{ "sci_version": "1.5", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "fork:pmid:28529692:abnormal-expression-of-atp1a1-and-atp1a2-in-breast-cancer-30ee8f18", "kind": "science-record", "revision": 8, "content_hash": "sha256:26c4153596d79a37288fac302e042eedf392341ff41d031a6c3fdb56881fa565", "created_at": "2026-11-03T10:54:57.000000Z", "updated_at": "2026-11-03T15:45:20.889630Z", "generator": { "name": "automated-assays", "session_id": "assays-session-30ee8f18-43ad-40ff-864f-b10e1b899c27" }, "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). Coincidently, ATP1A2 expression decreased by more than 2 times (p<0.05)." } ], "state": "complete" }, { "id": "claim-data-access", "statement": "Raw data for Table 1 are available at:\nhttps://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE65194&format=file 22.", "kind": "methodological", "target": null, "evidence": [ { "asset": "source:pmid:28529692", "locator": "sections[4] \"Data and software availability\" paragraphs 1-3", "quote": "Raw data for Table 1 are available at:\nhttps://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE65194&format=file 22." } ], "state": "complete" } ], "gaps": [] }, "experiment": { "state": "complete", "objective": "In GSE65194 Affymetrix microarray data analyzed by one-way between-subjects ANOVA, ATP1A1 was overexpressed approximately 1.5-fold in all breast cancer groups (p<0.05), while ATP1A2 expression decreased by more than 2-fold (p<0.05).", "steps": [ { "id": "assay:1-step-1", "order": 1, "name": "Validate the dataset schema and hash it", "kind": "computational", "state": "complete", "parameters": {}, "inputs": [], "outputs": [], "duration_hours": null }, { "id": "assay:1-step-2", "order": 2, "name": "Confirm at least two groups with at least two observations each", "kind": "computational", "state": "complete", "parameters": {}, "inputs": [], "outputs": [], "duration_hours": null }, { "id": "assay:1-step-3", "order": 3, "name": "Compute per-group descriptives", "kind": "computational", "state": "complete", "parameters": {}, "inputs": [], "outputs": [], "duration_hours": null }, { "id": "assay:1-step-4", "order": 4, "name": "Test variance homogeneity and screen each group for normality", "kind": "computational", "state": "complete", "parameters": {}, "inputs": [], "outputs": [], "duration_hours": null }, { "id": "assay:1-step-5", "order": 5, "name": "Run the one-way analysis of variance", "kind": "computational", "state": "complete", "parameters": {}, "inputs": [], "outputs": [], "duration_hours": null }, { "id": "assay:1-step-6", "order": 6, "name": "Compare every pair of groups and correct across the pairs", "kind": "computational", "state": "complete", "parameters": {}, "inputs": [], "outputs": [], "duration_hours": null }, { "id": "assay:1-step-7", "order": 7, "name": "Package the result and its hashes", "kind": "computational", "state": "complete", "parameters": {}, "inputs": [], "outputs": [], "duration_hours": null } ], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": [] }, "data": { "state": "partial", "assets": [ { "id": "source:pmid:28529692", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.12688/f1000research.10481.1", "sha256": "sha256:b52c152ee6cd127bf20948915bce7ef4e8d743048657f0fe8c3441f877d98c57", "bytes": 8810, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.12688/f1000research.10481.1", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": { "pmcid": "PMC5428514", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body" } }, { "id": "data:geo:GSE65194", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65194", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE65194", "version": null, "note": "Raw data for Table 1 are available at:\nhttps://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE65194&format=file 22.", "structure": { "repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Raw data for Table 1 are available at:\nhttps://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE65194&format=file 22.", "access_statement_kind": "data_availability_statement", "sample_accessions": [ "GSM1588970", "GSM1588971", "GSM1588972", "GSM1588973", "GSM1588974", "GSM1588975", "GSM1588976", "GSM1588977", "GSM1588978", "GSM1588979", "GSM1588980", "GSM1588981", "GSM1588982", "GSM1588983", "GSM1588984", "GSM1588985", "GSM1588986", "GSM1588987", "GSM1588988", "GSM1588989", "GSM1588990", "GSM1588991", "GSM1588992", "GSM1588993", "GSM1588994", "GSM1588995", "GSM1588996", "GSM1588997", "GSM1588998", "GSM1588999", "GSM1589000", "GSM1589001", "GSM1589002", "GSM1589003", "GSM1589004", "GSM1589005", "GSM1589006", "GSM1589007", "GSM1589008", "GSM1589009", "GSM1589010", "GSM1589011", "GSM1589012", "GSM1589013", "GSM1589014", "GSM1589015", "GSM1589016", "GSM1589017", "GSM1589018", "GSM1589019", "GSM1589020", "GSM1589021", "GSM1589022", "GSM1589023", "GSM1589024", "GSM1589025", "GSM1589026", "GSM1589027", "GSM1589028", "GSM1589029", "GSM1589030", "GSM1589031", "GSM1589032", "GSM1589033", "GSM1589034", "GSM1589035", "GSM1589036", "GSM1589037", "GSM1589038", "GSM1589039", "GSM1589040", "GSM1589041", "GSM1589042", "GSM1589043", "GSM1589044", "GSM1589045", "GSM1589046", "GSM1589047", "GSM1589048", "GSM1589049", "GSM1589050", "GSM1589051", "GSM1589052", "GSM1589053", "GSM1589054", "GSM1589055", "GSM1589056", "GSM1589057", "GSM1589058", "GSM1589059", "GSM1589060", "GSM1589061", "GSM1589062", "GSM1589063", "GSM1589064", "GSM1589065", "GSM1589066", "GSM1589067", "GSM1589068", "GSM1589069", "GSM1589070", "GSM1589071", "GSM1589072", "GSM1589073", "GSM1589074", "GSM1589075", "GSM1589076", "GSM1589077", "GSM1589078", "GSM1589079", "GSM1589080", "GSM1589081", "GSM1589082", "GSM1589083", "GSM1589084", "GSM1589085", "GSM1589086", "GSM1589087", "GSM1589088", "GSM1589089", "GSM1589090", "GSM1589091", "GSM1589092", "GSM1589093", "GSM1589094", "GSM1589095", "GSM1589097", "GSM1589098", "GSM1589099", "GSM1589101", "GSM1589103", "GSM1589105", "GSM1589107", "GSM1589109", "GSM1589110", "GSM1589111", "GSM1589112", "GSM1589113", "GSM1589114", "GSM1589115", "GSM1589116", "GSM1589117", "GSM1589118", "GSM1589119", "GSM1589120", "GSM1589121", "GSM1589122", "GSM1589123", "GSM1589124", "GSM1589125", "GSM1589126", "GSM1589127", "GSM1589128", "GSM1589129", "GSM1589130", "GSM1589131", "GSM1589132", "GSM1589133", "GSM1589134", "GSM1589135", "GSM1589136", "GSM1589137", "GSM1589138", "GSM1589139", "GSM1589140", "GSM1589141", "GSM1589142", "GSM1589143", "GSM1589144", "GSM1589145", "GSM1589146", "GSM1589147", "GSM1589148", "GSM1589149", "GSM1589150", "GSM1589151", "GSM1589152", "GSM1589153" ], "sample_count": 178, "group_sizes": { "Luminal A": 29, "Luminal B": 30, "Her2": 39, "TNBC": 55, "Healthy": 11, "CellLine": 14 }, "group_sizes_basis": "GEO sample metadata for GSE65194: 178 samples in six groups. 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, "software_access_statement_verbatim": "Expression Console 1.4 software and Transcriptome Analysis Console 3.0 software (Affymetrix, Inc. USA) are available after free customer registration at:\nhttp://www.affymetrix.com/support/technical/software_downloads.affx.", "software_access_statement_kind": "software_availability_statement", "software_access_uri": "http://www.affymetrix.com/support/technical/software_downloads.affx" } }, { "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 licence not read", "asset:data:geo:GSE65194 not downloaded", "data.group_sizes_conflict", "data.sample_set_unresolved" ], "group_sizes": { "CellLine": 14, "Healthy": 11, "Her2": 39, "Luminal A": 29, "Luminal B": 30, "TNBC": 55 }, "paper_group_sizes": { "sizes": { "Her2": 30, "Lum A": 29, "Lum B": 30, "TNBC": 41, "normal breast tissue": 11 }, "total": 141, "source": "Array data for 41 triple negative samples (TNBC group), 30 Her2-positive (Her2 group), 30 Luminal B (Lum B group), 29 Luminal A (Lum A group) breast cancer samples and 11 normal breast tissue samples were investigated.", "reference_group": "normal breast tissue" } }, "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:microarray_rma_normalise", "axes": { "method": { "tier": "R4", "expressible": false, "required_operations": [ "group_comparison_anova", "microarray_rma_normalise", "group_relative_expression" ], "missing_operations": [ "microarray_rma_normalise", "group_relative_expression" ], "basis": "The DSL catalogue has no operation for: microarray_rma_normalise, group_relative_expression." }, "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. No dataset was downloaded and no licence was read." } }, "can_run": { "dsl_operations": [ "group_comparison_anova" ], "assets": [ "source:pmid:28529692", "data:geo:GSE65194", "asset:table:pmid:28529692:1" ], "steps": [] }, "must_build": { "dsl_operations": [ { "operation": "microarray_rma_normalise", "unlocks_papers": null, "priority": null }, { "operation": "group_relative_expression", "unlocks_papers": null, "priority": null } ], "converters": [], "readers": [], "capabilities": [], "data_gaps": [ "data:geo:GSE65194" ] }, "gaps": [ "method:microarray_rma_normalise" ] }, "review": { "state": "absent", "machine_critique": null, "human_critique": null, "stages": [], "gaps": [ "review.absent: this document is a working version. Review and publication are separate actions, and they belong to the Journal." ] }, "execution": { "state": "complete", "status": "run", "mode": "computational", "runs": [ { "id": "2d090760-f2ae-423e-849f-dc58da829431", "record": "fork:pmid:28529692:abnormal-expression-of-atp1a1-and-atp1a2-in-breast-cancer-30ee8f18", "operation": "group_comparison_anova", "version": "0.1.0", "status": "complete", "provider": "automated-assays-computational", "result_hash": "9dd46f386a0e57d0d15cb2c6ecea5f48be988ebee6bdb03185e9373809493ac6", "evidence": "87ff3155b911ad594efd4d06168102fdee0c005e2f51b9edc0aae846081b9709" }, { "id": "ccdb9e35-1e46-47c8-9fde-b096e3b2dca6", "record": "fork:pmid:28529692:abnormal-expression-of-atp1a1-and-atp1a2-in-breast-cancer-30ee8f18", "operation": "group_comparison_anova", "version": "0.1.0", "status": "complete", "provider": "automated-assays-computational", "result_hash": "9dd46f386a0e57d0d15cb2c6ecea5f48be988ebee6bdb03185e9373809493ac6", "evidence": "7d6e68368f4e57c5bf3fc7c047891d14bed7a479b42bcbc59828dea0b10faf95" }, { "id": "30eab1f1-9658-4752-b04a-b6aa17a14a3a", "record": "fork:pmid:28529692:abnormal-expression-of-atp1a1-and-atp1a2-in-breast-cancer-30ee8f18", "operation": "group_comparison_anova", "version": "0.1.0", "status": "complete", "provider": "automated-assays-computational", "result_hash": "9dd46f386a0e57d0d15cb2c6ecea5f48be988ebee6bdb03185e9373809493ac6", "evidence": "9009b2063e89db5f8eb54e0d978d07e199de641c17497f35e6696b3878fded3e" }, { "id": "b1a80714-f07f-4e92-8712-5875211bd4a5", "record": "fork:pmid:28529692:abnormal-expression-of-atp1a1-and-atp1a2-in-breast-cancer-30ee8f18", "operation": "group_comparison_anova", "version": "0.1.0", "status": "complete", "provider": "automated-assays-computational", "result_hash": "d2e043b2c582c00897bbf0561ebfbe31771e5768aebf6717eb8e7dc5c0e258e0", "evidence": "8f5d82deb63559b72eede3efa16f7ee2c8a0513caf5b1624801931b243d98a4e" }, { "id": "b3d84aac-f651-4db8-b6d7-952c1067bc68", "record": "pmid:28529692", "operation": "group_comparison_anova", "version": "0.1.0", "status": "complete", "provider": "automated-assays-computational", "result_hash": "9dd46f386a0e57d0d15cb2c6ecea5f48be988ebee6bdb03185e9373809493ac6", "evidence": "39a33cc135b9e908a814f0854ae4337d69a77e91b6b4b08118eb1cfad1f00226" }, { "id": "35855d74-da28-419b-9aff-6a2faab1cbb3", "record": "pmid:28529692", "operation": "group_comparison_anova", "version": "0.1.0", "status": "complete", "provider": "automated-assays-computational", "result_hash": "9dd46f386a0e57d0d15cb2c6ecea5f48be988ebee6bdb03185e9373809493ac6", "evidence": "54d4257e859ea5a046fd1aeeda50771d69be127be8ce5af864e03b330244e861" }, { "id": "55e62ab5-1896-49a6-8660-084755f20b6b", "record": "pmid:28529692", "operation": "group_comparison_anova", "version": "0.1.0", "status": "complete", "provider": "automated-assays-computational", "result_hash": "54a410ca80264c03e91ef940661500f76af0af12ce97cf3f6005c0e6005d3608", "evidence": "ae2c9c04e9c7fa7fe01d8d2bca37c7d04d98d3e6adce5552011b255e09f4dffa" }, { "id": "dad39f8c-48e8-4efd-b166-d521049482f4", "record": "pmid:28529692", "operation": "group_comparison_anova", "version": "0.1.0", "status": "failed", "provider": "automated-assays-computational", "result_hash": null, "evidence": null }, { "id": "17fdc411-b820-446f-ad1c-2707e0c7c7ce", "record": "pmid:28529692", "operation": "group_comparison_anova", "version": "0.1.0", "status": "complete", "provider": "automated-assays-computational", "result_hash": "d2e043b2c582c00897bbf0561ebfbe31771e5768aebf6717eb8e7dc5c0e258e0", "evidence": "5cb7247f5e740f9c91e38661e930c9d423780dac50bcca5d1d8bc03344f8e131" }, { "id": "ddf18337-22c9-41f3-b428-91903ba5cb5e", "record": "pmid:28529692", "operation": "group_comparison_anova", "version": "0.1.0", "status": "complete", "provider": "automated-assays-computational", "result_hash": "d2e043b2c582c00897bbf0561ebfbe31771e5768aebf6717eb8e7dc5c0e258e0", "evidence": "a75426d81c2d534d0a5bf54f37a781bec8b8284e29638684c51eb2ea618e8135" }, { "id": "9d2dcc1b-00f2-479b-9e50-1f99a52a1649", "record": "pmid:28529692", "operation": "group_comparison_anova", "version": "0.1.0", "status": "complete", "provider": "automated-assays-computational", "result_hash": "d2e043b2c582c00897bbf0561ebfbe31771e5768aebf6717eb8e7dc5c0e258e0", "evidence": "e5d965c9dcfd87e1f460d9f3b43d9e083c72ce77f348babd44d81c5ebda1c83e" }, { "id": "7ee6eac8-e2d2-4cf7-832b-5a26f5c1626f", "record": "pmid:28529692", "operation": "group_comparison_anova", "version": "0.1.0", "status": "complete", "provider": "automated-assays-computational", "result_hash": "234ce160fd565c75d79da6bf3ff7703e74c34fce7f29f6b13fcb8b89adebf766", "evidence": "ce4c4c84ffa6fedfde751d02c3661158467b917cd83e93a36b6902816971e97b" }, { "id": "818d9213-ad32-4a5e-8325-2d7c59a7743c", "record": "pmid:28529692", "operation": "group_comparison_anova", "version": "0.1.0", "status": "complete", "provider": "automated-assays-computational", "result_hash": "e109c9ff1d16759ac889e64591e5b8c2bbc149ce55335d783758c9e2c4805105", "evidence": "e6477384c3bbc834c3a15bd9b952f3a75c23a54e09340b4c3fe721081b2ec4e6" }, { "id": "40b97cc2-c3b4-429f-b4ec-6ad4ef7d5085", "record": "pmid:28529692", "operation": "group_comparison_anova", "version": "0.1.0", "status": "complete", "provider": "automated-assays-computational", "result_hash": "e109c9ff1d16759ac889e64591e5b8c2bbc149ce55335d783758c9e2c4805105", "evidence": "37d41c54a1cf0055162706aa6b42103569b6471c1a9e91310d48d09c2158fe5b" } ], "gaps": [] }, "provenance": { "entities": [ { "id": "experiment:30ee8f18-43ad-40ff-864f-b10e1b899c27", "type": "experiment", "label": "Abnormal expression of ATP1A1 and ATP1A2 in breast cancer", "owner": "automated-assays", "version": "0.1.0", "digest": null }, { "id": "science-record:pmid:28529692", "type": "science_record", "label": "The Corpus Engine science record this experiment was opened against", "owner": "corpus-engine", "version": 6, "digest": "sha256:116bf117cc3112c78abf15a5c35878e88e5fab508f979460005284568439dbe5" }, { "id": "assay-definition:group-comparison-analysis@0.1.0", "type": "assay_definition", "label": "Group comparison analysis", "owner": "automated-assays", "version": "0.1.0", "digest": "sha256:f1c5d3dfb8ca3c3061030d0f366addd1f61dd994520aa65a406632940618b75a", "definition": { "name": "Group comparison analysis", "slug": "group-comparison-analysis", "version": "0.1.0", "owner": "automated-assays", "execution_mode": "computational", "purpose": "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. Implements the operation the Corpus Engine ranks first in its build list.", "operation": "group_comparison_anova", "operation_version": "0.1.0", "dsl_family": "group_comparison", "dsl_operations": [ "group_comparison_anova" ], "catalogued_by_corpus": true, "catalogue_note": "The Corpus Engine catalogues `group_comparison_anova` in the `group_comparison` family and ranks it first in its build list. The platform runs it over real, published data through the dataset runner, and answers a request for it over the observations the request carries.", "inputs": { "observations": { "type": "array", "description": "The measurements to compare. Each carries the group the observation belongs to and the value that was measured.", "required": true } }, "parameters": { "alpha": { "type": "number", "description": "The significance level, declared before the run and recorded with the result.", "default": 0.05 } }, "outputs": { "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" }, "controls": [ "Positive control group with a known difference", "Negative or blank control group", "Replicate policy recorded with the dataset", "Significance level declared before the run and recorded with the result" ], "refusals": { "observations_missing": "The request carried no observations to compare.", "observation_unlabelled": "An observation carries no group label.", "observation_not_numeric": "An observation carries a value that is not a number.", "too_few_groups": "A one-way analysis of variance needs at least two groups, each with at least two observations." }, "procedure": [ { "order": 1, "step": "Validate the dataset schema and hash it" }, { "order": 2, "step": "Confirm at least two groups with at least two observations each" }, { "order": 3, "step": "Compute per-group descriptives" }, { "order": 4, "step": "Test variance homogeneity and screen each group for normality" }, { "order": 5, "step": "Run the one-way analysis of variance" }, { "order": 6, "step": "Compare every pair of groups and correct across the pairs" }, { "order": 7, "step": "Package the result and its hashes" } ], "execution": { "default_provider": "automated-assays-computational", "provider_rule": "A request may name a provider that supports the exact operation. A provider that does not support it is refused, and is never substituted for one that does.", "request": { "required": { "source_record_id": "The science record the work is about.", "source_content_hash": "The exact version of that record, as sha256:. The request is refused if the platform does not hold that version.", "operation": "The operation to run.", "operation_version": "The version of that operation.", "inputs": "The inputs the operation takes." }, "optional": { "request_id": "The identity of the request. A retry with the same identity and the same request returns the execution that already exists, rather than running the work twice. A retry with the same identity and a different request — a different source, operation, set of inputs, set of parameters or provider — is refused, and the execution that already exists is left unchanged.", "parameters": "The parameters of the run.", "provider": "A provider that supports the exact operation. The default is Automated Assays. A provider that does not support the operation is refused and never substituted for one that does.", "assay_id": "The identity of the assay entry the work concerns, inside the source record. A record of version 1.2 carries an ordered set of assays and every entry has an identity, so a request that names one says exactly which assay of the record the work belongs to. The entry has to be one the record holds and the operation has to be one that entry requires, or the request is refused rather than run against some other assay.", "assay_entry": "The assay entry the work concerns, inside the source record. A science record carries an ordered set of assays, so a record and an operation do not on their own say which of that record's assays the work belongs to. Give definition_id, and definition_version and definition_digest when they are known. When the entry is given and does not match the operation named, the request is refused rather than quietly run against the other entry. 