{ "sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "fork:pmid:28529692:check-pmid28529692-figures-fd0a993d", "kind": "science-record", "revision": 7, "content_hash": "sha256:6803696d12a8098d47823d250008744b159fdf353fac02c84671a77b46f26234", "created_at": "2026-11-01T16:04:20.000000Z", "updated_at": "2026-11-02T04:29:08.928514Z", "generator": { "name": "automated-assays", "session_id": "assays-session-fd0a993d-d7cb-46b3-bcf9-8e31b5a8888b" }, "paper": { "state": "complete", "title": "Abnormal expression of ATP1A1 and ATP1A2 in breast cancer", "doi": "10.12688/f1000research.10481.1", "pmid": "28529692", "authors": [ "Alexey Bogdanov", "Fedor Moiseenko", "Michael Dubina" ], "journal": "F1000Research", "year": 2017, "abstract": "Breast cancer is the first in incidence and the second in death among all solid tumors occurring in women. The identification of molecular genetic abnormalities in breast cancer is important to improve the results of treatment. In the present study, we analyzed microarray data of breast cancer expression profiling (NCBI GEO database, accession GSE65194), focusing on Na +/K +-ATPase coding genes. We found overexpression of the ATP1A1 and down-regulation of the ATP1A2. We expect that our research could help to improve the understanding of predictive and prognostic features of breast cancer.\nKeywords: breast cancer, Na+/K+-ATPase, gene expression, abnormality, ATP1A1, ATP1A2", "claims": [ { "id": "claim-method", "statement": "We utilized Transcriptome Analysis Console 3.0 software (Affymetrix, Inc. USA) to analyze the obtained CHP files and to detect differentially expressed genes using one-way between subjects ANOVA.", "kind": "methodological", "target": null, "evidence": [ { "asset": "source:pmid:28529692", "locator": "sections[2] \"Methods\" paragraph 2", "quote": "We utilized Transcriptome Analysis Console 3.0 software (Affymetrix, Inc. USA) to analyze the obtained CHP files and to detect differentially expressed genes using one-way between subjects ANOVA." } ], "state": "complete" }, { "id": "claim-target-result", "statement": "ATP1A1 was overexpressed approximately 1.5 times in all groups of breast cancer samples (p<0.05). Coincidently, ATP1A2 expression decreased by more than 2 times (p<0.05).", "kind": "quantitative", "target": { "value": 1.5, "unit": "fold change (ATP1A1)", "tolerance": null, "source": "ATP1A1 was overexpressed approximately 1.5 times in all groups of breast cancer samples (p<0.05). Coincidently, ATP1A2 expression decreased by more than 2 times (p<0.05)." }, "evidence": [ { "asset": "source:pmid:28529692", "locator": "sections[1] \"Introduction\" paragraph 4", "quote": "ATP1A1 was overexpressed approximately 1.5 times in all groups of breast cancer samples (p<0.05). 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The tumour and healthy cohort is 164 of them; the other 14 are cell-line samples. Sample metadata only; no data was downloaded.", "platform": "570", "taxon": "Homo sapiens", "title": "Expression profiling of breast cancer samples from Institut Curie (Maire cohort) --Affy CDF", "resolution_checked_at": "2026-11-01T11:38:18Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false } }, { "id": "asset:table:pmid:28529692:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:093de1b1ff705f0e3a405721e80dff9250fdee11708bf051db5b2299349651b4", "bytes": 598, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#T1", "version": null, "note": "NKA genes expression in breast cancer samples relative to normal breast tissue.", "structure": { "pmcid": "PMC5428514", "section_index": 1, "section_title": "Introduction", "row_count": 5, "column_count": 5 }, "table": { "label": "Table 1.", "caption": "NKA genes expression in breast cancer samples relative to normal breast tissue.", "rows": [ [ "Breast cancer group", "Lum A", "Lum B", "Her2", "TNBC" ], [ "Gene", "Relative expression/(ANOVA P-value)" ], [ "ATP1A1", "1.53 (0.009016)", "1.38 (0.04454)", "1.66 (0.005926)", "1.44 (0.015725)" ], [ "ATP1A2", "-2.49 (1.85·10 -07)", "-2.52 (8.50·10 -09)", "-2.78 (5.48·10 -08)", "-2.87 (2.08·10-11)" ], [ "ATP1A3", "-1.05 (0.429089)", "1.03 (0.308298)", "-1.04 (0.768041)", "-1.04 (0.527878)" ] ], "row_count": 5, "column_count": 5, "numeric_cells": 12, "header_rows": 2, "locator": "section[1]/table-wrap[1]#T1" } } ], "gaps": [ "asset:data:geo:GSE65194 not downloaded", "asset:data:geo:GSE65194 licence not read" ], "group_sizes": { "CellLine": 14, "Healthy": 11, "Her2": 39, "Luminal A": 29, "Luminal B": 30, "TNBC": 55 } }, "analysis": { "state": "complete", "methods": [ { "id": "group_comparison_anova", "family": "group_comparison", "specific": "group_comparison_anova", "label": "Group comparison analysis", "dsl_operations": [ "group_comparison_anova" ], "missing_operations": [], "expressible": true, "parameters": { "alpha": { "type": "number", "description": "The significance level, declared before the run and recorded with the result.", "default": 0.05 } }, "data_shapes": [ "observations" ], "evidence": { "score": 1.0, "band": "implemented", "quote": "Compare a continuous measurement across two or more groups with a one-way analysis of variance, report the assumption checks the test depends on, and compare every pair of groups with Welch's unequal-variance t statistic under Holm's correction." } } ], "targets": [], "gaps": [] }, "capability": { "state": "complete", "requirements": [ { "capability_id": "provider:automated-assays-computational#group_comparison_anova", "label": "Group comparison analysis", "assay_families": [ "group_comparison" ], "availability_state": "available", "tier_unlocked": null, "candidate": "Automated Assays computational service" } ], "gaps": [] }, "readiness": { "state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": { "method": { "tier": "R1", "expressible": true, "required_operations": [ "group_comparison_anova" ], "missing_operations": [], "basis": "The named method is represented in the DSL catalogue." }, "capability": { "tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The corpus capability table owns computational analysis." }, "data": { "tier": "R1", "reachable": true, "accessions": [ "GSE65194" ], "statements": [ "Raw data for Table 1 are available at:\nhttps://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE65194&format=file 22." ], "basis": "The GEO series resolves and its sample accessions are listed. 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The code and the reason are in the response." } } }, "result": { "request_id": "The identity of the request.", "execution_id": "The identity of the execution.", "status": "complete, refused or failed.", "provider": "The provider that actually ran it, with the capability key and version.", "source": "The record and the exact version it was bound to.", "input_hash": "The canonical hash of the request inputs and parameters.", "result_hash": "The canonical hash of the result.", "evidence_hash": "The canonical hash of the evidence manifest.", "finding": "What was found, in bounded words.", "result": "The full result, in the shape the operation defines." } }, "limitations": [ "The analysis says whether the groups differ under the assumptions it screens for. It does not establish why they differ, and a non-significant result is not proof that the groups are the same.", "The groups, the measurements and the significance level are declared by the caller. The platform does not infer them, and a comparison between groups that were not declared as comparable is the caller's responsibility." ] } } ], "activities": [ { "id": "activity:fork:pmid:28529692", "type": "fork", "label": "Opened from pmid:28529692 at version sha256:597ab1b2b4d3af05deac209ed6b3bef79d7ad5fa1eabc8484a99c7b5ecd63c1d", "used": [ "pmid:28529692" ], "agent": "agent:user:0195616cec89" }, { "id": "activity:request-contract:group_comparison_anova", "type": "assay_request_contract", "label": "The request and result contract for this assay", "used": [ "assay-definition:group-comparison-analysis@0.1.0" ], "agent": "agent:automated-assays", "request": { "required": { "source_record_id": "The science record the work is about.", "source_content_hash": "The exact version of that record, as sha256:. 