{ "sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "fork:pmid:26981379:gene-expression-profiling-of-human-calcific-aortic-valve-disease-8db11e48", "kind": "science-record", "revision": 22, "content_hash": "sha256:71f971a55237fe178b6a50c6fc30b94dfacd30914972e4e0b4ef2a774298a996", "created_at": "2026-11-01T16:10:49.000000Z", "updated_at": "2026-11-03T08:03:44.105145Z", "generator": { "name": "automated-assays", "session_id": "assays-session-8db11e48-2149-4d81-b70c-0b751de5f0f5" }, "paper": { "state": "complete", "title": "Gene expression profiling of human calcific aortic valve disease", "doi": "10.1016/j.gdata.2015.12.015", "pmid": "26981379", "authors": [ "Jaana Rysä" ], "journal": "Genomics Data", "year": 2015, "abstract": "Calcific aortic valve disease is a slowly progressive disorder that ranges from mild valve thickening (i.e. aortic sclerosis) to severe calcification of valves (i.e. aortic stenosis). Gene expression profiling analysis of non-calcified controls, sclerotic, and calcified aortic valves was performed to better understand the progression of calcific aortic valve disease. The complementary information related to processing and statistical analysis of the DNA microarray data is provided in this article. Interpretation of this data can be found in a research article entitled “MicroRNA-125b and chemokine CCL4 expression are associated with calcific aortic valve disease” [1]. 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paragraph 2", "quote": "All samples are separately available in GEO database under accession number GSE51472 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE51472." } ], "state": "complete" } ], "gaps": [] }, "experiment": { "state": "complete", "objective": "The study identified differentially expressed genes using a ≥2.0-fold change with one-way ANOVA and Benjamini–Hochberg false discovery rate (P < 0.05), and the source microarray data were deposited in GEO under accession number GSE51472.", "steps": [ { "id": "assay:1-step-1", "order": 1, "name": "Validate the dataset schema and hash it", "kind": "computational", "state": "complete", "parameters": { "reference_group": "Normal aortic valve", "contrast_groups": [ "Sclerotic aortic valve", "Calcified aortic valve" ], "alpha": 0.05, "fold_change_threshold": 1.5 }, "inputs": [], "outputs": [], "duration_hours": null }, { "id": "assay:1-step-2", "order": 2, "name": "Confirm at least two groups with at least two observations each", 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This is the earlier form of the same reference and is still accepted; assay_id names the entry by the identity it has inside the record." }, "refusals": { "unsupported_operation": "This platform does not run the operation named.", "unsupported_version": "This platform does not run that operation at the version named.", "provider_unknown": "No provider is registered under the name given.", "provider_unsupported": "The provider named does not offer the operation at a version that is available for execution.", "no_provider_available": "The default provider does not offer the operation, and no provider that does something else is substituted for one.", "source_record_missing": "The request did not name the science record the work is about.", "source_hash_missing": "The request did not bind the exact version of the record, as a sha256 content hash.", "source_record_not_held": "This platform holds no science record under that identifier.", "source_hash_mismatch": "The version of the record the platform holds is not the version the request names.", "request_id_conflict": "The request identity has already been answered by a different request. 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"Calcified aortic valve": -0.6531570299441861 }, "fold_change": { "Sclerotic aortic valve": 0.8837837837837837, "Calcified aortic valve": 0.6358872865402716 }, "max_abs_log2_fold_change": 0.6531570299441861 }, { "feature": "1558184_s_at", "symbol": "ZNF17", "f_statistic": 22.308464909, "p_value": 9.0658720608e-5, "q_value": 0.02917780546707603, "log2_fold_change": { "Sclerotic aortic valve": -0.18543088769053048, "Calcified aortic valve": -0.9758380268958426 }, "fold_change": { "Sclerotic aortic valve": 0.8793863916048744, "Calcified aortic valve": 0.5084444171067547 }, "max_abs_log2_fold_change": 0.9758380268958426 } ], "differential_bound": { "state": "bounded", "shown": 