--- type: "firecrawl-provider" description: "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." use_when: "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." categories: "Life sciences" capabilities: 4 credits_per_call: 5 --- # Reactome: biological pathways and pathway enrichment on Firecrawl Alexandria 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. - Categories: Life sciences - Category index: [Life sciences category](https://firecrawl.dev/alexandria/agents/categories/life-sciences) - Provider key: `reactome-org` - Access: Firecrawl credits - Cost: 5 credits per call ## More - [Human guide](https://firecrawl.dev/app/alexandria/reactome-org) - [OpenAPI spec](https://firecrawl.dev/alexandria/agents/providers/reactome-org/openapi.json) ## Capabilities - [Enrichment](https://firecrawl.dev/alexandria/agents/providers/reactome-org/pathways/enrichment): Over-representation analysis of a gene, protein or chemical list with Reactome's Analysis Service: which pathways hold more of the listed molecules than chance predicts, by hypergeometric test with Benjamini-Hochberg FDR. Accepts up to 1,000 gene symbols, UniProt, Ensembl, NCBI Gene or ChEBI identifiers for one species. Each significant pathway has the molecules found out of its total, p-value, FDR, reactions found and which of the submitted identifiers it contains, most significant first. Also counts identifiers found and lists those Reactome does not know, and returns the analysis token and a Pathway Browser link to view the result, valid for about a week. - [Get](https://firecrawl.dev/alexandria/agents/providers/reactome-org/pathways/get): One Reactome pathway in full: name and synonyms, species, Reactome's curated summary, whether it is a disease pathway or inferred from human by orthology (with its source), review status and dates, DOI, the GO biological process it maps to, Disease Ontology terms, the normal pathway a disease variant perturbs, literature references with PubMed IDs, cross-references (BioModels, Rhea...), and its place in the hierarchy: direct parents, every path up to a top-level pathway, the top-level pathways, and its sub-pathways and reactions. Also orthologous pathways in other species, disease variants, the Reactome release and a ready citation. A reaction or molecule ID is refused with the pathways it belongs to. - [Participants](https://firecrawl.dev/alexandria/agents/providers/reactome-org/pathways/participants): The molecules taking part in a Reactome pathway and all its sub-pathways: proteins (UniProt), genes and RNAs (Ensembl, miRBase), small molecules (ChEBI), drugs (Guide to Pharmacology) and other references, each listed once with its database, identifier, name, link and how many of the pathway's physical entities (complexes, sets, modified forms) it is part of. Ordered by type, then name. `type_counts` counts every type, `types` filters, and `offset` pages through large pathways (Signal Transduction has over 2,500 proteins). - [Search](https://firecrawl.dev/alexandria/agents/providers/reactome-org/pathways/search): Find Reactome pathways in one of two modes. Gene mode (`gene`): every pathway, at every level of the hierarchy, that contains a gene, protein or chemical, given as a gene symbol (`EGFR`), UniProt accession (`P00533`), Ensembl gene ID, NCBI Gene ID or ChEBI ID, through Reactome's Analysis Service. Rows come most specific first (Reactome's p-value for that one identifier, which ranks small pathways where the molecule is a larger share first), each flagged lowest-level (drawn in a pathway diagram, not a grouping of pathways), top-level or disease, with the pathway's size; `top_level_pathways` lists the broad areas (Signal Transduction, Immune System...) the molecule sits in. Text mode (`query`): pathways whose name or summary match words or a topic (`apoptosis`, `insulin receptor signaling`), in Reactome's relevance order, each with the start of its summary. Both page with `offset`; `total_count` counts every match. An identifier Reactome does not know, or a query with no match, is an empty page with a warning. ## 1. Choose this provider when 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. ## 2. Minimal request Call `POST https://api.firecrawl.dev/v2/scrape` with `{ alexandria: { provider, capability, options } }`. For a batch, send `{ alexandria: [...] }` with up to 10 calls. ```json { "provider": "reactome-org", "capability": "pathways/enrichment", "options": { "identifiers": [ "TP53", "MDM2", "CDKN1A" ] } } ``` ## 3. Add provider options Use only the options needed for the task: - `identifiers` (string[], required): Genes, proteins or chemicals of one species: gene symbols (`TP53`, human only), UniProt accessions (`P04637`), Ensembl IDs, NCBI Gene IDs or ChEBI IDs, one per item. Repeats are dropped. Example: `["TP53"]` - `include_disease` (boolean): Include Reactome's disease pathways in the analysis. Default true. Example: `false` - `limit` (number): Most pathways to return. Example: `25` - `lowest_level_only` (boolean): Keep only Reactome's lowest-level pathways (those drawn in a pathway diagram), dropping broader groupings such as Signal Transduction. Default false. Example: `false` - `max_fdr` (number): Largest FDR (Benjamini-Hochberg adjusted p-value) a pathway may have to be listed. Example: `0.05` - `species` (string): Species: human by default. A name (`Homo sapiens`, `human`, `mouse`, `rat`, `zebrafish`, `yeast`), an NCBI taxonomy ID (`9606`, `10090`) or Reactome's three-letter code (`HSA`, `MMU`). Reactome curates human pathways and infers them for 15 model organisms: mouse, rat, cow, dog, pig, chicken, frog (X. tropicalis), zebrafish, fruit fly, C. elegans, budding and fission yeast, Dictyostelium, P. falciparum and M. tuberculosis. Example: `Homo sapiens` ## 4. Request through your preferred interface ### JavaScript ```javascript const result = await firecrawl.scrape({ alexandria: { provider: "reactome-org", capability: "pathways/enrichment", options: { identifiers: [ "TP53", "MDM2", "CDKN1A", ], }, }, }); ``` ### Python ```python result = firecrawl.scrape_alexandria({ "provider": "reactome-org", "capability": "pathways/enrichment", "options": { "identifiers": [ "TP53", "MDM2", "CDKN1A" ] } }) ``` ### cURL ```sh curl https://api.firecrawl.dev/v2/scrape \ -H "Authorization: Bearer $FIRECRAWL_API_KEY" \ -H "Content-Type: application/json" \ -d '{ "alexandria": { "provider": "reactome-org", "capability": "pathways/enrichment", "options": { "identifiers": [ "TP53", "MDM2", "CDKN1A" ] } } }' ``` ### CLI ```sh firecrawl scrape 'reactome-org/pathways/enrichment' \ --options '{"identifiers":["TP53","MDM2","CDKN1A"]}' ``` ### MCP Call the FCX MCP retrieve tool with this object: ```json { "provider": "reactome-org", "capability": "pathways/enrichment", "options": { "identifiers": [ "TP53", "MDM2", "CDKN1A" ] } } ``` Ask for only the returned fields needed by the task. ## 5. Full request shape ```json { "provider": "reactome-org", "capability": "pathways/enrichment", "options": { "identifiers": [ "TP53", "MDM2", "CDKN1A" ] } } ``` ## 6. Response data The response includes `success`, `provider`, `capability`, `creditsCost` and `data`. This example shows the provider payload in `data`: ```json { "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" } } ``` ## API reference-derived contract The following capability contract is generated from the same normalized Alexandria API reference exposed in the API spec. ### Enrichment - Capability: `pathways/enrichment` - Description: Over-representation analysis of a gene, protein or chemical list with Reactome's Analysis Service: which pathways hold more of the listed molecules than chance predicts, by hypergeometric test with Benjamini-Hochberg FDR. Accepts up to 1,000 gene symbols, UniProt, Ensembl, NCBI Gene or ChEBI identifiers for one species. Each significant pathway has the molecules found out of its total, p-value, FDR, reactions found and which of the submitted identifiers it contains, most significant first. Also counts identifiers found and lists those Reactome does not know, and returns the analysis token and a Pathway Browser link to view the result, valid for about a week. - Instructions: For a list of genes ("enriched pathways for TP53, MDM2, CDKN1A", "which pathways are over-represented in these 10 genes", a differential expression hit list). For one gene's pathways use `pathways/search` with `gene`. Raise `max_fdr` (default 0.05) to see weaker hits; gene symbols match only for human, so use UniProt accessions for other species. - Cost: 5 credits per call - Capability file: [Enrichment](https://firecrawl.dev/alexandria/agents/providers/reactome-org/pathways/enrichment) Accepted options: - `identifiers` (string[], required): Genes, proteins or chemicals of one species: gene symbols (`TP53`, human only), UniProt accessions (`P04637`), Ensembl IDs, NCBI Gene IDs or ChEBI IDs, one per item. Repeats are dropped. Example: `["TP53"]` - `include_disease` (boolean): Include Reactome's disease pathways in the analysis. Default true. Example: `false` - `limit` (number): Most pathways to return. Example: `25` - `lowest_level_only` (boolean): Keep only Reactome's lowest-level pathways (those drawn in a pathway diagram), dropping broader groupings such as Signal Transduction. Default false. Example: `false` - `max_fdr` (number): Largest FDR (Benjamini-Hochberg adjusted p-value) a pathway may have to be listed. Example: `0.05` - `species` (string): Species: human by default. A name (`Homo sapiens`, `human`, `mouse`, `rat`, `zebrafish`, `yeast`), an NCBI taxonomy ID (`9606`, `10090`) or Reactome's three-letter code (`HSA`, `MMU`). Reactome curates human pathways and infers them for 15 model organisms: mouse, rat, cow, dog, pig, chicken, frog (X. tropicalis), zebrafish, fruit fly, C. elegans, budding and fission yeast, Dictyostelium, P. falciparum and M. tuberculosis. Example: `Homo sapiens` Response schema example: ```json { "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" } } ``` ### Get - Capability: `pathways/get` - Description: One Reactome pathway in full: name and synonyms, species, Reactome's curated summary, whether it is a disease pathway or inferred from human by orthology (with its source), review status and dates, DOI, the GO biological process it maps to, Disease Ontology terms, the normal pathway a disease variant perturbs, literature references with PubMed IDs, cross-references (BioModels, Rhea...), and its place in the hierarchy: direct parents, every path up to a top-level pathway, the top-level pathways, and its sub-pathways and reactions. Also orthologous pathways in other species, disease variants, the Reactome release and a ready citation. A reaction or molecule ID is refused with the pathways it belongs to. - Instructions: After `pathways/search`, to explain what a pathway does and where it sits ("what is R-HSA-177929", "what is Signaling by EGFR part of"). Its literature PMIDs open in Europe PMC or PubMed providers, its GO ID in QuickGO. For the genes and chemicals in the pathway use `pathways/participants`. - Cost: 5 credits per call - Capability file: [Get](https://firecrawl.dev/alexandria/agents/providers/reactome-org/pathways/get) Accepted options: - `pathway` (string, required): A Reactome pathway: stable ID (`R-HSA-177929`, version suffix allowed: `R-HSA-177929.6`), database ID (`177929`) or a reactome.org pathway page (`https://reactome.org/content/detail/R-HSA-177929`, `https://reactome.org/PathwayBrowser/#/R-HSA-177929`). `pathways/search` finds the ID from a gene or a name. Example: `R-HSA-177929` Response schema example: ```json { "browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-177929", "citation": "Signaling by EGFR. Reactome, release 98, https://reactome.org/content/detail/R-HSA-177929, doi:10.3180/R-HSA-177929.5", "cross_references": [ { "database": "BioModels Database", "identifier": "BIOMD0000000175", "url": "https://www.ebi.ac.uk/biomodels/BIOMD0000000175" }, { "database": "BioModels Database", "identifier": "BIOMD0000000477", "url": "https://www.ebi.ac.uk/biomodels/BIOMD0000000477" }, { "database": "BioModels Database", "identifier": "BIOMD0000000653", "url": "https://www.ebi.ac.uk/biomodels/BIOMD0000000653" }, { "database": "BioModels Database", "identifier": "BIOMD0000000255", "url": "https://www.ebi.ac.uk/biomodels/BIOMD0000000255" }, { "database": "BioModels Database", "identifier": "BIOMD0000000223", "url": "https://www.ebi.ac.uk/biomodels/BIOMD0000000223" }, { "database": "BioModels Database", "identifier": "BIOMD0000000652", "url": "https://www.ebi.ac.uk/biomodels/BIOMD0000000652" }, { "database": "BioModels Database", "identifier": "BIOMD0000000594", "url": "https://www.ebi.ac.uk/biomodels/BIOMD0000000594" }, { "database": "BioModels Database", "identifier": "BIOMD0000000399", "url": "https://www.ebi.ac.uk/biomodels/BIOMD0000000399" }, { "database": "BioModels Database", "identifier": "BIOMD0000000019", "url": "https://www.ebi.ac.uk/biomodels/BIOMD0000000019" }, { "database": "BioModels Database", "identifier": "BIOMD0000000656", "url": "https://www.ebi.ac.uk/biomodels/BIOMD0000000656" }, { "database": "BioModels Database", "identifier": "BIOMD0000000883", "url": "https://www.ebi.ac.uk/biomodels/BIOMD0000000883" }, { "database": "BioModels Database", "identifier": "BIOMD0000000648", "url": "https://www.ebi.ac.uk/biomodels/BIOMD0000000648" }, { "database": "BioModels Database", "identifier": "BIOMD0000000468", "url": "https://www.ebi.ac.uk/biomodels/BIOMD0000000468" }, { "database": "BioModels Database", "identifier": "BIOMD0000000654", "url": "https://www.ebi.ac.uk/biomodels/BIOMD0000000654" }, { "database": "BioModels Database", "identifier": "BIOMD0000000595", "url": "https://www.ebi.ac.uk/biomodels/BIOMD0000000595" }, { "database": "BioModels Database", "identifier": "BIOMD0000000655", "url": "https://www.ebi.ac.uk/biomodels/BIOMD0000000655" }, { "database": "BioModels Database", "identifier": "BIOMD0000000466", "url": "https://www.ebi.ac.uk/biomodels/BIOMD0000000466" } ], "db_id": 177929, "disease_variants": [ { "in_disease": true, "inferred": false, "name": "Signaling by Overexpressed Wild-Type EGFR in Cancer", "species": "Homo sapiens", "st_id": "R-HSA-5638302", "type": "pathway" }, { "in_disease": true, "inferred": false, "name": "Signaling by EGFRvIII in Cancer", "species": "Homo sapiens", "st_id": "R-HSA-5637812", "type": "pathway" }, { "in_disease": true, "inferred": false, "name": "Signaling by Ligand-Responsive EGFR Variants in Cancer", "species": "Homo sapiens", "st_id": "R-HSA-5637815", "type": "pathway" } ], "diseases": [], "doi": "10.3180/R-HSA-177929.5", "go_biological_process": { "id": "GO:0007173", "name": "epidermal growth factor receptor signaling pathway", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0007173" }, "has_diagram": true, "hierarchy": { "ancestor_paths": [ [ { "name": "Signal Transduction", "st_id": "R-HSA-162582" }, { "name": "Signaling by Receptor Tyrosine Kinases", "st_id": "R-HSA-9006934" } ] ], "children": [ { "in_disease": false, "inferred": true, "name": "Pro-EGF is cleaved to form mature EGF", "species": "Homo sapiens", "st_id": "R-HSA-177946", "type": "reaction" }, { "in_disease": false, "inferred": false, "name": "AAMP binds EGFR", "species": "Homo sapiens", "st_id": "R-HSA-9674531", "type": "reaction" }, { "in_disease": false, "inferred": false, "name": "FAM83B, (FAM83A, FAM83D) bind EGFR", "species": "Homo sapiens", "st_id": "R-HSA-9851407", "type": "reaction" }, { "in_disease": false, "inferred": false, "name": "EGFR binds EGF ligand", "species": "Homo sapiens", "st_id": "R-HSA-177942", "type": "reaction" }, { "in_disease": false, "inferred": false, "name": "EGFR