Firecrawl Alexandria
Reactome: biological pathways and pathway enrichment
Reactome, the open, expert-curated knowledgebase of biological pathways and reactions (OICR, EMBL-EBI, NYU Langone and OHSU), through its Content Service and Analysis Service. Finds the pathways a gene, protein or chemical takes part in (gene symbol, UniProt, Ensembl, NCBI Gene or ChEBI ID), or pathways by name or topic; reads one pathway's curated summary, literature with PubMed IDs, GO process, disease terms, orthologs and its place in the pathway hierarchy; lists a pathway's participating proteins (UniProt), genes, RNAs and chemicals (ChEBI); and runs over-representation analysis of a gene list (hypergeometric test, FDR) with the genes found per pathway. Human pathways are curated and inferred for 15 model organisms; about 2,700 human pathways and 16,000 reactions. Reactome data is CC0 1.0; every answer carries the release and Reactome's citation.
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const result = await firecrawl.scrape({
alexandria: {
provider: "reactome-org",
capability: "pathways/enrichment",
options: {
identifiers: [
"TP53",
"MDM2",
"CDKN1A",
],
},
},
});2Response example
This is a sample shape. Press Run to see live data from Reactome: biological pathways and pathway enrichment.
{
"analysis_token": "MjAyNjEwMzAyMTIxMDhfMTYxODA%3D",
"analysis_url": "https://reactome.org/PathwayBrowser/#/DTAB=AN&ANALYSIS=MjAyNjEwMzAyMTIxMDhfMTYxODA%3D",
"identifiers_found": 3,
"identifiers_submitted": 3,
"include_disease": true,
"license": {
"attribution": "Data from Reactome (https://reactome.org), release 98, dedicated to the public domain under CC0 1.0 (https://reactome.org/license). Reactome asks that you cite: Ragueneau E et al. The Reactome Knowledgebase 2026. Nucleic Acids Res. 2025. doi:10.1093/nar/gkaf1223",
"name": "CC0 1.0",
"url": "https://creativecommons.org/publicdomain/zero/1.0/"
},
"limit": 25,
"lowest_level_only": false,
"max_fdr": 0.05,
"not_found": [],
"observed_at_ms": 1793395318752,
"pathways_found": 179,
"pathways_significant": 69,
"release": "98",
"results": [
{
"browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-69560",
"entities_found": 4,
"entities_total": 6,
"fdr": 8.996773770419964e-9,
"found_identifiers": [
"TP53",
"CDKN1A"
],
"in_disease": false,
"lowest_level": true,
"name": "Transcriptional activation of p53 responsive genes",
"p_value": 8.907696802396003e-11,
"reactions_found": 5,
"reactions_total": 5,
"st_id": "R-HSA-69560",
"url": "https://reactome.org/content/detail/R-HSA-69560"
},
{
"browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-69895",
"entities_found": 4,
"entities_total": 6,
"fdr": 8.996773770419964e-9,
"found_identifiers": [
"TP53",
"CDKN1A"
],
"in_disease": false,
"lowest_level": true,
"name": "Transcriptional activation of cell cycle inhibitor p21",
"p_value": 8.907696802396003e-11,
"reactions_found": 5,
"reactions_total": 5,
"st_id": "R-HSA-69895",
"url": "https://reactome.org/content/detail/R-HSA-69895"
},
{
"browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-69563",
"entities_found": 5,
"entities_total": 58,
"fdr": 4.261721808784813e-7,
"found_identifiers": [
"TP53",
"MDM2",
"CDKN1A"
],
"in_disease": false,
"lowest_level": true,
"name": "p53-Dependent G1 DNA Damage Response",
"p_value": 8.523443617569626e-9,
"reactions_found": 18,
"reactions_total": 22,
"st_id": "R-HSA-69563",
"url": "https://reactome.org/content/detail/R-HSA-69563"
},
{
"browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-69580",
"entities_found": 5,
"entities_total": 58,
"fdr": 4.261721808784813e-7,
"found_identifiers": [
"TP53",
"MDM2",
"CDKN1A"
],
"in_disease": false,
"lowest_level": false,
"name": "p53-Dependent G1/S DNA damage checkpoint",
"p_value": 8.523443617569626e-9,
"reactions_found": 18,
"reactions_total": 22,
"st_id": "R-HSA-69580",
"url": "https://reactome.org/content/detail/R-HSA-69580"
},
{
"browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-6804116",
"entities_found": 4,
"entities_total": 21,
"fdr": 5.284120518922464e-7,
"found_identifiers": [
"TP53",
"CDKN1A"
],
"in_disease": false,
"lowest_level": true,
"name": "TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest",
"p_value": 1.321030129730616e-8,
"reactions_found": 12,
"reactions_total": 17,
"st_id": "R-HSA-6804116",
"url": "https://reactome.org/content/detail/R-HSA-6804116"
},
{
"browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-69615",
"entities_found": 5,
"entities_total": 72,
"fdr": 8.202994656869578e-7,
"found_identifiers": [
"TP53",
"MDM2",
"CDKN1A"
],
"in_disease": false,
"lowest_level": false,
"name": "G1/S DNA Damage Checkpoints",
"p_value": 2.4857559566271448e-8,
"reactions_found": 18,
"reactions_total": 33,
"st_id": "R-HSA-69615",
"url": "https://reactome.org/content/detail/R-HSA-69615"
},
{
"browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-8941855",
"entities_found": 3,
"entities_total": 8,
"fdr": 0.0000039020066634476436,
"found_identifiers": [
"TP53",
"CDKN1A"
],
"in_disease": false,
"lowest_level": true,
"name": "RUNX3 regulates CDKN1A transcription",
"p_value": 1.345519539119877e-7,
"reactions_found": 4,
"reactions_total": 6,
"st_id": "R-HSA-8941855",
"url": "https://reactome.org/content/detail/R-HSA-8941855"
},
{
"browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-6806003",
"entities_found": 4,
"entities_total": 46,
"fdr": 0.000007455255437993635,
"found_identifiers": [
"TP53",
"MDM2"
],
"in_disease": false,
"lowest_level": true,
"name": "Regulation of TP53 Expression and Degradation",
"p_value": 2.982102175197454e-7,
"reactions_found": 33,
"reactions_total": 35,
"st_id": "R-HSA-6806003",
"url": "https://reactome.org/content/detail/R-HSA-6806003"
},
{
"browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-3700989",
"entities_found": 7,
"entities_total": 488,
"fdr": 0.000024880475493205267,
"found_identifiers": [
"TP53",
"MDM2",
"CDKN1A"
],
"in_disease": false,
"lowest_level": true,
"name": "Transcriptional Regulation by TP53",
"p_value": 0.0000011967338258145332,
"reactions_found": 188,
"reactions_total": 258,
"st_id": "R-HSA-3700989",
"url": "https://reactome.org/content/detail/R-HSA-3700989"
},
{
"browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-6791312",
"entities_found": 4,
"entities_total": 66,
"fdr": 0.000024880475493205267,
"found_identifiers": [
"TP53",
"CDKN1A"
],
"in_disease": false,
"lowest_level": true,
"name": "TP53 Regulates Transcription of Cell Cycle Genes",
"p_value": 0.0000012440237746602634,
"reactions_found": 28,
"reactions_total": 42,
"st_id": "R-HSA-6791312",
"url": "https://reactome.org/content/detail/R-HSA-6791312"
},
{
"browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-9617828",
"entities_found": 3,
"entities_total": 27,
"fdr": 0.00009173178155874595,
"found_identifiers": [
"CDKN1A"
],
"in_disease": false,
"lowest_level": true,
"name": "FOXO-mediated transcription of cell cycle genes",
"p_value": 0.000005096210086596997,