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. 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. 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 fork:pmid:28529692:abnormal-expression-of-atp1a1-and-atp1a2-in-breast-cancer-30ee8f18 at version sha256:ba5107d1ce6eda8cb1bc4309689cbade3a4eef170b65343d9166cb012e7aaae6", "used": [ "fork:pmid:28529692:abnormal-expression-of-atp1a1-and-atp1a2-in-breast-cancer-30ee8f18" ], "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:. The request is refused if the platform does not hold that version.", "operation": "The operation to run.", "operation_version": "The version of that operation.", "inputs": "The inputs the operation takes." }, "optional": { "request_id": "The identity of the request. A retry with the same identity and the same request returns the execution that already exists, rather than running the work twice. A retry with the same identity and a different request — a different source, operation, set of inputs, set of parameters or provider — is refused, and the execution that already exists is left unchanged.", "parameters": "The parameters of the run.", "provider": "A provider that supports the exact operation. The default is Automated Assays. A provider that does not support the operation is refused and never substituted for one that does.", "assay_id": "The identity of the assay entry the work concerns, inside the source record. A record of version 1.2 carries an ordered set of assays and every entry has an identity, so a request that names one says exactly which assay of the record the work belongs to. The entry has to be one the record holds and the operation has to be one that entry requires, or the request is refused rather than run against some other assay.", "assay_entry": "The assay entry the work concerns, inside the source record. A science record carries an ordered set of assays, so a record and an operation do not on their own say which of that record's assays the work belongs to. Give definition_id, and definition_version and definition_digest when they are known. When the entry is given and does not match the operation named, the request is refused rather than quietly run against the other entry. 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. 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. 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." } } ], "agents": [ { "id": "agent:user:0195616cec89", "type": "person", "label": "Automated Assays Administrator", "identity": "admin@automated-assays.local", "role": "author" }, { "id": "agent:automated-assays", "type": "software", "label": "Automated Assays" } ], "source_run_id": "assays-session-30ee8f18-43ad-40ff-864f-b10e1b899c27", "dsl_catalogue_fingerprint": null, "capability_table_fingerprint": null, "snapshot_id": null }, "lineage": { "parent_id": "fork:pmid:28529692:abnormal-expression-of-atp1a1-and-atp1a2-in-breast-cancer-30ee8f18", "parent_hash": "sha256:ba5107d1ce6eda8cb1bc4309689cbade3a4eef170b65343d9166cb012e7aaae6", "fork_of": "pmid:28529692", "generation": 7 }, "gaps": [ "execution.unbound: 2 runs against this record are not bound to a version of it, so are not published as evidence on an assay entry." ], "assays": [ { "id": "assay:1", "role": "primary", "order_basis": "platform_plan_order:0", "definition_id": "group-comparison-analysis", "definition_version": "0.1.0", "definition_digest": "sha256:f1c5d3dfb8ca3c3061030d0f366addd1f61dd994520aa65a406632940618b75a", "required_operations": [ "group_comparison_rank_sum", "group_comparison_wilcoxon", "group_comparison_mann_whitney", "student_t", "welch_t", "group_comparison_anova" ], "support_state": "supported", "source_hashes": { "assay_definition": "sha256:f1c5d3dfb8ca3c3061030d0f366addd1f61dd994520aa65a406632940618b75a", "science_record": "sha256:116bf117cc3112c78abf15a5c35878e88e5fab508f979460005284568439dbe5" }, "definition": { "definition_id": "group-comparison-analysis", "definition_version": "0.1.0", "definition_digest": "sha256:f1c5d3dfb8ca3c3061030d0f366addd1f61dd994520aa65a406632940618b75a", "required_operations": [ "group_comparison_rank_sum", "group_comparison_wilcoxon", "group_comparison_mann_whitney", "student_t", "welch_t", "group_comparison_anova" ], "support_state": "supported", "input_contract": { "observations": { "type": "array", "description": "The measurements to compare. 