dimerization", "species": "Homo sapiens", "st_id": "R-HSA-177922", "type": "reaction" }, { "in_disease": false, "inferred": false, "name": "EGFR autophosphorylation", "species": "Homo sapiens", "st_id": "R-HSA-177934", "type": "reaction" }, { "in_disease": false, "inferred": false, "name": "Phosphorylation of EGFR by SRC kinase", "species": "Homo sapiens", "st_id": "R-HSA-177937", "type": "reaction" }, { "in_disease": false, "inferred": false, "name": "EGFR interacts with phospholipase C-gamma", "species": "Homo sapiens", "st_id": "R-HSA-212718", "type": "pathway" }, { "in_disease": false, "inferred": false, "name": "GRB2 events in EGFR signaling", "species": "Homo sapiens", "st_id": "R-HSA-179812", "type": "pathway" }, { "in_disease": false, "inferred": false, "name": "SHC1 events in EGFR signaling", "species": "Homo sapiens", "st_id": "R-HSA-180336", "type": "pathway" }, { "in_disease": false, "inferred": false, "name": "GAB1 signalosome", "species": "Homo sapiens", "st_id": "R-HSA-180292", "type": "pathway" }, { "in_disease": false, "inferred": false, "name": "EGFR downregulation", "species": "Homo sapiens", "st_id": "R-HSA-182971", "type": "pathway" } ], "parents": [ { "in_disease": false, "inferred": false, "name": "Signaling by Receptor Tyrosine Kinases", "species": "Homo sapiens", "st_id": "R-HSA-9006934", "type": "pathway" } ], "top_level": [ { "name": "Signal Transduction", "st_id": "R-HSA-162582" } ] }, "in_disease": false, "inferred": false, "inferred_from": [], "last_updated": "2023-03-29", "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/" }, "literature": [ { "journal": "Nat Rev Mol Cell Biol", "pmid": 21252999, "title": "Feedback regulation of EGFR signalling: decision making by early and delayed loops", "type": "article", "url": "https://www.ncbi.nlm.nih.gov/pubmed/21252999", "year": 2011 }, { "journal": "Oncotarget", "pmid": 27221039, "title": "FAM83 proteins: Fostering new interactions to drive oncogenic signaling and therapeutic resistance", "type": "article", "url": "https://www.ncbi.nlm.nih.gov/pubmed/27221039", "year": 2016 }, { "journal": "Int J Radiat Oncol Biol Phys", "pmid": 15142631, "title": "Review of epidermal growth factor receptor biology", "type": "article", "url": "https://www.ncbi.nlm.nih.gov/pubmed/15142631", "year": 2004 }, { "journal": "Biochem Pharmacol", "pmid": 36191627, "title": "Overview of the multifaceted resistances toward EGFR-TKIs and new chemotherapeutic strategies in non-small cell lung cancer", "type": "article", "url": "https://www.ncbi.nlm.nih.gov/pubmed/36191627", "year": 2022 }, { "journal": "Int J Biochem Cell Biol", "pmid": 10404636, "title": "EGF receptor", "type": "article", "url": "https://www.ncbi.nlm.nih.gov/pubmed/10404636", "year": 1999 }, { "journal": "J Cell Biol", "pmid": 10459005, "title": "Employment of the epidermal growth factor receptor in growth factor-independent signaling pathways", "type": "article", "url": "https://www.ncbi.nlm.nih.gov/pubmed/10459005", "year": 1999 }, { "journal": "Cell", "pmid": 12297041, "title": "Ligand-induced, receptor-mediated dimerization and activation of EGF receptor", "type": "article", "url": "https://www.ncbi.nlm.nih.gov/pubmed/12297041", "year": 2002 }, { "journal": "Cancers (Basel)", "pmid": 34206026, "title": "EGFR in Cancer: Signaling Mechanisms, Drugs, and Acquired Resistance", "type": "article", "url": "https://www.ncbi.nlm.nih.gov/pubmed/34206026", "year": 2021 } ], "name": "Signaling by EGFR", "normal_pathway": null, "observed_at_ms": 1793395318775, "orthologs": [ { "species": "Mus musculus", "st_id": "R-MMU-177929" }, { "species": "Rattus norvegicus", "st_id": "R-RNO-177929" }, { "species": "Canis familiaris", "st_id": "R-CFA-177929" }, { "species": "Bos taurus", "st_id": "R-BTA-177929" }, { "species": "Sus scrofa", "st_id": "R-SSC-177929" }, { "species": "Danio rerio", "st_id": "R-DRE-177929" }, { "species": "Drosophila melanogaster", "st_id": "R-DME-177929" }, { "species": "Caenorhabditis elegans", "st_id": "R-CEL-177929" }, { "species": "Gallus gallus", "st_id": "R-GGA-177929" }, { "species": "Xenopus tropicalis", "st_id": "R-XTR-177929" } ], "release": "98", "release_date": "2007-02-20", "review_status": "five stars", "species": "Homo sapiens", "st_id": "R-HSA-177929", "st_id_version": "R-HSA-177929.6", "summary": "The epidermal growth factor receptor (EGFR) is one member of the ERBB family of transmembrane glycoprotein tyrosine receptor kinases (RTK). Binding of EGFR to its ligands induces conformational change that unmasks the dimerization interface in the extracellular domain of EGFR, leading to receptor homo- or heterodimerization at the cell surface. Dimerization of the extracellular regions of EGFR triggers additional conformational change of the cytoplasmic EGFR regions, enabling the kinase domains of two EGFR molecules to achieve the catalytically active conformation. Ligand activated EGFR dimers trans-autophosphorylate on tyrosine residues in the cytoplasmic tail of the receptor. Phosphorylated tyrosines serve as binding sites for the recruitment of signal transducers and activators of intracellular substrates, which then stimulate intracellular