{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.tr.nr1h4","code":"thing-q14905041","url":"https://ver.cy/models/thing/q14905041/","name":"NR1H4","alternateNames":[],"kind":"thing","status":"published","version":"0.1.0-research.1","language":"en","classifiers":{"family":"Thing Registry","category":"Physical world and living systems","entryKind":"thing","plane":"PHY","domain":["PHY.OBJ"],"industry":[],"navPath":"","tags":[],"facets":{}},"whatItIs":"NR1H4 is a gene encoding the farnesoid X receptor (FXR), a bile-acid-activated nuclear receptor that regulates transcription involved in bile acid homeostasis and lipid and glucose metabolism.","purpose":"Enable an agent to identify NR1H4, distinguish its gene and receptor forms, and interpret evidence about its expression, molecular state and experimental manipulation.","scope":{"in":["NR1H4 identity, species and gene-to-protein relationships","Reference sequences, transcript variants and receptor isoforms","Expression and receptor localization in specified biological contexts","Ligand response and transcriptional activity","Sequence alterations and experimentally supported functional effects"],"out":["Complete bile acid synthesis and transport pathways","Independent models of NR1H4 ligands or medicinal products","Whole-organ liver and intestinal physiology","Diagnosis and treatment of diseases associated with NR1H4","Other nuclear receptors and their independent molecular identities"],"boundaries":[]},"distinguishingFeatures":["Resolve the symbol through a species-specific identifier: human NR1H4 maps to NCBI Gene 9971, rather than treating the name alone as sufficient identification. [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene/9971/)","Distinguish the coding locus from its protein product: UniProt Q96RI1 identifies the human bile acid receptor protein. [UniProt](https://www.uniprot.org/uniprotkb/Q96RI1/entry)","Require sequence or accession evidence when separating NR1H4 from similarly named nuclear receptors.","Distinguish receptor identification from a functional bile acid response; a response alone does not establish which receptor mediated it.","Separate an endogenous NR1H4 isoform from a tagged, truncated or otherwise engineered experimental construct."],"structure":{"bundles":[{"id":"nr1h4-identity","name":"NR1H4 identity and registry boundary","description":"Resolve what the registered name denotes before attaching biological observations.","layers":[{"id":"registry-referent","name":"Registry referent","description":"Establish the molecular and taxonomic scope of this entry.","findings":[{"id":"gene-protein-boundary","name":"Gene and receptor boundary","description":"Require an explicit referent instead of inferring it from PHY.OBJ.","questions":[{"text":"Does the originating registry record denote the NR1H4 gene, its protein product or a deliberately combined molecular concept?","id":"gene-protein-boundary-q01","kind":"boundary"},{"text":"Which original identifier and organism support that interpretation?","id":"gene-protein-boundary-q02","kind":"provenance"}]}]},{"id":"identifier-resolution","name":"Identifier resolution","description":"Reconcile symbols, aliases and accessions without conflating related receptors.","findings":[{"id":"alias-disambiguation","name":"Alias disambiguation","description":"Treat names such as FXR as lookup aids that require accession confirmation.","questions":[{"text":"Which authoritative record connects the supplied NR1H4 or FXR label to the intended species and molecular form?","id":"alias-disambiguation-q01","kind":"provenance"},{"text":"What accession or sequence check excludes a similarly named receptor or an ortholog from another species?","id":"alias-disambiguation-q02","kind":"boundary"}]}]}]},{"id":"nr1h4-sequence-forms","name":"NR1H4 sequences and molecular forms","description":"Connect locus, transcripts, receptor isoforms and experimental constructs.","layers":[{"id":"transcript-isoform-mapping","name":"Transcript and isoform mapping","description":"Preserve the reference chain from coding sequence to receptor product.","findings":[{"id":"reference-sequence-chain","name":"Reference sequence chain","description":"Record versioned references and the evidence linking each transcript to its protein sequence.","questions":[{"text":"Which versioned transcript and protein accessions describe the NR1H4 form being observed?","id":"reference-sequence-chain-q01","kind":"definition"},{"text":"Does the experiment distinguish that isoform from other NR1H4 transcripts or proteins?","id":"reference-sequence-chain-q02","kind":"measurement"}]}]},{"id":"receptor-sequence-integrity","name":"Receptor sequence integrity","description":"Assess changes affecting the receptor regions required by a particular experiment.","findings":[{"id":"native-versus-engineered-receptor","name":"Native versus engineered receptor","description":"Document domain coverage, substitutions, deletions and tags before interpreting function.","questions":[{"text":"Which DNA-binding and ligand-binding regions are present in the tested NR1H4 sequence?","id":"native-versus-engineered-receptor-q01","kind":"definition"},{"text":"Could a truncation, tag or substitution limit what this experiment establishes about endogenous NR1H4?","id":"native-versus-engineered-receptor-q02","kind":"boundary"}]}]}]},{"id":"nr1h4-cellular-context","name":"NR1H4 expression and cellular context","description":"Situate receptor observations in a defined tissue, cell population and cellular compartment.","layers":[{"id":"expression-context","name":"Expression context","description":"Separate endogenous expression from experimentally introduced receptor