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" } }, "depends_on": [], "operations": [ { "operation": "group_comparison_rank_sum", "operation_version": "0.1.0", "support_state": "supported", "input_contract": { "observations": { "type": "array", "description": "The measurements to compare. Each carries the group the observation belongs to and the value that was measured. Exactly two groups must be present.", "required": true } }, "parameter_contract": { "alpha": { "type": "number", "description": "The significance level, declared before the run and recorded with the result.", "default": 0.05 }, "method": { "type": "string", "description": "How the p-value is computed: `exact` counts the ways the ranks can be split between the groups and reads the tail of that count; `asymptotic` uses the normal approximation with the continuity and tie corrections; `auto` chooses between them, using the exact distribution only when there are no ties and at least one group is small enough for the count to be worth making.", "default": "auto", "allowed": [ "auto", "exact", "asymptotic" ] } }, "output_contract": { "status": "complete", "summary": "How many observations were compared and how the p-value was computed", "parameters": "The parameters the run was made under", "dataset": "The rows the run was made over, with their hash", "result": "The rank sums, the U statistic, the p-value, the effect sizes and the per-group descriptives", "result_sha256": "The canonical hash of the result", "interpretation": "What the result does and does not say" }, "limitations": [ "The test compares the distribution of the ranks between the two groups. It does not compare the medians, and a significant result is not a statement about the size of the difference.", "The observations are taken to be independent. Where they are paired or repeated measures from the same subject, this test is the wrong test and the platform refuses it rather than answering a question that was not asked.", "The exact p-value assumes every observation has a rank of its own. Where the observations are tied, the normal approximation is used and the result says so.", "The groups and the measurements 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." ], "interpretation": "This operation is computed by this platform over the data the record names. Its result is a re-analysis of that data, not a reproduction of the pipeline the paper used." }, { "operation": "group_comparison_wilcoxon", "operation_version": "0.1.0", "support_state": "supported", "input_contract": { "observations": { "type": "array", "description": "The measurements to compare. Each carries the group the observation belongs to and the value that was measured. Exactly two groups must be present.", "required": true } }, "parameter_contract": { "alpha": { "type": "number", "description": "The significance level, declared before the run and recorded with the result.", "default": 0.05 }, "method": { "type": "string", "description": "How the p-value is computed: `exact` counts the ways the ranks can be split between the groups and reads the tail of that count; `asymptotic` uses the normal approximation with the continuity and tie corrections; `auto` chooses between them, using the exact distribution only when there are no ties and at least one group is small enough for the count to be worth making.", "default": "auto", "allowed": [ "auto", "exact", "asymptotic" ] } }, "output_contract": { "status": "complete", "summary": "How many observations were compared and how the p-value was computed", "parameters": "The parameters the run was made under", "dataset": "The rows the run was made over, with their hash", "result": "The rank sums, the U statistic, the p-value, the effect sizes and the per-group descriptives", "result_sha256": "The canonical hash of the result", "interpretation": "What the result does and does not say" }, "limitations": [ "The test compares the distribution of the ranks between the two groups. It does not compare the medians, and a significant result is not a statement about the size of the difference.", "The observations are taken to be independent. Where they are paired or repeated measures from the same subject, this test is the wrong test and the platform refuses it rather than answering a question that was not asked.", "The exact p-value assumes every observation has a rank of its own. Where the observations are tied, the normal approximation is used and the result says so.", "The groups and the measurements 