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The execution that already exists is unchanged.", "assay_entry_mismatch": "The assay entry named is not one the record holds, or it does not require the operation named, so the request does not say which assay of the record the work concerns." }, "endpoint": { "method": "POST", "path": "/api/v1/executions", "authentication": "A bearer token, checked by the paper-assay-api middleware.", "responses": { "201": "The work ran, or the answer to this request had already been given.", "202": "The work is already under way under this identity. The execution is named in the response and can be read back.", "409": "The request identity has already been answered by a different request. The execution that already exists is unchanged.", "422": "The request was refused. 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Each carries the group the observation belongs to and the value that was measured.", "required": true } }, "parameter_contract": { "alpha": { "type": "number", "description": "The significance level, declared before the run and recorded with the result.", "default": 0.05 } }, "output_contract": { "status": "complete", "summary": "How many observations were compared and across how many groups", "parameters": "The parameters the run was made under", "dataset": "The rows the run was made over, with their hash", "result": "The analysis of variance, the effect sizes, the assumption checks and the pairwise comparisons", "result_sha256": "The canonical hash of the result", "interpretation": "What the result does and does not say" } }, "request": { "assay_id": "assay:1", "source_record_id": "fork:pmid:28529692:check-pmid28529692-figures-fd0a993d", "source_content_hash": "sha256:5b8308595aed02f36d9649fc2666319f6d942806598db65c97d428cf85f88a58", "operation": "group_comparison_anova", 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The complete result is the run's own result, named by its hash." }, "sample_count": 164, "group_count": 6, "recipe_source": { "source": "published_run", "run_id": "17fdc411-b820-446f-ad1c-2707e0c7c7ce", "record_id": "pmid:28529692" }, "published_target": { "record_id": "pmid:28529692", "source": { "authority": "Corpus Engine", "record_id": "pmid:28529692", "content_hash": "sha256:597ab1b2b4d3af05deac209ed6b3bef79d7ad5fa1eabc8484a99c7b5ecd63c1d", "document_sha256": "64b68ff5025807df588812cf2f3665738e159303d28602de0a5099412f94ee90", "sci_version": "1.2", "revision": 4, "table_asset": { "id": "asset:table:pmid:28529692:1", "sha256": "sha256:093de1b1ff705f0e3a405721e80dff9250fdee11708bf051db5b2299349651b4", "locator": "section[1]/table-wrap[1]#T1", "note": "NKA genes expression in breast cancer samples relative to normal breast tissue." }, "built_by": "App\\Support\\Science\\CorpusReplicationTarget", "built_at": "2026-11-02T04:26:45+00:00" }, "statement": "ATP1A1 was overexpressed approximately 1.5 times in all groups of breast cancer samples (p<0.05). Coincidently, ATP1A2 expression decreased by more than 2 times (p<0.05).", "design": { "reference_group": "Healthy", "contrast_groups": [ "TNBC", "Her2", "Luminal A", "Luminal B" ], "alpha": 0.05, "group_map": { "Lum A": "Luminal A", "Lum B": "Luminal B", "Her2": "Her2", "TNBC": "TNBC" }, "unmapped_paper_groups": [], "expected_group_sizes": { "CellLine": 14, "Healthy": 11, "Her2": 39, "Luminal A": 29, "Luminal B": 30, "TNBC": 55 } }, "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": [ { "symbol": "ATP1A1", "reference_group": "Healthy", "contrast_groups": [ "Luminal A", "Luminal B", "Her2", "TNBC" ], "direction": "up", "named_in_claim": true, "alpha": 0.05, "expected": { "Luminal A": { "paper_group": "Lum A", "fold_factor": 1.53, "expected_ratio": 1.53, "p_value": 0.009016, "significant": true, "source_cell": "1.53 (0.009016)", "asset_id": "asset:table:pmid:28529692:1", "tolerance": 0.25 }, "Luminal B": { "paper_group": "Lum B", "fold_factor": 1.38, "expected_ratio": 1.38, "p_value": 0.04454, "significant": true, "source_cell": "1.38 (0.04454)", "asset_id": "asset:table:pmid:28529692:1", "tolerance": 0.25 }, "Her2": { "paper_group": "Her2", "fold_factor": 1.66, "expected_ratio": 1.66, "p_value": 0.005926, "significant": true, "source_cell": "1.66 (0.005926)", "asset_id": "asset:table:pmid:28529692:1", "tolerance": 0.25 }, "TNBC": { "paper_group": "TNBC", "fold_factor": 1.44, "expected_ratio": 1.44, "p_value": 0.015725, "significant": true, "source_cell": "1.44 (0.015725)", "asset_id": "asset:table:pmid:28529692:1", "tolerance": 0.25 } } }, { "symbol": "ATP1A2", "reference_group": "Healthy", "contrast_groups": [ "Luminal A", "Luminal B", "Her2", "TNBC" ], "direction": "down", "named_in_claim": true, "alpha": 0.05, "expected": { "Luminal A": { "paper_group": "Lum A", "fold_factor": -2.49, "expected_ratio": 0.4016064257028112, "p_value": 1.85e-7, "significant": true, "source_cell": "-2.49 (1.85·10 -07)", "asset_id": "asset:table:pmid:28529692:1", "tolerance": 0.25 }, "Luminal B": { "paper_group": "Lum B", "fold_factor": -2.52, "expected_ratio": 0.3968253968253968, "p_value": 8.5e-9, "significant": true, "source_cell": "-2.52 (8.50·10 -09)", "asset_id": "asset:table:pmid:28529692:1", "tolerance": 0.25 }, "Her2": { "paper_group": "Her2", "fold_factor": -2.78, "expected_ratio": 0.3597122302158274, "p_value": 5.480000000000001e-8, "significant": true, "source_cell": "-2.78 (5.48·10 -08)", "asset_id": "asset:table:pmid:28529692:1", "tolerance": 0.25 }, "TNBC": { "paper_group": "TNBC", "fold_factor": -2.87, "expected_ratio": 0.3484320557491289, "p_value": 2.08e-11, "significant": true, "source_cell": "-2.87 (2.08·10-11)", "asset_id": "asset:table:pmid:28529692:1", "tolerance": 0.25 } } }, { "symbol": "ATP1A3", "reference_group": "Healthy", "contrast_groups": [ "Luminal A", "Luminal B", "Her2", "TNBC" ], "direction": "down", "named_in_claim": false, "alpha": 0.05, "expected": { "Luminal A": { "paper_group": "Lum A", "fold_factor": -1.05, "expected_ratio": 0.9523809523809523, "p_value": 0.429089, "significant": false, "source_cell": "-1.05 (0.429089)", "asset_id": "asset:table:pmid:28529692:1", "tolerance": 0.25 }, "Luminal B": { "paper_group": "Lum B", "fold_factor": 1.03, "expected_ratio": 1.03, "p_value": 0.308298, "significant": false, "source_cell": "1.03 (0.308298)", "asset_id": "asset:table:pmid:28529692:1", "tolerance": 0.25 }, "Her2": { "paper_group": "Her2", "fold_factor": -1.04, "expected_ratio": 0.9615384615384615, "p_value": 0.768041, "significant": false, "source_cell": "-1.04 (0.768041)", "asset_id": "asset:table:pmid:28529692:1", "tolerance": 0.25 }, "TNBC": { "paper_group": "TNBC", "fold_factor": -1.04, "expected_ratio": 0.9615384615384615, "p_value": 