50, "total": 645, "omitted": 595, "complete_result_hash": "50a679ddbb8d627ce71d6e39139826a902378a9a0d0afa7390dbc49888af70a5", "complete_result_run": "2f3bceb6-55ca-44fe-bc02-75359983f659", "note": "This record carries the first 50 of these. The complete result is the run's own result, named by its hash." }, "sample_count": 15, "group_count": 3, "published_target": { "record_id": "pmid:26981379", "source": { "authority": "Corpus Engine", "record_id": "pmid:26981379", "content_hash": "sha256:a353b105e3521f7b07a6b31bade25f25e99afd2ffdad634bd102f06188b57966", "document_sha256": "50d022cecd574931e4ca91d8d4e6ddc94e7206dee2df9ac7605c8aa80ef6917f", "sci_version": "1.2", "revision": 4, "table_asset": { "id": "asset:table:pmid:26981379:1", "sha256": "sha256:899445f8a1682cc33fee2cc9dd59a6c66ab864e9975cfe0b1e3e9da343876edd", "locator": "section[1]/table-wrap[1]#t0005", "note": null }, "built_by": "App\\Support\\Science\\CorpusReplicationTarget", "built_at": "2026-11-02T02:45:12+00:00" }, "statement": "Genes were defined as differentially expressed if the change was at least 2.0-fold and statistically significant (P < 0.05, one-way ANOVA and Benjamini and Hochberg false discovery rate).", "design": { "reference_group": "Normal aortic valve", "contrast_groups": [ "Sclerotic aortic valve", "Calcified aortic valve" ], "alpha": 0.05, "group_map": [], "unmapped_paper_groups": [], "expected_group_sizes": { "Calcified aortic valve": 5, "Normal aortic valve": 5, "Sclerotic aortic valve": 5 } }, "equivalence": { "fold_change_relative_tolerance": 0.25, "rule": "A published fold factor is a ratio: a positive value is the factor by which the expression is higher, a negative value the factor by which it is lower. The run agrees when the ratio it observes is within the declared relative tolerance of the published ratio and the run reaches the published significance. A run that gets the direction right but not the size is recorded as direction_only, not as a contradiction.", "significance_rule": "A published p-value below the alpha is tested by asking whether the run also reaches that alpha. A published p-value above it is tested by asking whether the run stays above it, because the paper reports no difference there." }, "claims": [], "cross_check": [ { "target_id": "target-fold-change-threshold", "kind": "threshold", "unit": "fold-change threshold", "published_value": 2, "status": "threshold", "detail": "The target states a threshold and is applied to the run, not compared with a cell." }, { "target_id": "target-p-value-threshold", "kind": "threshold", "unit": "exclusive p-value threshold", "published_value": 0.05, "status": "threshold", "detail": "The target states a threshold and is applied to the run, not compared with a cell." } ], "gaps": [] }, "replication": null, "sample_set_fidelity": { "verdict": "matches_the_paper", "expected_group_sizes": { "Calcified aortic valve": 5, "Normal aortic valve": 5, "Sclerotic aortic valve": 5 }, "observed_group_sizes": { "Calcified aortic valve": 5, "Normal aortic valve": 5, "Sclerotic aortic valve": 5 }, "differences": [], "detail": "every group matches the size the paper states" }, "method_inference": { "operation": "infer_probe_mapping", "operation_version": "0.1.0", "record_id": "pmid:26981379", "source": { "authority": "Corpus Engine", "record_id": "pmid:26981379", "content_hash": "sha256:a353b105e3521f7b07a6b31bade25f25e99afd2ffdad634bd102f06188b57966", "document_sha256": "50d022cecd574931e4ca91d8d4e6ddc94e7206dee2df9ac7605c8aa80ef6917f", "sci_version": "1.2", "revision": 4, "table_asset": { "id": "asset:table:pmid:26981379:1", "sha256": "sha256:899445f8a1682cc33fee2cc9dd59a6c66ab864e9975cfe0b1e3e9da343876edd", "locator": "section[1]/table-wrap[1]#t0005", "note": null }, "built_by": "App\\Support\\Science\\CorpusReplicationTarget", "built_at": "2026-11-02T02:45:12+00:00" }, "reference_group": "Normal aortic valve", "tolerance": 0.25, "genes": [], "summary": { "genes_considered": 0, "genes_resolved": 0, "genes_ambiguous": 0, "genes_unresolved": 0, "discriminating_genes": 0, "discriminating_genes_resolved": 0, "selected_features": [], "selected_probe_classes": [], "probe_class_consistency": "not_determined", "probe_class_consistency_detail": "No gene with more than one candidate probe was resolved, so no probe class can be read from the result." }, "gaps": [] }, "probe_stats": [] } } } ] }