signal transduction cascades that are involved in regulating cellular proliferation, differentiation, and survival. Recruitment of complexes containing GRB2 and SOS1 to phosphorylated EGFR dimers either directly, through phosphotyrosine residues that serve as GRB2 docking sites, or indirectly, through SHC1 recruitment, promotes GDP to GTP exchange on RAS, resulting in the activation of RAF/MAP kinase cascade. Binding of complexes of GRB2 and GAB1 to phosphorylated EGFR dimers leads to formation of the active PI3K complex, conversion of PIP2 into PIP3, and activation of AKT signaling. Phospholipase C-gamma1 (PLCG1) can also be recruited directly, through EGFR phosphotyrosine residues that serve as PLCG1 docking sites, which leads to PLCG1 phosphorylation by EGFR and activation of DAG and IP3 signaling. EGFR signaling is downregulated by the action of ubiquitin ligase CBL. CBL binds directly to the phosphorylated EGFR dimer through the phosphotyrosine Y1069 (i.e. Y1045 in the mature protein) in the C-tail of EGFR, and after CBL is phosphorylated by EGFR, it becomes active and ubiquitinates phosphorylated EGFR dimers, targeting them for degradation. Positive regulation of EGFR signaling by direct association of EGFR with accessory proteins such as AAMP and FAM83B is being investigated. For review of EGFR signaling, please refer to Carpenter 1999, Wells 1999, Schlessinger 2002, Herbst 2004, Avraham and Yarden, 2011, Bartel et al. 2016, Uribe et al. 2021, Keflee et al. 2022.", "synonyms": [ "Epidermal Growth Factor Receptor (EGFR) signaling" ], "taxon_id": "9606", "type": "pathway", "url": "https://reactome.org/content/detail/R-HSA-177929" } ``` ### Participants - Capability: `pathways/participants` - Description: The molecules taking part in a Reactome pathway and all its sub-pathways: proteins (UniProt), genes and RNAs (Ensembl, miRBase), small molecules (ChEBI), drugs (Guide to Pharmacology) and other references, each listed once with its database, identifier, name, link and how many of the pathway's physical entities (complexes, sets, modified forms) it is part of. Ordered by type, then name. `type_counts` counts every type, `types` filters, and `offset` pages through large pathways (Signal Transduction has over 2,500 proteins). - Instructions: To list the genes, proteins or chemicals in a pathway ("which proteins are in Signaling by EGFR"), for example to build a gene set or to look the proteins up in uniprot-org or the chemicals in ChEMBL. Find the pathway first with `pathways/search`. - Cost: 5 credits per call - Capability file: [Participants](https://firecrawl.dev/alexandria/agents/providers/reactome-org/pathways/participants) Accepted options: - `limit` (number): Rows per page. Example: `200` - `offset` (number): Rows to skip: `next_offset` from the previous page. Repeat the other inputs with it. Example: `0` - `pathway` (string, required): A Reactome pathway: stable ID (`R-HSA-177929`, version suffix allowed: `R-HSA-177929.6`), database ID (`177929`) or a reactome.org pathway page (`https://reactome.org/content/detail/R-HSA-177929`, `https://reactome.org/PathwayBrowser/#/R-HSA-177929`). `pathways/search` finds the ID from a gene or a name. Example: `R-HSA-177929` - `types` (string[]): Only these molecule types: `protein` (UniProt), `gene` (DNA), `rna` (RNA, e.g. miRBase), `chemical` (ChEBI small molecules), `drug` (therapeutics), `other`. Default all. Example: `[]` Response schema example: ```json { "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": 200, "next_offset": null, "observed_at_ms": 1793395318800, "offset": 0, "pathway": { "name": "Signaling by EGFR", "species": "Homo sapiens", "st_id": "R-HSA-177929", "taxon_id": "9606" }, "physical_entity_count": 88, "release": "98", "results": [ { "database": "UniProt", "entity_count": 2, "identifier": "Q13685", "name": "AAMP", "type": "protein", "url": "https://purl.uniprot.org/uniprot/Q13685" }, { "database": "UniProt", "entity_count": 1, "identifier": "O14672", "name": "ADAM10", "type": "protein", "url": "https://purl.uniprot.org/uniprot/O14672" }, { "database": "UniProt", "entity_count": 1, "identifier": "O43184", "name": "ADAM12", "type": "protein", "url": "https://purl.uniprot.org/uniprot/O43184" }, { "database": "UniProt", "entity_count": 1, "identifier": "P78536", "name": "ADAM17", "type": "protein", "url": "https://purl.uniprot.org/uniprot/P78536" }, { "database": "UniProt", "entity_count": 32, "identifier": "P15514", "name": "AREG", "type": "protein", "url": "https://purl.uniprot.org/uniprot/P15514" }, { "database": "UniProt", "entity_count": 5, "identifier": "Q14155", "name": "ARHGEF7", "type": "protein", "url": "https://purl.uniprot.org/uniprot/Q14155" }, { "database": "UniProt", "entity_count": 32, "identifier": "P35070", "name": "BTC", "type": "protein", "url": "https://purl.uniprot.org/uniprot/P35070" }, { "database": "UniProt", "entity_count": 20, "identifier": "P22681", "name": "CBL", "type": "protein", "url": "https://purl.uniprot.org/uniprot/P22681" }, { "database": "UniProt", "entity_count": 5, "identifier": "P60953", "name": "CDC42", "type": "protein", "url": "https://purl.uniprot.org/uniprot/P60953" }, { "database": "UniProt", "entity_count": 