0.527878, "significant": false, "source_cell": "-1.04 (0.527878)", "asset_id": "asset:table:pmid:28529692:1", "tolerance": 0.25 } } } ], "cross_check": [ { "target_id": "target-atp1a1-summary", "kind": "summary", "unit": "fold change (ATP1A1)", "published_value": 1.5, "status": "summary", "detail": "The target restates the published claim in words and is checked through the table values." }, { "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." }, { "target_id": "target-atp1a1-lum-a", "kind": "cell", "symbol": "ATP1A1", "paper_group": "Lum A", "unit": "relative expression fold change", "published_value": 1.53, "table_value": 1.53, "status": "agreed", "detail": "The machine-readable target and the published table cell state the same value." }, { "target_id": "target-atp1a1-lum-a-p", "kind": "cell", "symbol": "ATP1A1", "paper_group": "Lum A", "unit": "ANOVA p-value", "published_value": 0.009016, "table_value": 0.009016, "status": "agreed", "detail": "The machine-readable target and the published table cell state the same value." }, { "target_id": "target-atp1a1-lum-b", "kind": "cell", "symbol": "ATP1A1", "paper_group": "Lum B", "unit": "relative expression fold change", "published_value": 1.38, "table_value": 1.38, "status": "agreed", "detail": "The machine-readable target and the published table cell state the same value." }, { "target_id": "target-atp1a1-lum-b-p", "kind": "cell", "symbol": "ATP1A1", "paper_group": "Lum B", "unit": "ANOVA p-value", "published_value": 0.04454, "table_value": 0.04454, "status": "agreed", "detail": "The machine-readable target and the published table cell state the same value." }, { "target_id": "target-atp1a1-her2", "kind": "cell", "symbol": "ATP1A1", "paper_group": "Her2", "unit": "relative expression fold change", "published_value": 1.66, "table_value": 1.66, "status": "agreed", "detail": "The machine-readable target and the published table cell state the same value." }, { "target_id": "target-atp1a1-her2-p", "kind": "cell", "symbol": "ATP1A1", "paper_group": "Her2", "unit": "ANOVA p-value", "published_value": 0.005926, "table_value": 0.005926, "status": "agreed", "detail": "The machine-readable target and the published table cell state the same value." }, { "target_id": "target-atp1a1-tnbc", "kind": "cell", "symbol": "ATP1A1", "paper_group": "TNBC", "unit": "relative expression fold change", "published_value": 1.44, "table_value": 1.44, "status": "agreed", "detail": "The machine-readable target and the published table cell state the same value." }, { "target_id": "target-atp1a1-tnbc-p", "kind": "cell", "symbol": "ATP1A1", "paper_group": "TNBC", "unit": "ANOVA p-value", "published_value": 0.015725, "table_value": 0.015725, "status": "agreed", "detail": "The machine-readable target and the published table cell state the same value." }, { "target_id": "target-atp1a2-lum-a", "kind": "cell", "symbol": "ATP1A2", "paper_group": "Lum A", "unit": "relative expression fold change", "published_value": -2.49, "table_value": -2.49, "status": "agreed", "detail": "The machine-readable target and the published table cell state the same value." }, { "target_id": "target-atp1a2-lum-a-p", "kind": "cell", "symbol": "ATP1A2", "paper_group": "Lum A", "unit": "ANOVA p-value", "published_value": 1.85e-7, "table_value": 1.85e-7, "status": "agreed", "detail": "The machine-readable target and the published table cell state the same value." }, { "target_id": "target-atp1a2-lum-b", "kind": "cell", "symbol": "ATP1A2", "paper_group": "Lum B", "unit": "relative expression fold change", "published_value": -2.52, "table_value": -2.52, "status": "agreed", "detail": "The machine-readable target and the published table cell state the same value." }, { "target_id": "target-atp1a2-lum-b-p", "kind": "cell", "symbol": "ATP1A2", "paper_group": "Lum B", "unit": "ANOVA p-value", "published_value": 8.5e-9, "table_value": 8.5e-9, "status": "agreed", "detail": "The machine-readable target and the published table cell state the same value." }, { "target_id": "target-atp1a2-her2", "kind": "cell", "symbol": "ATP1A2", "paper_group": "Her2", "unit": "relative expression fold change", "published_value": -2.78, "table_value": -2.78, "status": "agreed", "detail": "The machine-readable target and the published table cell state the same value." }, { "target_id": "target-atp1a2-her2-p", "kind": "cell", "symbol": "ATP1A2", "paper_group": "Her2", "unit": "ANOVA p-value", "published_value": 5.48e-8, "table_value": 5.480000000000001e-8, "status": "agreed", "detail": "The machine-readable target and the published table cell state the same value." }, { "target_id": "target-atp1a2-tnbc", "kind": "cell", "symbol": "ATP1A2", "paper_group": "TNBC", "unit": "relative expression fold change", "published_value": -2.87, "table_value": -2.87, "status": "agreed", "detail": "The machine-readable target and the published table cell state the same value." }, { "target_id": "target-atp1a2-tnbc-p", "kind": "cell", "symbol": "ATP1A2", "paper_group": "TNBC", "unit": "ANOVA p-value", "published_value": 2.08e-11, "table_value": 2.08e-11, "status": "agreed", "detail": "The machine-readable target and the published table cell state the same value." } ], "gaps": [] }, "replication": { "target": { "record_id": "pmid:28529692", "source": { "authority": "Corpus Engine", "record_id": "pmid:28529692", "content_hash": "sha256:597ab1b2b4d3af05deac209ed6b3bef79d7ad5fa1eabc8484a99c7b5ecd63c1d", "document_sha256": "64b68ff5025807df588812cf2f3665738e159303d28602de0a5099412f94ee90", "sci_version": "1.2", "revision": 4, "table_asset": { "id": "asset:table:pmid:28529692:1", "sha256": "sha256:093de1b1ff705f0e3a405721e80dff9250fdee11708bf051db5b2299349651b4", "locator": "section[1]/table-wrap[1]#T1", "note": "NKA genes expression in breast cancer samples relative to normal breast tissue." }, "built_by": "App\\Support\\Science\\CorpusReplicationTarget", "built_at": "2026-11-02T04:26:45+00:00" }, "statement": "ATP1A1 was overexpressed approximately 1.5 times in all groups of breast cancer samples (p<0.05). Coincidently, ATP1A2 expression decreased by more than 2 times (p<0.05)." }, "claims": [ { "symbol": "ATP1A1", "reference_group": "Healthy", "direction": "up", "verdict": "partly_reproduced", "reason": "Luminal A: the observed change is not an increase; the run goes the other way (published ratio 1.5300, run ratio 0.9676); Luminal B: the observed change is not an increase; the run goes the other way (published ratio 1.3800, run ratio 0.9737); the run agrees with the published ratio 1.3800 but reaches a significance the paper did not (published p 0.044540, run p 0.096332 against the same two groups); Her2: the observed change is not an increase; the run goes the other way (published ratio 1.6600, run ratio 0.9778); TNBC: the observed change is not an increase; the run goes the other way (published ratio 1.4400, run ratio 0.9758)", "contrasts": [ { "contrast_group": "Luminal A", "reference_group": "Healthy", "verdict": "partly_reproduced", "reason": "the observed change is not an increase; the run goes the other way (published ratio 1.5300, run ratio 0.9676)", "probes_tested": 2, "probes_reproduced": 1, "probes_direction_only": 0, "probes_significance_only": 0, "probes_contradicted": 1, "observed": [ { "feature": "244606_at", "log2_fold_change": -0.04748830676000004, "observed_ratio": 0.9676194627982302, "p_value": 1.90084445347e-6, "q_value": 3.860077584391238e-6, "f_statistic": 8.80610513583, "contrast_p_value": 