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." ], "interpretation": "This operation is computed by this platform over the data the record names. Its result is a re-analysis of that data, not a reproduction of the pipeline the paper used." }, { "operation": "group_comparison_mann_whitney", "operation_version": "0.1.0", "support_state": "supported", "input_contract": { "observations": { "type": "array", "description": "The measurements to compare. Each carries the group the observation belongs to and the value that was measured. Exactly two groups must be present.", "required": true } }, "parameter_contract": { "alpha": { "type": "number", "description": "The significance level, declared before the run and recorded with the result.", "default": 0.05 }, "method": { "type": "string", "description": "How the p-value is computed: `exact` counts the ways the ranks can be split between the groups and reads the tail of that count; `asymptotic` uses the normal approximation with the continuity and tie corrections; `auto` chooses between them, using the exact distribution only when there are no ties and at least one group is small enough for the count to be worth making.", "default": "auto", "allowed": [ "auto", "exact", "asymptotic" ] } }, "output_contract": { "status": "complete", "summary": "How many observations were compared and how the p-value was computed", "parameters": "The parameters the run was made under", "dataset": "The rows the run was made over, with their hash", "result": "The rank sums, the U statistic, the p-value, the effect sizes and the per-group descriptives", "result_sha256": "The canonical hash of the result", "interpretation": "What the result does and does not say" }, "limitations": [ "The test compares the distribution of the ranks between the two groups. It does not compare the medians, and a significant result is not a statement about the size of the difference.", "The observations are taken to be independent. Where they are paired or repeated measures from the same subject, this test is the wrong test and the platform refuses it rather than answering a question that was not asked.", "The exact p-value assumes every observation has a rank of its own. Where the observations are tied, the normal approximation is used and the result says so.", "The groups and the measurements 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." ], "interpretation": "This operation is computed by this platform over the data the record names. Its result is a re-analysis of that data, not a reproduction of the pipeline the paper used." }, { "operation": "student_t", "operation_version": "0.1.0", "support_state": "supported", "input_contract": { "observations": { "type": "array", "description": "The measurements to compare. Each carries the group the observation belongs to and the value that was measured. Exactly two groups must be present, with at least two observations in each.", "required": true } }, "parameter_contract": { "alpha": { "type": "number", "description": "The significance level, declared before the run and recorded with the result. The interval for the difference in means is at one minus this level.", "default": 0.05 }, "equal_variances": { "type": "boolean", "description": "Whether the two groups are assumed to share a variance. True is the pooled form of Student's t test, whose degrees of freedom are n1 + n2 - 2. False is Welch's form, whose degrees of freedom are the Welch-Satterthwaite quantity. The form that ran is recorded in the result.", "default": true } }, "output_contract": { "status": "complete", "summary": "How many observations were compared and which form of the test ran", "parameters": "The parameters the run was made under", "dataset": "The rows the run was made over, with their hash", "result": "The means, the difference in means, the standard error, the t statistic, its degrees of freedom, the p-value, the interval and the per-group descriptives", "result_sha256": "The canonical hash of the result", "interpretation": "What the result does and does not say" }, "limitations": [ "The test compares the means of two groups under an assumption about the distribution of the measurement. The pooled form additionally assumes the two groups share a variance, and that assumption is the platform's to state and the caller's to judge.", "The observations are taken to be independent. Where they are paired or repeated measures from the same subject, this test is the wrong test and the platform refuses it rather than answering a question that was not asked.", "The groups and the measurements 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." ], "interpretation": "This operation is computed by this platform over the data the record names. Its result is a re-analysis of that data, not a reproduction of the pipeline the paper