"reactions_found": 5,
"reactions_total": 22,
"st_id": "R-HSA-9617828",
"url": "https://reactome.org/content/detail/R-HSA-9617828"
},
{
"browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-8878159",
"entities_found": 4,
"entities_total": 108,
"fdr": 0.00013807011976041395,
"found_identifiers": [
"TP53",
"MDM2",
"CDKN1A"
],
"in_disease": false,
"lowest_level": true,
"name": "Transcriptional regulation by RUNX3",
"p_value": 0.000008629382485025872,
"reactions_found": 6,
"reactions_total": 47,
"st_id": "R-HSA-8878159",
"url": "https://reactome.org/content/detail/R-HSA-8878159"
},
{
"browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-6804754",
"entities_found": 2,
"entities_total": 4,
"fdr": 0.00016392720574121,
"found_identifiers": [
"TP53"
],
"in_disease": false,
"lowest_level": true,
"name": "Regulation of TP53 Expression",
"p_value": 0.000011443288277734887,
"reactions_found": 5,
"reactions_total": 5,
"st_id": "R-HSA-6804754",
"url": "https://reactome.org/content/detail/R-HSA-6804754"
},
{
"browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-9700206",
"entities_found": 4,
"entities_total": 119,
"fdr": 0.00016392720574121,
"found_identifiers": [
"TP53",
"MDM2",
"CDKN1A"
],
"in_disease": true,
"lowest_level": false,
"name": "Signaling by ALK in cancer",
"p_value": 0.000012609785057016154,
"reactions_found": 4,
"reactions_total": 71,
"st_id": "R-HSA-9700206",
"url": "https://reactome.org/content/detail/R-HSA-9700206"
},
{
"browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-9725370",
"entities_found": 4,
"entities_total": 119,
"fdr": 0.00016392720574121,
"found_identifiers": [
"TP53",
"MDM2",
"CDKN1A"
],
"in_disease": true,
"lowest_level": true,
"name": "Signaling by ALK fusions and activated point mutants",
"p_value": 0.000012609785057016154,
"reactions_found": 4,
"reactions_total": 63,
"st_id": "R-HSA-9725370",
"url": "https://reactome.org/content/detail/R-HSA-9725370"
},
{
"browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-69620",
"entities_found": 5,
"entities_total": 279,
"fdr": 0.00022211807147831664,
"found_identifiers": [
"TP53",
"MDM2",
"CDKN1A"
],
"in_disease": false,
"lowest_level": false,
"name": "Cell Cycle Checkpoints",
"p_value": 0.00001850983928985972,
"reactions_found": 23,
"reactions_total": 63,
"st_id": "R-HSA-69620",
"url": "https://reactome.org/content/detail/R-HSA-69620"
},
{
"browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-6804757",
"entities_found": 3,
"entities_total": 43,
"fdr": 0.00022362020136756922,
"found_identifiers": [
"TP53",
"MDM2"
],
"in_disease": false,
"lowest_level": true,
"name": "Regulation of TP53 Degradation",
"p_value": 0.000020329109215233565,
"reactions_found": 28,
"reactions_total": 30,
"st_id": "R-HSA-6804757",
"url": "https://reactome.org/content/detail/R-HSA-6804757"
},
{
"browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-8866911",
"entities_found": 2,
"entities_total": 6,
"fdr": 0.00028280413526193815,
"found_identifiers": [
"CDKN1A"
],
"in_disease": false,
"lowest_level": true,
"name": "TFAP2 (AP-2) family regulates transcription of cell cycle factors",
"p_value": 0.000025709466841994377,
"reactions_found": 3,
"reactions_total": 4,
"st_id": "R-HSA-8866911",
"url": "https://reactome.org/content/detail/R-HSA-8866911"
},
{
"browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-5633007",
"entities_found": 4,
"entities_total": 179,
"fdr": 0.0006157208373491763,
"found_identifiers": [
"TP53",
"MDM2"
],
"in_disease": false,