2, "identifier": "P41240", "name": "CSK", "type": "protein", "url": "https://purl.uniprot.org/uniprot/P41240" }, { "database": "UniProt", "entity_count": 36, "identifier": "P01133", "name": "EGF", "type": "protein", "url": "https://purl.uniprot.org/uniprot/P01133" }, { "database": "UniProt", "entity_count": 36, "identifier": "P00533", "name": "EGFR", "type": "protein", "url": "https://purl.uniprot.org/uniprot/P00533" }, { "database": "UniProt", "entity_count": 32, "identifier": "Q6UW88", "name": "EPGN", "type": "protein", "url": "https://purl.uniprot.org/uniprot/Q6UW88" }, { "database": "UniProt", "entity_count": 6, "identifier": "Q9Y6I3", "name": "EPN1", "type": "protein", "url": "https://purl.uniprot.org/uniprot/Q9Y6I3" }, { "database": "UniProt", "entity_count": 6, "identifier": "P42566", "name": "EPS15", "type": "protein", "url": "https://purl.uniprot.org/uniprot/P42566" }, { "database": "UniProt", "entity_count": 6, "identifier": "Q9UBC2", "name": "EPS15L1", "type": "protein", "url": "https://purl.uniprot.org/uniprot/Q9UBC2" }, { "database": "UniProt", "entity_count": 32, "identifier": "O14944", "name": "EREG", "type": "protein", "url": "https://purl.uniprot.org/uniprot/O14944" }, { "database": "UniProt", "entity_count": 2, "identifier": "Q86UY5", "name": "FAM83A", "type": "protein", "url": "https://purl.uniprot.org/uniprot/Q86UY5" }, { "database": "UniProt", "entity_count": 2, "identifier": "Q5T0W9", "name": "FAM83B", "type": "protein", "url": "https://purl.uniprot.org/uniprot/Q5T0W9" }, { "database": "UniProt", "entity_count": 2, "identifier": "Q9H4H8", "name": "FAM83D", "type": "protein", "url": "https://purl.uniprot.org/uniprot/Q9H4H8" }, { "database": "UniProt", "entity_count": 10, "identifier": "Q13480", "name": "GAB1", "type": "protein", "url": "https://purl.uniprot.org/uniprot/Q13480" }, { "database": "UniProt", "entity_count": 22, "identifier": "P62993-1", "name": "GRB2", "type": "protein", "url": "https://purl.uniprot.org/uniprot/P62993-1" }, { "database": "UniProt", "entity_count": 32, "identifier": "Q99075", "name": "HBEGF", "type": "protein", "url": "https://purl.uniprot.org/uniprot/Q99075" }, { "database": "UniProt", "entity_count": 6, "identifier": "O14964", "name": "HGS", "type": "protein", "url": "https://purl.uniprot.org/uniprot/O14964" }, { "database": "UniProt", "entity_count": 2, "identifier": "P01112", "name": "HRAS", "type": "protein", "url": "https://purl.uniprot.org/uniprot/P01112" }, { "database": "UniProt", "entity_count": 2, "identifier": "P01116-1", "name": "KRAS", "type": "protein", "url": "https://purl.uniprot.org/uniprot/P01116-1" }, { "database": "UniProt", "entity_count": 2, "identifier": "P01116-2", "name": "KRAS", "type": "protein", "url": "https://purl.uniprot.org/uniprot/P01116-2" }, { "database": "UniProt", "entity_count": 1, "identifier": "Q96JA1", "name": "LRIG1", "type": "protein", "url": "https://purl.uniprot.org/uniprot/Q96JA1" }, { "database": "UniProt", "entity_count": 2, "identifier": "P01111", "name": "NRAS", "type": "protein", "url": "https://purl.uniprot.org/uniprot/P01111" }, { "database": "UniProt", "entity_count": 2, "identifier": "Q9NWQ8", "name": "PAG1", "type": "protein", "url": "https://purl.uniprot.org/uniprot/Q9NWQ8" }, { "database": "UniProt", "entity_count": 2, "identifier": "P42336", "name": "PIK3CA", "type": "protein", "url": "https://purl.uniprot.org/uniprot/P42336" }, { "database": "UniProt", "entity_count": 2, "identifier": "P27986", "name": "PIK3R1", "type": "protein", "url": "https://purl.uniprot.org/uniprot/P27986" }, { "database": "UniProt", "entity_count": 4, "identifier": "P19174", "name": "PLCG1", "type": "protein", "url": "https://purl.uniprot.org/uniprot/P19174" }, { "database": "UniProt", "entity_count": 4, "identifier": "Q06124", "name": "PTPN11", "type": "protein", "url": "https://purl.uniprot.org/uniprot/Q06124" }, { "database": "UniProt", "entity_count": 1, "identifier": "Q05209", "name": "PTPN12", "type": "protein", "url": "https://purl.uniprot.org/uniprot/Q05209" }, { "database": "UniProt", "entity_count": 1, "identifier": "P26045", "name": "PTPN3", "type": "protein", "url": "https://purl.uniprot.org/uniprot/P26045" }, { "database": "UniProt", "entity_count": 1, "identifier": "Q15262", "name": "PTPRK", "type": "protein", "url": "https://purl.uniprot.org/uniprot/Q15262" }, { "database": "UniProt", "entity_count": 2, "identifier": "P49023", "name": "PXN", "type": "protein", "url": "https://purl.uniprot.org/uniprot/P49023" }, { "database": "UniProt", "entity_count": 5, "identifier": "P62979", "name": "RPS27A", "type": "protein", "url": "https://purl.uniprot.org/uniprot/P62979" }, { "database": "UniProt", "entity_count": 8, "identifier": "Q99961", "name": "SH3GL1", "type": "protein", "url": "https://purl.uniprot.org/uniprot/Q99961" }, { "database": "UniProt", "entity_count": 8, "identifier": "Q99962", "name": "SH3GL2", "type": "protein", "url": "https://purl.uniprot.org/uniprot/Q99962" }, { "database": "UniProt", "entity_count": 8, "identifier": "Q99963", "name": "SH3GL3", "type": "protein", "url": "https://purl.uniprot.org/uniprot/Q99963" }, { "database": "UniProt", "entity_count": 