0.00148360288536, "contrast_p_value_holm": 0.0148360288536, "contrast_t_statistic": -3.86517935188, "contrast_degrees_of_freedom": 15.2538799979, "verdict": "contradicted", "problems": [ "the observed change is not an increase" ], "against_published": { "verdict": "contradicted", "detail": "the run goes the other way (published ratio 1.5300, run ratio 0.9676)", "fold_verdict": "contradicted", "significance_verdict": "reproduced", "published_fold_factor": 1.53, "published_ratio": 1.53, "published_p_value": 0.009016, "observed_ratio": 0.9676194627982302, "observed_p_value": 0.00148360288536, "relative_difference": 0.36756897856324827, "tolerance": 0.25, "source_cell": "1.53 (0.009016)", "asset_id": "asset:table:pmid:28529692:1" } }, { "feature": "220948_s_at", "log2_fold_change": 0.562951256969999, "observed_ratio": 1.4772881509433262, "p_value": 0.00202411595674, "q_value": 0.002850634751882899, "f_statistic": 4.4278555666, "contrast_p_value": 0.0416425003723, "contrast_p_value_holm": 0.291497502606, "contrast_t_statistic": 2.26184990944, "contrast_degrees_of_freedom": 12.895191892, "verdict": "reproduced", "problems": [], "against_published": { "verdict": "reproduced", "detail": null, "fold_verdict": "reproduced", "significance_verdict": "reproduced", "published_fold_factor": 1.53, "published_ratio": 1.53, "published_p_value": 0.009016, "observed_ratio": 1.4772881509433262, "observed_p_value": 0.0416425003723, "relative_difference": 0.03445218892593059, "tolerance": 0.25, "source_cell": "1.53 (0.009016)", "asset_id": "asset:table:pmid:28529692:1" } } ] }, { "contrast_group": "Luminal B", "reference_group": "Healthy", "verdict": "contradicted", "reason": "the observed change is not an increase; the run goes the other way (published ratio 1.3800, run ratio 0.9737); the run agrees with the published ratio 1.3800 but reaches a significance the paper did not (published p 0.044540, run p 0.096332 against the same two groups)", "probes_tested": 2, "probes_reproduced": 0, "probes_direction_only": 0, "probes_significance_only": 1, "probes_contradicted": 1, "observed": [ { "feature": "244606_at", "log2_fold_change": -0.038398123599999945, "observed_ratio": 0.9737355211122102, "p_value": 1.90084445347e-6, "q_value": 3.860077584391238e-6, "f_statistic": 8.80610513583, "contrast_p_value": 0.00610310256891, "contrast_p_value_holm": 0.0549279231202, "contrast_t_statistic": -3.27920485801, "contrast_degrees_of_freedom": 12.784201539, "verdict": "contradicted", "problems": [ "the observed change is not an increase" ], "against_published": { "verdict": "contradicted", "detail": "the run goes the other way (published ratio 1.3800, run ratio 0.9737)", "fold_verdict": "contradicted", "significance_verdict": "reproduced", "published_fold_factor": 1.38, "published_ratio": 1.38, "published_p_value": 0.04454, "observed_ratio": 0.9737355211122102, "observed_p_value": 0.00610310256891, "relative_difference": 0.29439454991868824, "tolerance": 0.25, "source_cell": "1.38 (0.04454)", "asset_id": "asset:table:pmid:28529692:1" } }, { "feature": "220948_s_at", "log2_fold_change": 0.44965726877000023, "observed_ratio": 1.365715774423173, "p_value": 0.00202411595674, "q_value": 0.002850634751882899, "f_statistic": 4.4278555666, "contrast_p_value": 0.0963315854148, "contrast_p_value_holm": 0.481657927074, "contrast_t_statistic": 1.78841127867, "contrast_degrees_of_freedom": 13.4001713778, "verdict": "significance_only", "problems": [], "against_published": { "verdict": "significance_only", "detail": "the run agrees with the published ratio 1.3800 but reaches a significance the paper did not (published p 0.044540, run p 0.096332 against the same two groups)", "fold_verdict": "reproduced", "significance_verdict": "contradicted", "published_fold_factor": 1.38, "published_ratio": 1.38, "published_p_value": 0.04454, "observed_ratio": 1.365715774423173, "observed_p_value": 0.0963315854148, "relative_difference": 0.01035088809914997, "tolerance": 0.25, "source_cell": "1.38 (0.04454)", "asset_id": "asset:table:pmid:28529692:1" } } ] }, { "contrast_group": "Her2", "reference_group": "Healthy", "verdict": "partly_reproduced", "reason": "the observed change is not an increase; the run goes the other way (published ratio 1.6600, run ratio 0.9778)", "probes_tested": 2, "probes_reproduced": 1, "probes_direction_only": 0, "probes_significance_only": 0, "probes_contradicted": 1, "observed": [ { "feature": "244606_at", "log2_fold_change": -0.032421399760000025, "observed_ratio": 0.9777778305959733, "p_value": 1.90084445347e-6, "q_value": 3.860077584391238e-6, "f_statistic": 8.80610513583, "contrast_p_value": 0.0150446757769, "contrast_p_value_holm": 0.105312730438, "contrast_t_statistic": -2.87354288166, "contrast_degrees_of_freedom": 11.0797779058, "verdict": "contradicted", "problems": [ "the observed change is not an increase" ], "against_published": { "verdict": "contradicted", "detail": "the run goes the other way (published ratio 1.6600, run ratio 0.9778)", "fold_verdict": "contradicted", "significance_verdict": "reproduced", "published_fold_factor": 1.66, "published_ratio": 1.66, "published_p_value": 0.005926, "observed_ratio": 0.9777778305959733, "observed_p_value": 0.0150446757769, "relative_difference": 0.4109772104843534, "tolerance": 0.25, "source_cell": "1.66 (0.005926)", "asset_id": "asset:table:pmid:28529692:1" } }, { "feature": "220948_s_at", "log2_fold_change": 0.7729704707699998, "observed_ratio": 1.7087845058450737, "p_value": 0.00202411595674, "q_value": 0.002850634751882899, "f_statistic": 4.4278555666, "contrast_p_value": 0.00886749685122, "contrast_p_value_holm": 0.0886749685122, "contrast_t_statistic": 3.03285995425, "contrast_degrees_of_freedom": 14.1361553299, "verdict": "reproduced", "problems": [], "against_published": { "verdict": "reproduced", "detail": null, "fold_verdict": "reproduced", "significance_verdict": "reproduced", "published_fold_factor": 1.66, "published_ratio": 1.66, "published_p_value": 0.005926, "observed_ratio": 1.7087845058450737, "observed_p_value": 0.00886749685122, "relative_difference": 0.02938825653317697, "tolerance": 0.25, "source_cell": "1.66 (0.005926)", "asset_id": "asset:table:pmid:28529692:1" } } ] }, { "contrast_group": "TNBC", "reference_group": "Healthy", "verdict": "partly_reproduced", "reason": "the observed change is not an increase; the run goes the other way (published ratio 1.4400, run ratio 0.9758)", "probes_tested": 2, "probes_reproduced": 1, "probes_direction_only": 0, "probes_significance_only": 0, "probes_contradicted": 1, "observed": [ { "feature": "244606_at", "log2_fold_change": -0.035399219769999934, "observed_ratio": 0.9757617125281737, "p_value": 1.90084445347e-6, "q_value": 3.860077584391238e-6, "f_statistic": 8.80610513583, "contrast_p_value": 0.0094244035113, "contrast_p_value_holm": 0.0753952280904, "contrast_t_statistic": -3.12233224814, "contrast_degrees_of_freedom": 11.2962025645, "verdict": "contradicted", "problems": [ "the observed change is not an increase" ], "against_published": { "verdict": "contradicted", "detail": "the run goes the other way (published ratio 1.4400, run ratio 0.9758)", "fold_verdict": "contradicted", "significance_verdict": "reproduced", "published_fold_factor": 1.44, "published_ratio": 1.44, "published_p_value": 0.015725, "observed_ratio": 0.9757617125281737, "observed_p_value": 0.0094244035113, "relative_difference": 0.3223876996332127, "tolerance": 0.25, "source_cell": "1.44 (0.015725)", "asset_id": "asset:table:pmid:28529692:1" } }, { "feature": "220948_s_at", "log2_fold_change": 0.6851228651699994, "observed_ratio": 1.607838905079381, "p_value": 0.00202411595674, "q_value": 0.002850634751882899, "f_statistic": 4.4278555666, "contrast_p_value": 0.0163080667888, "contrast_p_value_holm": 0.146772601099, "contrast_t_statistic": 2.768185608, "contrast_degrees_of_freedom": 12.6593029046, "verdict": "reproduced", "problems": [], "against_published": { "verdict": "reproduced", "detail": null, "fold_verdict": "reproduced", "significance_verdict": "reproduced", "published_fold_factor": 1.44, "published_ratio": 1.44, "published_p_value": 0.015725, "observed_ratio": 1.607838905079381, "observed_p_value": 0.0163080667888, "relative_difference": 0.1165547951940147, "tolerance": 0.25, "source_cell": "1.44 (0.015725)", "asset_id": "asset:table:pmid:28529692:1" } } ] } ], "contrasts_tested": 4, "contrasts_reproduced": 0, "contrasts_direction_only": 0, "contrasts_significance_only": 0, "contrasts_partly_reproduced": 3, "contrasts_contradicted": 1, "contrasts_not_testable": 0 }, { "symbol": "ATP1A2", "reference_group": "Healthy", "direction": "down", "verdict": "direction_only", "reason": "Luminal A: the run gets the direction right but its ratio 0.0362 is 91.0% from the published ratio 0.4016, outside the declared tolerance of 25%; the run gets the direction right but its ratio 0.2244 is 44.1% from the published ratio 0.4016, outside the declared tolerance of 25%; Luminal B: the run gets the direction right but its ratio 0.0282 is 92.9% from the published ratio 0.3968, outside the declared tolerance of 25%; the run gets the direction right but its ratio 0.2226 is 43.9% from the published ratio 0.3968, outside the declared tolerance of 25%; Her2: the run gets the direction right but its ratio 0.0290 is 91.9% from the published ratio 0.3597, outside the declared tolerance of 25%; the run gets the direction right but its ratio 0.2247 is 37.5% from the published ratio 0.3597, outside the declared tolerance of 25%; TNBC: the run gets the direction right but its ratio 0.0305 is 91.2% from the published ratio 0.3484, outside the declared tolerance of 25%; the run gets the direction right but its ratio 0.2308 is 33.8% from the published ratio 0.3484, outside the declared tolerance of 25%", "contrasts": [ { "contrast_group": "Luminal A", "reference_group": "Healthy", "verdict": "direction_only", "reason": "the run gets the direction right but its ratio 0.0362 is 91.0% from the published ratio 0.4016, outside the declared tolerance of 25%; the run gets the direction right but its ratio 0.2244 is 44.1% from the published ratio 0.4016, outside the declared tolerance of 25%", "probes_tested": 2, "probes_reproduced": 0, "probes_direction_only": 2, "probes_significance_only": 0, "probes_contradicted": 0, "observed": [ { "feature": "203296_s_at", "log2_fold_change": -4.787550438, "observed_ratio": 0.036207931284621436, "p_value": 1.70777666013e-44, "q_value": 5.90944767970174e-42, "f_statistic": 108.901660795, "contrast_p_value": 1.63436299015e-5, "contrast_p_value_holm": 0.000134200371803, "contrast_t_statistic": -7.07014678756, "contrast_degrees_of_freedom": 11.5006724008, "verdict": "direction_only", "problems": [], "against_published": { "verdict": "direction_only", "detail": "the run gets the direction right but its ratio 0.0362 is 91.0% from the published ratio 0.4016, outside the declared tolerance of 25%", "fold_verdict": "direction_only", "significance_verdict": "reproduced", "published_fold_factor": -2.49, "published_ratio": 0.4016064257028112, "published_p_value": 1.85e-7, "observed_ratio": 0.036207931284621436, "observed_p_value": 1.63436299015e-5, "relative_difference": 0.9098422511012926, "tolerance": 0.25, "source_cell": "-2.49 (1.85·10 -07)", "asset_id": "asset:table:pmid:28529692:1" } }, { "feature": "203295_s_at", "log2_fold_change": -2.1557998152999995, "observed_ratio": 0.22440864888078413, 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outside the declared tolerance of 25%", "fold_verdict": "direction_only", "significance_verdict": "reproduced", "published_fold_factor": -2.52, "published_ratio": 0.3968253968253968, "published_p_value": 8.5e-9, "observed_ratio": 0.028243552904532433, "observed_p_value": 1.34200371803e-5, "relative_difference": 0.9288262466805782, "tolerance": 0.25, "source_cell": "-2.52 (8.50·10 -09)", "asset_id": "asset:table:pmid:28529692:1" } }, { "feature": "203295_s_at", "log2_fold_change": -2.16779527859, "observed_ratio": 0.22255051145041047, "p_value": 3.01690308625e-19, "q_value": 3.1180178153978495e-18, "f_statistic": 31.352214066, "contrast_p_value": 0.0112038683302, "contrast_p_value_holm": 0.112038683302, "contrast_t_statistic": -3.1023516865, "contrast_degrees_of_freedom": 10.0014097853, "verdict": "direction_only", "problems": [], "against_published": { "verdict": "direction_only", "detail": "the run gets the direction right but its ratio 0.2226 is 43.9% from the published ratio 0.3968, outside the declared tolerance of 25%", "fold_verdict": "direction_only", "significance_verdict": "reproduced", "published_fold_factor": -2.52, "published_ratio": 0.3968253968253968, "published_p_value": 8.5e-9, "observed_ratio": 0.22255051145041047, "observed_p_value": 0.0112038683302, "relative_difference": 0.4391727111449656, "tolerance": 0.25, "source_cell": "-2.52 (8.50·10 -09)", "asset_id": "asset:table:pmid:28529692:1" } } ] }, { "contrast_group": "Her2", "reference_group": "Healthy", "verdict": "direction_only", "reason": "the run gets the direction right but its ratio 0.0290 is 91.9% from the published ratio 0.3597, outside the declared tolerance of 25%; the run gets the direction right but its ratio 0.2247 is 37.5% from the published ratio 0.3597, outside the declared tolerance of 25%", "probes_tested": 2, "probes_reproduced": 0, "probes_direction_only": 2, "probes_significance_only": 0, "probes_contradicted": 0, "observed": [ { "feature": "203296_s_at", "log2_fold_change": -5.106493906000001, "observed_ratio": 0.029026332217344884, "p_value": 1.70777666013e-44, "q_value": 5.90944767970174e-42, "f_statistic": 108.901660795, "contrast_p_value": 1.44491227827e-5, "contrast_p_value_holm": 0.000134200371803, "contrast_t_statistic": -7.81228402325, "contrast_degrees_of_freedom": 10.0045721046, "verdict": "direction_only", "problems": [], "against_published": { "verdict": "direction_only", "detail": "the run gets the direction right but its ratio 0.0290 is 91.9% from the published ratio 0.3597, outside the declared tolerance of 25%", "fold_verdict": "direction_only", "significance_verdict": "reproduced", "published_fold_factor": -2.78, "published_ratio": 0.3597122302158274, "published_p_value": 5.480000000000001e-8, "observed_ratio": 0.029026332217344884, "observed_p_value": 1.44491227827e-5, "relative_difference": 0.9193067964357812, "tolerance": 0.25, "source_cell": "-2.78 (5.48·10 -08)", "asset_id": "asset:table:pmid:28529692:1" } }, { "feature": "203295_s_at", "log2_fold_change": -2.1542176696999995, "observed_ratio": 0.22465488380951953, "p_value": 3.01690308625e-19, "q_value": 3.1180178153978495e-18, "f_statistic": 31.352214066, "contrast_p_value": 0.0115808831397, "contrast_p_value_holm": 0.112038683302, "contrast_t_statistic": -3.08296961367, "contrast_degrees_of_freedom": 10.000774393, "verdict": "direction_only", "problems": [], "against_published": { "verdict": "direction_only", "detail": "the run gets the direction