abundance.","findings":[{"id":"measured-receptor-abundance","name":"Measured receptor abundance","description":"Require tissue, cell identity, molecular analyte and normalization for abundance claims.","questions":[{"text":"In which species, tissue and cell population was NR1H4 RNA or protein measured?","id":"measured-receptor-abundance-q01","kind":"measurement"},{"text":"Does the abundance reflect endogenous expression or an introduced construct, and how was it normalized?","id":"measured-receptor-abundance-q02","kind":"provenance"}]}]},{"id":"localization-context","name":"Localization context","description":"Record where the receptor was observed under the tested conditions.","findings":[{"id":"receptor-compartment-evidence","name":"Receptor compartment evidence","description":"Keep observed distribution separate from assumed activity.","questions":[{"text":"What method establishes NR1H4 compartment distribution, and at what time after treatment?","id":"receptor-compartment-evidence-q01","kind":"measurement"},{"text":"What additional evidence is required before interpreting the observed localization as transcriptional activation?","id":"receptor-compartment-evidence-q02","kind":"boundary"}]}]}]},{"id":"nr1h4-ligand-transcription","name":"NR1H4 ligand response and transcription","description":"Connect ligand exposure to receptor engagement and separately measured transcriptional output.","layers":[{"id":"ligand-engagement","name":"Ligand engagement","description":"Characterize a specified ligand against a specified NR1H4 form.","findings":[{"id":"binding-versus-response","name":"Binding versus functional response","description":"Preserve assay type, concentration and exposure when assessing ligand effects.","questions":[{"text":"Was direct NR1H4 binding measured, or was engagement inferred from a functional response?","id":"binding-versus-response-q01","kind":"measurement"},{"text":"Which ligand identity, concentration range, exposure duration and controls support the reported response?","id":"binding-versus-response-q02","kind":"provenance"}]}]},{"id":"transcriptional-output","name":"Transcriptional output","description":"Resolve DNA-associated receptor activity from indirect downstream effects.","findings":[{"id":"target-regulation-evidence","name":"Target regulation evidence","description":"Ask which target, regulatory sequence and molecular partners are supported in the tested context.","questions":[{"text":"Which endogenous target or reporter was measured, and what evidence distinguishes direct regulation from an indirect response?","id":"target-regulation-evidence-q01","kind":"measurement"},{"text":"Were RXR participation and relevant coregulators tested, inferred or left unresolved in this NR1H4 experiment?","id":"target-regulation-evidence-q02","kind":"provenance"}]}]}]},{"id":"nr1h4-perturbation-evidence","name":"NR1H4 perturbation and causal interpretation","description":"Determine what receptor alterations and experimental interventions actually establish.","layers":[{"id":"variant-function","name":"Variant function","description":"Connect sequence alterations to measured molecular consequences.","findings":[{"id":"alteration-functional-consequence","name":"Alteration and functional consequence","description":"Distinguish predicted effects from observed changes in abundance, binding or transcription.","questions":[{"text":"Against which reference accession is the NR1H4 alteration described?","id":"alteration-functional-consequence-q01","kind":"definition"},{"text":"Which functional consequences were directly measured, and which remain predictions?","id":"alteration-functional-consequence-q02","kind":"measurement"}]}]},{"id":"perturbation-specificity","name":"Perturbation specificity","description":"Assess whether genetic or chemical interventions support attribution to NR1H4.","findings":[{"id":"causal-attribution-controls","name":"Causal attribution controls","description":"Use specificity and rescue evidence to bound claims about receptor-dependent phenotypes.","questions":[{"text":"What independent perturbation, rescue or receptor-deficient control supports attribution of the observed effect to NR1H4?","id":"causal-attribution-controls-q01","kind":"provenance"},{"text":"Which additional control is needed before using this result to choose a subsequent NR1H4 experiment?","id":"causal-attribution-controls-q02","kind":"action"}]}]}]},{"id":"evidence-and-external-alignment","name":"Evidence and external alignment","description":"What the world already says about this thing, gathered so the model can be checked against it.","layers":[{"id":"reported-evidence","name":"Reported evidence","description":"Findings from the breadth pass, kept separate from the structural claims.","findings":[{"id":"evidence-confidence-notes","name":"Check these first","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these check these first hold for the sense of NR1H4 this model covers, and on what evidence?","id":"evidence-confidence-notes-q01","kind":"provenance"}]},{"id":"evidence-identifiers","name":"Identifiers and schemes","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these identifiers and schemes hold for the sense of NR1H4 this model covers, and on what evidence?","id":"evidence-identifiers-q01","kind":"provenance"}]},{"id":"evidence-real-world-use","name":"Real-world use","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these real-world use hold for the sense of NR1H4 this model covers, and on what evidence?","id":"evidence-real-world-use-q01","kind":"provenance"}]},{"id":"evidence-failure-modes-and-hazards","name":"Failure modes and hazards","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these failure modes and hazards hold for the sense of