8, "identifier": "Q96B97", "name": "SH3KBP1", "type": "protein", "url": "https://purl.uniprot.org/uniprot/Q96B97" }, { "database": "UniProt", "entity_count": 4, "identifier": "P29353", "name": "SHC1", "type": "protein", "url": "https://purl.uniprot.org/uniprot/P29353" }, { "database": "UniProt", "entity_count": 4, "identifier": "Q07889", "name": "SOS1", "type": "protein", "url": "https://purl.uniprot.org/uniprot/Q07889" }, { "database": "UniProt", "entity_count": 6, "identifier": "O43609", "name": "SPRY1", "type": "protein", "url": "https://purl.uniprot.org/uniprot/O43609" }, { "database": "UniProt", "entity_count": 7, "identifier": "O43597", "name": "SPRY2", "type": "protein", "url": "https://purl.uniprot.org/uniprot/O43597" }, { "database": "UniProt", "entity_count": 2, "identifier": "P12931", "name": "SRC", "type": "protein", "url": "https://purl.uniprot.org/uniprot/P12931" }, { "database": "UniProt", "entity_count": 1, "identifier": "P12931-1", "name": "SRC", "type": "protein", "url": "https://purl.uniprot.org/uniprot/P12931-1" }, { "database": "UniProt", "entity_count": 6, "identifier": "Q92783", "name": "STAM", "type": "protein", "url": "https://purl.uniprot.org/uniprot/Q92783" }, { "database": "UniProt", "entity_count": 6, "identifier": "O75886", "name": "STAM2", "type": "protein", "url": "https://purl.uniprot.org/uniprot/O75886" }, { "database": "UniProt", "entity_count": 32, "identifier": "P01135", "name": "TGFA", "type": "protein", "url": "https://purl.uniprot.org/uniprot/P01135" }, { "database": "UniProt", "entity_count": 5, "identifier": "P62987", "name": "UBA52", "type": "protein", "url": "https://purl.uniprot.org/uniprot/P62987" }, { "database": "UniProt", "entity_count": 5, "identifier": "P0CG47", "name": "UBB", "type": "protein", "url": "https://purl.uniprot.org/uniprot/P0CG47" }, { "database": "UniProt", "entity_count": 5, "identifier": "P0CG48", "name": "UBC", "type": "protein", "url": "https://purl.uniprot.org/uniprot/P0CG48" } ], "source_url": "https://reactome.org/ContentService/data/participants/R-HSA-177929", "total_count": 55, "type_counts": { "chemical": 9, "drug": 0, "gene": 0, "other": 0, "protein": 55, "rna": 0 }, "types": [ "protein" ], "url": "https://reactome.org/content/detail/R-HSA-177929" } ``` ### Search - Capability: `pathways/search` - Description: Find Reactome pathways in one of two modes. Gene mode (`gene`): every pathway, at every level of the hierarchy, that contains a gene, protein or chemical, given as a gene symbol (`EGFR`), UniProt accession (`P00533`), Ensembl gene ID, NCBI Gene ID or ChEBI ID, through Reactome's Analysis Service. Rows come most specific first (Reactome's p-value for that one identifier, which ranks small pathways where the molecule is a larger share first), each flagged lowest-level (drawn in a pathway diagram, not a grouping of pathways), top-level or disease, with the pathway's size; `top_level_pathways` lists the broad areas (Signal Transduction, Immune System...) the molecule sits in. Text mode (`query`): pathways whose name or summary match words or a topic (`apoptosis`, `insulin receptor signaling`), in Reactome's relevance order, each with the start of its summary. Both page with `offset`; `total_count` counts every match. An identifier Reactome does not know, or a query with no match, is an empty page with a warning. - Instructions: Start here for "which pathways is EGFR in" (gene mode) or "find the Reactome pathway for apoptosis" (text mode), then pass a row's `st_id` to `pathways/get` for its summary, literature and hierarchy, or to `pathways/participants` for its molecules. For a list of genes and which pathways are over-represented in it, use `pathways/enrichment` instead. Gene symbols match only for human; for other species pass the UniProt accession (from uniprot-org `map_ids`). - Cost: 5 credits per call - Capability file: [Search](https://firecrawl.dev/alexandria/agents/providers/reactome-org/pathways/search) Accepted options: - `gene` (string): Gene mode: one gene, protein or chemical identifier: a gene symbol (`EGFR`, human only), UniProt accession (`P00533`), Ensembl ID (`ENSG00000146648`), NCBI Gene ID or ChEBI ID (`CHEBI:15422`). Pass `gene` or `query`, not both. Example: `` - `limit` (number): Rows per page. Example: `25` - `lowest_level_only` (boolean): Gene mode only: keep only Reactome's lowest-level pathways (those drawn in a pathway diagram), dropping the broader groupings every hit is nested in, such as Signal Transduction or Disease. Default false. Example: `false` - `offset` (number): Rows to skip: `next_offset` from the previous page. Repeat the other inputs with it. Example: `0` - `query` (string): Text mode: words or a topic matched against pathway names and summaries, e.g. `apoptosis`, `insulin receptor signaling`. Pass `gene` or `query`, not both. Example: `` - `species` (string): Species: human by default. A name (`Homo sapiens`, `human`, `mouse`, `rat`, `zebrafish`, `yeast`), an NCBI taxonomy ID (`9606`, `10090`) or Reactome's three-letter code (`HSA`, `MMU`). Reactome curates human pathways and infers them for 15 model organisms: mouse, rat, cow, dog, pig, chicken, frog (X. tropicalis), zebrafish, fruit fly, C. elegans, budding and fission yeast, Dictyostelium, P. falciparum and M. tuberculosis. Example: `Homo sapiens` Response schema example: ```json { "gene": "EGFR", "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. 