right but its ratio 0.2247 is 37.5% from the published ratio 0.3597, outside the declared tolerance of 25%", "fold_verdict": "direction_only", "significance_verdict": "reproduced", "published_fold_factor": -2.78, "published_ratio": 0.3597122302158274, "published_p_value": 5.480000000000001e-8, "observed_ratio": 0.22465488380951953, "observed_p_value": 0.0115808831397, "relative_difference": 0.3754594230095358, "tolerance": 0.25, "source_cell": "-2.78 (5.48·10 -08)", "asset_id": "asset:table:pmid:28529692:1" } } ] }, { "contrast_group": "TNBC", "reference_group": "Healthy", "verdict": "direction_only", "reason": "the run gets the direction right but its ratio 0.0305 is 91.2% from the published ratio 0.3484, outside the declared tolerance of 25%; the run gets the direction right but its ratio 0.2308 is 33.8% from the published ratio 0.3484, outside the declared tolerance of 25%", "probes_tested": 2, "probes_reproduced": 0, "probes_direction_only": 2, "probes_significance_only": 0, "probes_contradicted": 0, "observed": [ { "feature": "203296_s_at", "log2_fold_change": -5.03508776262, "observed_ratio": 0.030499137131729297, "p_value": 1.70777666013e-44, "q_value": 5.90944767970174e-42, "f_statistic": 108.901660795, "contrast_p_value": 1.44129203061e-5, "contrast_p_value_holm": 0.000134200371803, "contrast_t_statistic": -7.63642011095, "contrast_degrees_of_freedom": 10.3576902485, "verdict": "direction_only", "problems": [], "against_published": { "verdict": "direction_only", "detail": "the run gets the direction right but its ratio 0.0305 is 91.2% from the published ratio 0.3484, outside the declared tolerance of 25%", "fold_verdict": "direction_only", "significance_verdict": "reproduced", "published_fold_factor": -2.87, "published_ratio": 0.3484320557491289, "published_p_value": 2.08e-11, "observed_ratio": 0.030499137131729297, "observed_p_value": 1.44129203061e-5, "relative_difference": 0.9124674764319369, "tolerance": 0.25, "source_cell": "-2.87 (2.08·10-11)", "asset_id": "asset:table:pmid:28529692:1" } }, { "feature": "203295_s_at", "log2_fold_change": -2.1155144594699995, "observed_ratio": 0.23076327371796562, "p_value": 3.01690308625e-19, "q_value": 3.1180178153978495e-18, "f_statistic": 31.352214066, "contrast_p_value": 0.0127494373135, "contrast_p_value_holm": 0.112038683302, "contrast_t_statistic": -3.02173967123, "contrast_degrees_of_freedom": 10.0782899956, "verdict": "direction_only", "problems": [], "against_published": { "verdict": "direction_only", "detail": "the run gets the direction right but its ratio 0.2308 is 33.8% from the published ratio 0.3484, outside the declared tolerance of 25%", "fold_verdict": "direction_only", "significance_verdict": "reproduced", "published_fold_factor": -2.87, "published_ratio": 0.3484320557491289, "published_p_value": 2.08e-11, "observed_ratio": 0.23076327371796562, "observed_p_value": 0.0127494373135, "relative_difference": 0.3377094044294386, "tolerance": 0.25, "source_cell": "-2.87 (2.08·10-11)", "asset_id": "asset:table:pmid:28529692:1" } } ] } ], "contrasts_tested": 4, "contrasts_reproduced": 0, "contrasts_direction_only": 4, "contrasts_significance_only": 0, "contrasts_partly_reproduced": 0, "contrasts_contradicted": 0, "contrasts_not_testable": 0 }, { "symbol": "ATP1A3", "reference_group": "Healthy", "direction": "down", "verdict": "reproduced", "reason": null, "contrasts": [ { "contrast_group": "Luminal A", "reference_group": "Healthy", "verdict": "reproduced", "reason": null, "probes_tested": 1, "probes_reproduced": 1, "probes_direction_only": 0, "probes_significance_only": 0, "probes_contradicted": 0, "observed": [ { "feature": "214432_at", "log2_fold_change": -0.018334374230000172, "observed_ratio": 0.9873719911695374, "p_value": 0.00433487566013, "q_value": 0.00586896778184061, "f_statistic": 3.95728898308, "contrast_p_value": 0.05665310841, "contrast_p_value_holm": 0.39657175887, "contrast_t_statistic": -2.08560773062, "contrast_degrees_of_freedom": 13.4077771495, "verdict": "reproduced", "problems": [], "against_published": { "verdict": "reproduced", "detail": null, "fold_verdict": "reproduced", "significance_verdict": "reproduced", "published_fold_factor": -1.05, "published_ratio": 0.9523809523809523, "published_p_value": 0.429089, "observed_ratio": 0.9873719911695374, "observed_p_value": 0.05665310841, "relative_difference": 0.036740590728014375, "tolerance": 0.25, "source_cell": "-1.05 (0.429089)", "asset_id": "asset:table:pmid:28529692:1" } } ] }, { "contrast_group": "Luminal B", "reference_group": "Healthy", "verdict": "reproduced", "reason": null, "probes_tested": 1, "probes_reproduced": 1, "probes_direction_only": 0, "probes_significance_only": 0, "probes_contradicted": 0, "observed": [ { "feature": "214432_at", "log2_fold_change": -0.01202323764000024, "observed_ratio": 0.9917007571817732, "p_value": 0.00433487566013, "q_value": 0.00586896778184061, "f_statistic": 3.95728898308, "contrast_p_value": 0.181435021246, "contrast_p_value_holm": 0.90717510623, "contrast_t_statistic": -1.42203233708, "contrast_degrees_of_freedom": 11.5591244434, "verdict": "reproduced", "problems": [], "against_published": { "verdict": "reproduced", "detail": null, "fold_verdict": "reproduced", "significance_verdict": "reproduced", "published_fold_factor": 1.03, "published_ratio": 1.03, "published_p_value": 0.308298, "observed_ratio": 0.9917007571817732, "observed_p_value": 0.181435021246, "relative_difference": 0.03718373089148236, "tolerance": 0.25, "source_cell": "1.03 (0.308298)", "asset_id": "asset:table:pmid:28529692:1" } } ] }, { "contrast_group": "Her2", "reference_group": "Healthy", "verdict": "reproduced", "reason": null, "probes_tested": 1, "probes_reproduced": 1, "probes_direction_only": 0, "probes_significance_only": 0, "probes_contradicted": 0, "observed": [ { "feature": "214432_at", "log2_fold_change": -0.005801424379999975, "observed_ratio": 0.9959868334105573, "p_value": 0.00433487566013, "q_value": 0.00586896778184061, "f_statistic": 3.95728898308, "contrast_p_value": 0.501532249509, "contrast_p_value_holm": 1, "contrast_t_statistic": -0.694893193844, "contrast_degrees_of_freedom": 11.0035914904, "verdict": "reproduced", "problems": [], "against_published": { "verdict": "reproduced", "detail": null, "fold_verdict": "reproduced", "significance_verdict": "reproduced", "published_fold_factor": -1.04, "published_ratio": 0.9615384615384615, "published_p_value": 0.768041, "observed_ratio": 0.9959868334105573, "observed_p_value": 0.501532249509, "relative_difference": 0.035826306746979654, "tolerance": 0.25, "source_cell": "-1.04 (0.768041)", "asset_id": "asset:table:pmid:28529692:1" } } ] }, { "contrast_group": "TNBC", "reference_group": "Healthy", "verdict": "reproduced", "reason": null, "probes_tested": 1, "probes_reproduced": 1, "probes_direction_only": 0, "probes_significance_only": 0, "probes_contradicted": 0, "observed": [ { "feature": "214432_at", "log2_fold_change": -0.009030129460000147, "observed_ratio": 0.9937603392656016, "p_value": 0.00433487566013, "q_value": 0.00586896778184061, "f_statistic": 3.95728898308, "contrast_p_value": 0.306832363475, "contrast_p_value_holm": 1, "contrast_t_statistic": -1.06931163861, "contrast_degrees_of_freedom": 11.515134431, "verdict": "reproduced", "problems": [], "against_published": { "verdict": "reproduced", "detail": null, "fold_verdict": "reproduced", "significance_verdict": "reproduced", "published_fold_factor": -1.04, "published_ratio": 