NR1H4 this model covers, and on what evidence?","id":"evidence-failure-modes-and-hazards-q01","kind":"provenance"}]},{"id":"evidence-neighbours","name":"Neighbouring kinds and how to tell them apart","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these neighbouring kinds and how to tell them apart hold for the sense of NR1H4 this model covers, and on what evidence?","id":"evidence-neighbours-q01","kind":"provenance"}]}]}]}]},"agentConduct":{"may":["Describe NR1H4 and the bile-acid receptor it encodes, citing sources.","Report what a variant or expression result shows, with source and limits."],"mustNot":["Interpret a person's NR1H4 variant as a diagnosis of liver disease.","Share genetic data without consent.","Recommend drugs acting on this receptor to a person.","Present supplement claims linked to it as proven."],"requiresHuman":["Using results in treatment decisions.","Research on patient samples without documented consent."]},"ethics":{"considerations":["Genetic findings about liver disease affect patients and their families.","Health claims about bile acid signalling can mislead consumers."],"affectedParties":["Patients and families","Consumers","Researchers"]},"owners":{"steward":"The person whose genome carries it; laboratories and biobanks hold records.","roles":[],"masterSystems":["Gene and variant databases"]},"relations":[{"target":"Q20747295","type":"parent","note":"registry parent class"}],"interaction":{"identity":{"applicability":"required","items":["Vercy registry: vr.tr.nr1h4","Wikidata: Q14905041 (https://www.wikidata.org/wiki/Q14905041)"]},"properties":{"applicability":"required","items":["Molecular referent: gene locus | transcript | protein isoform | engineered construct","Taxonomic identity: Organism name and taxonomy identifier","Reference identity: Versioned gene, transcript and protein accessions; assembly for genomic coordinates","Sequence alteration: Reference sequence | accession-relative variant | documented construct modification","Expression abundance: RNA abundance in a declared normalization system; protein abundance in assay-specific units","Subcellular distribution: Observed compartment distribution, method and observation time","Ligand response: Concentration in mol/L; response and baseline; EC50 or IC50 only when fitted appropriately","Transcriptional effect: Target-specific expression change or reporter activity relative to a stated control"]},"recognition":{"applicability":"required","items":["Not visible; known from sequence data and receptor assays.","Identified by its approved gene symbol; the receptor is often called by another name."]},"capabilities":{"applicability":"required","items":["Resolve an NR1H4 label to a species, molecular form and reference accession.","Check whether a sequence, reagent or construct actually targets the intended NR1H4 form.","Compare expression or activity observations under compatible biological and assay conditions.","Assess whether a ligand-response experiment supports NR1H4-specific activity.","Identify the controls and additional evidence needed before attributing a phenotype to NR1H4."]},"hazards":{"applicability":"required","items":["Confusion between the gene symbol and the receptor name in reports.","Overinterpretation of variant associations."]},"interfaces":{"applicability":"required","items":["Human gene nomenclature, HUGO Gene Nomenclature Committee (HGNC), which approves the gene symbol."]},"context":{"applicability":"required","items":["The human NR1H4 gene is encountered in studies of bile acid regulation and metabolism, particularly in liver and intestinal tissues.","Its sequence and transcript expression support investigation of the encoded farnesoid X receptor and its role in controlling gene transcription."]}},"sources":[{"title":"Wikidata item Q14905041: NR1H4","url":"https://www.wikidata.org/wiki/Q14905041","note":"identity and sense of the item"},{"title":"Wikipedia: Farnesoid X receptor","url":"https://en.wikipedia.org/wiki/Farnesoid_X_receptor","note":"general description of the item"}],"openQuestions":["Does the originating registry identifier intend human NR1H4, another species or the receptor family across species?","Should the entry primarily own the gene locus or receptor protein, and does an existing Vercy model already own that referent?","Which transcript and protein isoforms require distinct treatment because their differences affect recognition or functional interpretation?","Which ligand, partner and direct-target claims have sufficient primary evidence in each relevant tissue and species?","Which NR1H4 alterations have reproducible functional evidence, and where do phenotype associations remain mechanistically unresolved?"],"resources":{"spec":"/models/things/publications/thing-q14905041/spec.json"},"provenance":{"origin":"thing registry research (pass 2)","builtFrom":["models/things/publications/thing-q14905041/spec.json"],"providers":["Codex"],"researchStatus":"unreviewed","generatedAt":"2026-09-12T11:41:32Z","builder":"tools/build_cards.py@1.0.0"},"completeness":{"sections":{"classifiers":"filled","whatItIs":"filled","purpose":"filled","distinguishingFeatures":"filled","structure":"filled","agentConduct":"filled","ethics":"filled","owners":"filled","relations":"filled","interaction.identity":"filled","interaction.properties":"filled","interaction.recognition":"filled","interaction.capabilities":"filled","interaction.hazards":"filled","interaction.interfaces":"filled","interaction.context":"filled","sources":"filled"},"notes":{"_gate":"Published through the thing publication gate 1.0 on 2026-10-07T10:10:26+00:00: completeness 1.00; sense: Wikidata description; 2 live sources; review by codex: pass"},"score":1.0}}