	EvidenceTAS
GeneBPNT2	AuthorityHGNC:26019	Mapping file id54928 NCBI file	EvidenceTAS
GeneCBR3	AuthorityHGNC:1549	Mapping file id874 NCBI file	EvidenceTAS
GeneCES1	AuthorityHGNC:1863	Mapping file id1066 NCBI file	EvidenceTAS
GeneCES2	AuthorityHGNC:1864	Mapping file id8824 NCBI file	EvidenceTAS
GeneCES3	AuthorityHGNC:1865	Mapping file id23491 NCBI file	EvidenceTAS
GeneCHAC1	AuthorityHGNC:28680	Mapping file id79094 NCBI file	EvidenceTAS
GeneCHAC2	AuthorityHGNC:32363	Mapping file id494143 NCBI file	EvidenceTAS
GeneCMBL	AuthorityHGNC:25090	Mapping file id134147 NCBI file	EvidenceTAS
GeneCNDP2	AuthorityHGNC:24437	Mapping file id55748 NCBI file	EvidenceTAS
GeneCOMT	AuthorityHGNC:2228	Mapping file id1312 NCBI file	EvidenceTAS
GeneCYB5B	AuthorityHGNC:24374	Mapping file id80777 NCBI file	EvidenceTAS
GeneCYB5R3	AuthorityHGNC:2873	Mapping file id1727 NCBI file	EvidenceTAS
GeneCYP11A1	AuthorityHGNC:2590	Mapping file id1583 NCBI file	EvidenceTAS
GeneCYP11B1	AuthorityHGNC:2591	Mapping file id1584 NCBI file	EvidenceTAS
GeneCYP11B2	AuthorityHGNC:2592	Mapping file id1585 NCBI file	EvidenceTAS
GeneCYP19A1	AuthorityHGNC:2594	Mapping file id1588 NCBI file	EvidenceTAS
GeneCYP1A1	AuthorityHGNC:2595	Mapping file id1543 NCBI file	EvidenceTAS
GeneCYP1A2	AuthorityHGNC:2596	Mapping file id1544 NCBI file	EvidenceTAS
GeneCYP1B1	AuthorityHGNC:2597	Mapping file id1545 NCBI file	EvidenceTAS
GeneCYP21A2	AuthorityHGNC:2600	Mapping file id1589 NCBI file	EvidenceTAS
GeneCYP24A1	AuthorityHGNC:2602	Mapping file id1591 NCBI file	EvidenceTAS
GeneCYP26A1	AuthorityHGNC:2603	Mapping file id1592 NCBI file	EvidenceTAS
GeneCYP26B1	AuthorityHGNC:20581	Mapping file id56603 NCBI file	EvidenceTAS
GeneCYP26C1	AuthorityHGNC:20577	Mapping file id340665 NCBI file	EvidenceTAS
GeneCYP27A1	AuthorityHGNC:2605	Mapping file id1593 NCBI file	EvidenceTAS
GeneCYP27B1	AuthorityHGNC:2606	Mapping file id1594 NCBI file	EvidenceTAS
GeneCYP2A13	AuthorityHGNC:2608	Mapping file id1553 NCBI file	EvidenceTAS
GeneCYP2A6	AuthorityHGNC:2610	Mapping file id1548 NCBI file	EvidenceTAS
GeneCYP2A7	AuthorityHGNC:2611	Mapping file id1549 NCBI file	EvidenceTAS
GeneCYP2B6	AuthorityHGNC:2615	Mapping file id1555 NCBI file	EvidenceTAS
GeneCYP2C18	AuthorityHGNC:2620	Mapping file id1562 NCBI file	EvidenceTAS
GeneCYP2C19	AuthorityHGNC:2621	Mapping file id1557 NCBI file	EvidenceTAS
GeneCYP2C8	AuthorityHGNC:2622	Mapping file id1558 NCBI file	EvidenceTAS
GeneCYP2C9	AuthorityHGNC:2623	Mapping file id1559 NCBI file	EvidenceTAS
GeneCYP2D6	AuthorityHGNC:2625	Mapping file id1565 NCBI file	EvidenceTAS
GeneCYP2E1	AuthorityHGNC:2631	Mapping file id1571 NCBI file	EvidenceTAS
GeneCYP2F1	AuthorityHGNC:2632	Mapping file id1572 NCBI file	EvidenceTAS
GeneCYP2J2	AuthorityHGNC:2634	Mapping file id1573 NCBI file	EvidenceTAS
GeneCYP2R1	AuthorityHGNC:20580	Mapping file id120227 NCBI file	EvidenceTAS
GeneCYP2S1	AuthorityHGNC:15654	Mapping file id29785 NCBI file	EvidenceTAS
GeneCYP2U1	AuthorityHGNC:20582	Mapping file id113612 NCBI file	EvidenceTAS
GeneCYP2W1	AuthorityHGNC:20243	Mapping file id54905 NCBI file	EvidenceTAS
GeneCYP39A1	AuthorityHGNC:17449	Mapping file id51302 NCBI file	EvidenceTAS
GeneCYP3A4	AuthorityHGNC:2637	Mapping file id1576 NCBI file	EvidenceTAS
GeneCYP3A43	AuthorityHGNC:17450	Mapping file id64816 NCBI file	EvidenceTAS
GeneCYP3A5	AuthorityHGNC:2638	Mapping file id1577 NCBI file	EvidenceTAS
GeneCYP3A7	AuthorityHGNC:2640	Mapping file id1551 NCBI file	EvidenceTAS
GeneCYP3A7-CYP3A51P	AuthorityHGNC:51504	Mapping file id100861540 NCBI file	EvidenceTAS
GeneCYP46A1	AuthorityHGNC:2641	Mapping file id10858 NCBI file	EvidenceTAS
GeneCYP4A11	AuthorityHGNC:2642	Mapping file id1579 NCBI file	EvidenceTAS
GeneCYP4A22	AuthorityHGNC:20575	Mapping file id284541 NCBI file	EvidenceTAS
GeneCYP4B1	AuthorityHGNC:2644	Mapping file id1580 NCBI file	EvidenceTAS
GeneCYP4F11	AuthorityHGNC:13265	Mapping file id57834 NCBI file	EvidenceTAS
GeneCYP4F12	AuthorityHGNC:18857	Mapping file id66002 NCBI file	EvidenceTAS
GeneCYP4F2	AuthorityHGNC:2645	Mapping file id8529 NCBI file	EvidenceTAS
GeneCYP4F22	AuthorityHGNC:26820	Mapping file id126410 NCBI file	EvidenceTAS
GeneCYP4F3	AuthorityHGNC:2646	Mapping file id4051 NCBI file	EvidenceTAS
GeneCYP4F8	AuthorityHGNC:2648	Mapping file id11283 NCBI file	EvidenceTAS
GeneCYP4V2	AuthorityHGNC:23198	Mapping file id285440 NCBI file	EvidenceTAS
GeneCYP51A1	AuthorityHGNC:2649	Mapping file id1595 NCBI file	EvidenceTAS
GeneCYP7A1	AuthorityHGNC:2651	Mapping file id1581 NCBI file	EvidenceTAS

Evidence codes on this page: 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.