0.9615384615384615, "published_p_value": 0.527878, "observed_ratio": 0.9937603392656016, "observed_p_value": 0.306832363475, "relative_difference": 0.033510752836225746, "tolerance": 0.25, "source_cell": "-1.04 (0.527878)", "asset_id": "asset:table:pmid:28529692:1" } } ] } ], "contrasts_tested": 4, "contrasts_reproduced": 4, "contrasts_direction_only": 0, "contrasts_significance_only": 0, "contrasts_partly_reproduced": 0, "contrasts_contradicted": 0, "contrasts_not_testable": 0 } ], "summary": { "total": 3, "reproduced": 1, "direction_only": 1, "significance_only": 0, "partly_reproduced": 1, "contradicted": 0, "not_testable": 0, "verdict": "partly_reproduced" } }, "sample_set_fidelity": { "verdict": "matches_the_paper", "expected_group_sizes": { "CellLine": 14, "Healthy": 11, "Her2": 39, "Luminal A": 29, "Luminal B": 30, "TNBC": 55 }, "observed_group_sizes": { "CellLine": 14, "Healthy": 11, "Her2": 39, "Luminal A": 29, "Luminal B": 30, "TNBC": 55 }, "differences": [], "detail": "every group matches the size the paper states" }, "method_inference": { "operation": "infer_probe_mapping", "operation_version": "0.1.0", "record_id": "pmid:28529692", "source": { "authority": "Corpus Engine", "record_id": "pmid:28529692", "content_hash": "sha256:597ab1b2b4d3af05deac209ed6b3bef79d7ad5fa1eabc8484a99c7b5ecd63c1d", "document_sha256": "64b68ff5025807df588812cf2f3665738e159303d28602de0a5099412f94ee90", "sci_version": "1.2", "revision": 4, "table_asset": { "id": "asset:table:pmid:28529692:1", "sha256": "sha256:093de1b1ff705f0e3a405721e80dff9250fdee11708bf051db5b2299349651b4", "locator": "section[1]/table-wrap[1]#T1", "note": "NKA genes expression in breast cancer samples relative to normal breast tissue." }, "built_by": "App\\Support\\Science\\CorpusReplicationTarget", "built_at": "2026-11-02T04:26:45+00:00" }, "reference_group": "Healthy", "tolerance": 0.25, "genes": [ { "symbol": "ATP1A1", "state": "resolved", "reason": "Probe 220948_s_at reproduces the published value in every group (4 of 4), and no other candidate does.", "selected_feature": "220948_s_at", "closest_feature": "220948_s_at", "probe_class": "sequence_tagged", "candidates": [ { "feature": "220948_s_at", "symbol": "ATP1A1", "probe_class": "sequence_tagged", "groups_tested": 4, "groups_within_tolerance": 4, "groups_direction_agrees": 4, "mean_relative_difference": 0.04768653218806805, "max_relative_difference": 0.1165547951940147, "evidence": [ { "contrast_group": "Luminal A", "published_ratio": 1.53, "observed_ratio": 1.4772881509433262, "relative_difference": 0.03445218892593059, "within_tolerance": true, "direction_agrees": true, "source_cell": "1.53 (0.009016)", "note": null }, { "contrast_group": "Luminal B", "published_ratio": 1.38, "observed_ratio": 1.365715774423173, "relative_difference": 0.01035088809914997, "within_tolerance": true, "direction_agrees": true, "source_cell": "1.38 (0.04454)", "note": null }, { "contrast_group": "Her2", "published_ratio": 1.66, "observed_ratio": 1.7087845058450737, "relative_difference": 0.02938825653317697, "within_tolerance": true, "direction_agrees": true, "source_cell": "1.66 (0.005926)", "note": null }, { "contrast_group": "TNBC", "published_ratio": 1.44, "observed_ratio": 1.607838905079381, "relative_difference": 0.1165547951940147, "within_tolerance": true, "direction_agrees": true, "source_cell": "1.44 (0.015725)", "note": null } ] }, { "feature": "244606_at", "symbol": "ATP1A1", "probe_class": "legacy_clone", "groups_tested": 4, "groups_within_tolerance": 0, "groups_direction_agrees": 0, "mean_relative_difference": 0.34883210964987565, "max_relative_difference": 0.4109772104843534, "evidence": [ { "contrast_group": "Luminal A", "published_ratio": 1.53, "observed_ratio": 0.9676194627982302, "relative_difference": 0.36756897856324827, "within_tolerance": false, "direction_agrees": false, "source_cell": "1.53 (0.009016)", "note": null }, { "contrast_group": "Luminal B", "published_ratio": 1.38, "observed_ratio": 0.9737355211122102, "relative_difference": 0.29439454991868824, "within_tolerance": false, "direction_agrees": false, "source_cell": "1.38 (0.04454)", "note": null }, { "contrast_group": "Her2", "published_ratio": 1.66, "observed_ratio": 0.9777778305959733, "relative_difference": 0.4109772104843534, "within_tolerance": false, "direction_agrees": false, "source_cell": "1.66 (0.005926)", "note": null }, { "contrast_group": "TNBC", "published_ratio": 1.44, "observed_ratio": 0.9757617125281737, "relative_difference": 0.3223876996332127, "within_tolerance": false, "direction_agrees": false, "source_cell": "1.44 (0.015725)", "note": null } ] } ], "evidence": [ { "contrast_group": "Luminal A", "published_ratio": 1.53, "observed_ratio": 1.4772881509433262, "relative_difference": 0.03445218892593059, "within_tolerance": true, "direction_agrees": true, "source_cell": "1.53 (0.009016)", "note": null }, { "contrast_group": "Luminal B", "published_ratio": 1.38, "observed_ratio": 1.365715774423173, "relative_difference": 0.01035088809914997, "within_tolerance": true, "direction_agrees": true, "source_cell": "1.38 (0.04454)", "note": null }, { "contrast_group": "Her2", "published_ratio": 1.66, "observed_ratio": 1.7087845058450737, "relative_difference": 0.02938825653317697, "within_tolerance": true, "direction_agrees": true, "source_cell": "1.66 (0.005926)", "note": null }, { "contrast_group": "TNBC", "published_ratio": 1.44, "observed_ratio": 1.607838905079381, "relative_difference": 0.1165547951940147, "within_tolerance": true, "direction_agrees": true, "source_cell": "1.44 (0.015725)", "note": null } ] }, { "symbol": "ATP1A2", "state": "unresolved", "reason": "No candidate probe reproduces the published value within the declared tolerance. The closest is 203295_s_at, whose ratios sit 39.8% from the published values on average.", "selected_feature": null, "closest_feature": "203295_s_at", "probe_class": "sequence_tagged", "candidates": [ { "feature": "203295_s_at", "symbol": "ATP1A2", "probe_class": "sequence_tagged", "groups_tested": 4, "groups_within_tolerance": 0, "groups_direction_agrees": 4, "mean_relative_difference": 0.39839100071769684, "max_relative_difference": 0.4412224642868474, "evidence": [ { "contrast_group": "Luminal A", "published_ratio": 0.4016064257028112, "observed_ratio": 0.22440864888078413, "relative_difference": 0.4412224642868474, "within_tolerance": false, "direction_agrees": true, "source_cell": "-2.49 (1.85·10 -07)", "note": null }, { "contrast_group": "Luminal B", "published_ratio": 0.3968253968253968, "observed_ratio": 0.22255051145041047, "relative_difference": 0.4391727111449656, "within_tolerance": false, "direction_agrees": true, "source_cell": "-2.52 (8.50·10 -09)", "note": null }, { "contrast_group": "Her2", "published_ratio": 0.3597122302158274, "observed_ratio": 0.22465488380951953, "relative_difference": 0.3754594230095358, "within_tolerance": false, "direction_agrees": true, "source_cell": "-2.78 (5.48·10 -08)", "note": null }, { "contrast_group": "TNBC", "published_ratio": 0.3484320557491289, "observed_ratio": 0.23076327371796562, "relative_difference": 0.3377094044294386, "within_tolerance": false, "direction_agrees": true, "source_cell": "-2.87 (2.08·10-11)", "note": null } ] }, { "feature": "203296_s_at", "symbol": "ATP1A2", "probe_class": "sequence_tagged", "groups_tested": 4, "groups_within_tolerance": 0, "groups_direction_agrees": 4, "mean_relative_difference": 0.9176106926623973, "max_relative_difference": 