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"https://reactome.org/PathwayBrowser/#/R-HSA-8864260", "entities_total": 52, "in_disease": false, "lowest_level": true, "name": "Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors", "st_id": "R-HSA-8864260", "summary": null, "top_level": false, "url": "https://reactome.org/content/detail/R-HSA-8864260" }, { "browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-9924644", "entities_total": 81, "in_disease": false, "lowest_level": false, "name": "Developmental Lineages of the Mammary Gland", "st_id": "R-HSA-9924644", "summary": null, "top_level": false, "url": "https://reactome.org/content/detail/R-HSA-9924644" }, { "browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-9734779", "entities_total": 122, "in_disease": false, "lowest_level": false, "name": "Developmental Cell Lineages of the Integumentary System", "st_id": "R-HSA-9734779", "summary": null, "top_level": false, "url": "https://reactome.org/content/detail/R-HSA-9734779" }, { "browser_url": 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growth factor receptors and second messengers", "st_id": "R-HSA-5663202", "summary": null, "top_level": false, "url": "https://reactome.org/content/detail/R-HSA-5663202" }, { "browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-422475", "entities_total": 565, "in_disease": false, "lowest_level": false, "name": "Axon guidance", "st_id": "R-HSA-422475", "summary": null, "top_level": false, "url": "https://reactome.org/content/detail/R-HSA-422475" }, { "browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-9675108", "entities_total": 602, "in_disease": false, "lowest_level": false, "name": "Nervous system development", "st_id": "R-HSA-9675108", "summary": null, "top_level": false, "url": "https://reactome.org/content/detail/R-HSA-9675108" }, { "browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-9006934", "entities_total": 633, "in_disease": false, "lowest_level": false, "name": "Signaling by Receptor Tyrosine Kinases", "st_id": "R-HSA-9006934", "summary": null, "top_level": false, "url": "https://reactome.org/content/detail/R-HSA-9006934" }, { "browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-199991", "entities_total": 667, "in_disease": false, "lowest_level": false, "name": "Membrane Trafficking", "st_id": "R-HSA-199991", "summary": null, "top_level": false, "url": "https://reactome.org/content/detail/R-HSA-199991" }, { "browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-388396", "entities_total": 794, "in_disease": false, "lowest_level": false, "name": "GPCR downstream signalling", "st_id": "R-HSA-388396", "summary": null, "top_level": false, "url": "https://reactome.org/content/detail/R-HSA-388396" }, { "browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-5653656", "entities_total": 840, "in_disease": false, "lowest_level": false, "name": "Vesicle-mediated transport", "st_id": "R-HSA-5653656", "summary": null, "top_level": true, "url": "https://reactome.org/content/detail/R-HSA-5653656" }, { "browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-372790", "entities_total": 877, "in_disease": false, "lowest_level": false, "name": "Signaling by GPCR", "st_id": "R-HSA-372790", "summary": null, "top_level": false, "url": "https://reactome.org/content/detail/R-HSA-372790" }, { "browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-9824446", "entities_total": 1411, "in_disease": true, "lowest_level": false, "name": "Viral Infection Pathways", "st_id": "R-HSA-9824446", "summary": null, "top_level": false, "url": "https://reactome.org/content/detail/R-HSA-9824446" }, { "browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-5663205", "entities_total": 1968, "in_disease": true, "lowest_level": false, "name": "Infectious disease", "st_id": "R-HSA-5663205", "summary": null, "top_level": false, "url": "https://reactome.org/content/detail/R-HSA-5663205" }, { "browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-162582", "entities_total": 3054, "in_disease": false, "lowest_level": false, "name": "Signal Transduction", "st_id": "R-HSA-162582", "summary": null, "top_level": true, "url": "https://reactome.org/content/detail/R-HSA-162582" }, { "browser_url": "https://reactome.org/PathwayBrowser/#/R-HSA-1643685", "entities_total": 3094, "in_disease": true, "lowest_level": false, "name": "Disease", "st_id": "R-HSA-1643685", "summary": null, "top_level": true, "url": "https://reactome.org/content/detail/R-HSA-1643685" } ], "source_url": "https://reactome.org/AnalysisService/identifier/EGFR?species=9606&pageSize=5000&page=1&sortBy=ENTITIES_PVALUE&order=ASC&resource=TOTAL&includeDisease=true&interactors=false", "species": { "name": "Homo sapiens", "taxon_id": "9606" }, "top_level_pathways": [ { "name": "Gene expression (Transcription)", "st_id": "R-HSA-74160" }, { "name": "Developmental Biology", "st_id": "R-HSA-1266738" }, { "name": "Vesicle-mediated transport", "st_id": "R-HSA-5653656" }, { "name": "Signal Transduction", "st_id": "R-HSA-162582" }, { "name": "Disease", "st_id": "R-HSA-1643685" } ], "total_count": 78 } ```