"lowest_level": true,
"name": "Regulation of TP53 Activity",
"p_value": 0.00006157208373491763,
"reactions_found": 82,
"reactions_total": 97,
"st_id": "R-HSA-5633007",
"url": "https://reactome.org/content/detail/R-HSA-5633007"
},
{
"browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-2559586",
"entities_found": 3,
"entities_total": 71,
"fdr": 0.0008494493076508514,
"found_identifiers": [
"TP53",
"CDKN1A"
],
"in_disease": false,
"lowest_level": true,
"name": "DNA Damage/Telomere Stress Induced Senescence",
"p_value": 0.0000895289530208343,
"reactions_found": 7,
"reactions_total": 18,
"st_id": "R-HSA-2559586",
"url": "https://reactome.org/content/detail/R-HSA-2559586"
},
{
"browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-2559583",
"entities_found": 4,
"entities_total": 200,
"fdr": 0.0008494493076508514,
"found_identifiers": [
"TP53",
"MDM2",
"CDKN1A"
],
"in_disease": false,
"lowest_level": false,
"name": "Cellular Senescence",
"p_value": 0.00009438325640565015,
"reactions_found": 13,
"reactions_total": 90,
"st_id": "R-HSA-2559583",
"url": "https://reactome.org/content/detail/R-HSA-2559583"
},
{
"browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-6785807",
"entities_found": 4,
"entities_total": 211,
"fdr": 0.0010432216186526677,
"found_identifiers": [
"TP53",
"CDKN1A"
],
"in_disease": false,
"lowest_level": true,
"name": "Interleukin-4 and Interleukin-13 signaling",
"p_value": 0.00011591351318362975,
"reactions_found": 2,
"reactions_total": 47,
"st_id": "R-HSA-6785807",
"url": "https://reactome.org/content/detail/R-HSA-6785807"
},
{
"browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-198323",
"entities_found": 2,
"entities_total": 16,
"fdr": 0.0014518440864623727,
"found_identifiers": [
"MDM2",
"CDKN1A"
],
"in_disease": false,
"lowest_level": true,
"name": "AKT phosphorylates targets in the cytosol",
"p_value": 0.0001814805108077966,
"reactions_found": 2,
"reactions_total": 9,
"st_id": "R-HSA-198323",
"url": "https://reactome.org/content/detail/R-HSA-198323"
},
{
"browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-2559584",
"entities_found": 2,
"entities_total": 17,
"fdr": 0.0016377887554881454,
"found_identifiers": [
"TP53",
"CDKN1A"
],
"in_disease": false,
"lowest_level": true,
"name": "Formation of Senescence-Associated Heterochromatin Foci (SAHF)",
"p_value": 0.00020472359443601817,
"reactions_found": 1,
"reactions_total": 2,
"st_id": "R-HSA-2559584",
"url": "https://reactome.org/content/detail/R-HSA-2559584"
},
{
"browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-3232118",
"entities_found": 2,
"entities_total": 20,
"fdr": 0.002180353667100343,
"found_identifiers": [
"TP53",
"MDM2"
],
"in_disease": false,
"lowest_level": true,
"name": "SUMOylation of transcription factors",
"p_value": 0.00028272891015790336,
"reactions_found": 1,
"reactions_total": 11,
"st_id": "R-HSA-3232118",
"url": "https://reactome.org/content/detail/R-HSA-3232118"
}
],
"source_url": "https://reactome.org/AnalysisService/identifiers/?species=9606&pageSize=5000&page=1&sortBy=ENTITIES_FDR&order=ASC&resource=TOTAL&includeDisease=true&interactors=false",
"species": {
"name": "Homo sapiens",
"taxon_id": "9606"
}
}Data from Reactome (reactome.org), dedicated to the public domain under CC0 1.0. Reactome asks that you cite: Ragueneau E et al. The Reactome Knowledgebase 2026. Nucleic Acids Res. 2025, doi:10.1093/nar/gkaf1223. (https://reactome.org/license)
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