0.9288262466805782, "evidence": [ { "contrast_group": "Luminal A", "published_ratio": 0.4016064257028112, "observed_ratio": 0.036207931284621436, "relative_difference": 0.9098422511012926, "within_tolerance": false, "direction_agrees": true, "source_cell": "-2.49 (1.85·10 -07)", "note": null }, { "contrast_group": "Luminal B", "published_ratio": 0.3968253968253968, "observed_ratio": 0.028243552904532433, "relative_difference": 0.9288262466805782, "within_tolerance": false, "direction_agrees": true, "source_cell": "-2.52 (8.50·10 -09)", "note": null }, { "contrast_group": "Her2", "published_ratio": 0.3597122302158274, "observed_ratio": 0.029026332217344884, "relative_difference": 0.9193067964357812, "within_tolerance": false, "direction_agrees": true, "source_cell": "-2.78 (5.48·10 -08)", "note": null }, { "contrast_group": "TNBC", "published_ratio": 0.3484320557491289, "observed_ratio": 0.030499137131729297, "relative_difference": 0.9124674764319369, "within_tolerance": false, "direction_agrees": true, "source_cell": "-2.87 (2.08·10-11)", "note": null } ] } ], "evidence": [ { "contrast_group": "Luminal A", "published_ratio": 0.4016064257028112, "observed_ratio": 0.22440864888078413, "relative_difference": 0.4412224642868474, "within_tolerance": false, "direction_agrees": true, "source_cell": "-2.49 (1.85·10 -07)", "note": null }, { "contrast_group": "Luminal B", "published_ratio": 0.3968253968253968, "observed_ratio": 0.22255051145041047, "relative_difference": 0.4391727111449656, "within_tolerance": false, "direction_agrees": true, "source_cell": "-2.52 (8.50·10 -09)", "note": null }, { "contrast_group": "Her2", "published_ratio": 0.3597122302158274, "observed_ratio": 0.22465488380951953, "relative_difference": 0.3754594230095358, "within_tolerance": false, "direction_agrees": true, "source_cell": "-2.78 (5.48·10 -08)", "note": null }, { "contrast_group": "TNBC", "published_ratio": 0.3484320557491289, "observed_ratio": 0.23076327371796562, "relative_difference": 0.3377094044294386, "within_tolerance": false, "direction_agrees": true, "source_cell": "-2.87 (2.08·10-11)", "note": null } ] }, { "symbol": "ATP1A3", "state": "resolved", "reason": "The platform carries one probe for ATP1A3, so the published value is placed without a choice to make.", "selected_feature": "214432_at", "closest_feature": "214432_at", "probe_class": "legacy_clone", "candidates": [ { "feature": "214432_at", "symbol": "LOC101927137///ATP1A3", "probe_class": "legacy_clone", "groups_tested": 4, "groups_within_tolerance": 4, "groups_direction_agrees": 3, "mean_relative_difference": 0.03581534530067554, "max_relative_difference": 0.03718373089148236, "evidence": [ { "contrast_group": "Luminal A", "published_ratio": 0.9523809523809523, "observed_ratio": 0.9873719911695374, "relative_difference": 0.036740590728014375, "within_tolerance": true, "direction_agrees": true, "source_cell": "-1.05 (0.429089)", "note": null }, { "contrast_group": "Luminal B", "published_ratio": 1.03, "observed_ratio": 0.9917007571817732, "relative_difference": 0.03718373089148236, "within_tolerance": true, "direction_agrees": false, "source_cell": "1.03 (0.308298)", "note": null }, { "contrast_group": "Her2", "published_ratio": 0.9615384615384615, "observed_ratio": 0.9959868334105573, "relative_difference": 0.035826306746979654, "within_tolerance": true, "direction_agrees": true, "source_cell": "-1.04 (0.768041)", "note": null }, { "contrast_group": "TNBC", "published_ratio": 0.9615384615384615, "observed_ratio": 0.9937603392656016, "relative_difference": 0.033510752836225746, "within_tolerance": true, "direction_agrees": true, "source_cell": "-1.04 (0.527878)", "note": null } ] } ], "evidence": [ { "contrast_group": "Luminal A", "published_ratio": 0.9523809523809523, "observed_ratio": 0.9873719911695374, "relative_difference": 0.036740590728014375, "within_tolerance": true, "direction_agrees": true, "source_cell": "-1.05 (0.429089)", "note": null }, { "contrast_group": "Luminal B", "published_ratio": 1.03, "observed_ratio": 0.9917007571817732, "relative_difference": 0.03718373089148236, "within_tolerance": true, "direction_agrees": false, "source_cell": "1.03 (0.308298)", "note": null }, { "contrast_group": "Her2", "published_ratio": 0.9615384615384615, "observed_ratio": 0.9959868334105573, "relative_difference": 0.035826306746979654, "within_tolerance": true, "direction_agrees": true, "source_cell": "-1.04 (0.768041)", "note": null }, { "contrast_group": "TNBC", "published_ratio": 0.9615384615384615, "observed_ratio": 0.9937603392656016, "relative_difference": 0.033510752836225746, "within_tolerance": true, "direction_agrees": true, "source_cell": "-1.04 (0.527878)", "note": null } ] } ], "summary": { "genes_considered": 3, "genes_resolved": 2, "genes_ambiguous": 0, "genes_unresolved": 1, "discriminating_genes": 2, "discriminating_genes_resolved": 1, "selected_features": { "ATP1A1": "220948_s_at", "ATP1A3": "214432_at" }, "selected_probe_classes": { "ATP1A1": "sequence_tagged" }, "probe_class_consistency": "consistent", "probe_class_consistency_detail": "Every gene that had a choice is placed on a sequence_tagged probe." }, "gaps": [ { "kind": "no_candidate_within_tolerance", "symbol": "ATP1A2", "detail": "No candidate probe reproduces the published value within the declared tolerance. The closest is 203295_s_at, whose ratios sit 39.8% from the published values on average." } ] }, "probe_stats": [ { "feature": "203295_s_at", "symbol": "ATP1A2", "p_value": 3.01690308625e-19, "q_value": 3.1180178153978495e-18, "log2_fold_change": { "TNBC": -2.1155144594699995, "Her2": -2.1542176696999995, "Luminal A": -2.1557998152999995, "Luminal B": -2.16779527859 }, "fold_change": { "TNBC": 0.23076327371796562, "Her2": 0.22465488380951953, "Luminal A": 0.22440864888078413, "Luminal B": 0.22255051145041047 } }, { "feature": "203296_s_at", "symbol": "ATP1A2", "p_value": 1.70777666013e-44, "q_value": 5.90944767970174e-42, "log2_fold_change": { "TNBC": -5.03508776262, "Her2": -5.106493906000001, "Luminal A": -4.787550438, "Luminal B": -5.145934605580001 }, "fold_change": { "TNBC": 0.030499137131729297, "Her2": 0.029026332217344884, "Luminal A": 0.036207931284621436, "Luminal B": 0.028243552904532433 } }, { "feature": "214432_at", "symbol": "LOC101927137///ATP1A3", "p_value": 0.00433487566013, "q_value": 0.00586896778184061, "log2_fold_change": { "TNBC": -0.009030129460000147, "Her2": -0.005801424379999975, "Luminal A": -0.018334374230000172, "Luminal B": -0.01202323764000024 }, "fold_change": { "TNBC": 0.9937603392656016, "Her2": 0.9959868334105573, "Luminal A": 0.9873719911695374, "Luminal B": 0.9917007571817732 } }, { "feature": "220948_s_at", "symbol": "ATP1A1", "p_value": 0.00202411595674, "q_value": 0.002850634751882899, "log2_fold_change": { "TNBC": 0.6851228651699994, "Her2": 0.7729704707699998, "Luminal A": 0.562951256969999, "Luminal B": 0.44965726877000023 }, "fold_change": { "TNBC": 1.607838905079381, "Her2": 1.7087845058450737, "Luminal A": 1.4772881509433262, "Luminal B": 1.365715774423173 } }, { "feature": "244606_at", "symbol": "ATP1A1", "p_value": 1.90084445347e-6, "q_value": 3.860077584391238e-6, "log2_fold_change": { "TNBC": -0.035399219769999934, "Her2": -0.032421399760000025, "Luminal A": -0.04748830676000004, "Luminal B": -0.038398123599999945 }, "fold_change": { "TNBC": 0.9757617125281737, "Her2": 0.9777778305959733, "Luminal A": 0.9676194627982302, "Luminal B": 0.9737355211122102 } } ] } } } ] }