used." }, { "operation": "welch_t", "operation_version": "0.1.0", "support_state": "supported", "input_contract": { "observations": { "type": "array", "description": "The measurements to compare. Each carries the group the observation belongs to and the value that was measured. Exactly two groups must be present, with at least two observations in each.", "required": true } }, "parameter_contract": { "alpha": { "type": "number", "description": "The significance level, declared before the run and recorded with the result. The interval for the difference in means is at one minus this level.", "default": 0.05 } }, "output_contract": { "status": "complete", "summary": "How many observations were compared and which form of the test ran", "parameters": "The parameters the run was made under", "dataset": "The rows the run was made over, with their hash", "result": "The means, the difference in means, the standard error, the t statistic, its degrees of freedom, the p-value, the interval and the per-group descriptives", "result_sha256": "The canonical hash of the result", "interpretation": "What the result does and does not say" }, "limitations": [ "The test compares the means of two groups under an assumption about the distribution of the measurement. This form makes no equal-variance assumption, which is the reason to use it, and it costs a small loss of power when the assumption would have held.", "The observations are taken to be independent. Where they are paired or repeated measures from the same subject, this test is the wrong test and the platform refuses it rather than answering a question that was not asked.", "The groups and the measurements 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 responsibility." ], "interpretation": "This operation is computed by this platform over the data the record names. Its result is a re-analysis of that data, not a reproduction of the pipeline the paper used." }, { "operation": "group_comparison_anova", "operation_version": "0.1.0", "support_state": "supported", "input_contract": { "observations": { "type": "array", "description": "The measurements to compare. 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" }, "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." ], "interpretation": "This operation is computed by this platform over the data the record names. Its result is a re-analysis of that data, not a reproduction of the pipeline the paper used." } ], "request": { "assay_id": "assay:1", "source_record_id": "fork:pmid:28529692:abnormal-expression-of-atp1a1-and-atp1a2-in-breast-cancer-30ee8f18", "source_content_hash": "sha256:ba5107d1ce6eda8cb1bc4309689cbade3a4eef170b65343d9166cb012e7aaae6", "operation": "group_comparison_anova", "operation_version": "0.1.0", "inputs": [], "parameters": { "reference_group": "Healthy", "contrast_groups": [ "TNBC", "Her2", "Luminal A", "Luminal B" ], "alpha": 0.05, "fold_change_threshold": 1.5, "multiple_testing": "benjamini_hochberg" }, "request_id": null, "provider": "automated-assays-computational" }, "result": { "assay_id": "assay:1", "provider": "automated-assays-computational", "execution_id": "2d090760-f2ae-423e-849f-dc58da829431", "input_hash": null, "result_hash": "9dd46f386a0e57d0d15cb2c6ecea5f48be988ebee6bdb03185e9373809493ac6", "evidence_hash": "87ff3155b911ad594efd4d06168102fdee0c005e2f51b9edc0aae846081b9709", "status": "complete", "finding": null, "result": { "feature_count": 54673, "differential_count": 22426, "differential": [ { "feature": "211565_at", "symbol": "SH3GL3", "f_statistic": 694.482866849, "p_value": 2.06276814606e-89, "q_value": 1.127777228495384e-84, "log2_fold_change": { "TNBC": -6.35637434489, "Her2": -6.37902371601, "Luminal A": -6.343058452309999, "Luminal B": -6.350793852959999 }, "fold_change": { "TNBC": 0.012205080789960673, "Her2": 0.012014965232441227, "Luminal A": 0.0123182536224913, "Luminal B": 0.012252382715758526 }, "max_abs_log2_fold_change": 6.37902371601 }, { "feature": "243689_s_at", "symbol": "FRG1BP", "f_statistic": 356.724419097, "p_value": 4.93491345645e-71, "q_value": 1.3490326170224544e-66, "log2_fold_change": { "TNBC": -6.11933110022, "Her2": -6.08240435099, "Luminal A": -6.073333030700001, "Luminal B": -6.12509688013 }, "fold_change": { "TNBC": 0.014384599857277358, "Her2": 0.014757535771266582, "Luminal A": 0.014850619954437207, "Luminal B": 0.014327226038178336 }, "max_abs_log2_fold_change": 6.12509688013 }, { "feature": "1562755_at", "symbol": null, "f_statistic": 309.650393284, "p_value": 3.01241856554e-67, "q_value": 5.48993200779228e-63, "log2_fold_change": { "TNBC": -5.61425522733, "Her2": -5.58242022618, "Luminal A": -5.64678428259, "Luminal B": -5.642843354509999 }, "fold_change": { "TNBC": 0.02041459522443413, "Her2": 0.0208700775826067, "Luminal A": 0.01995944917929172, "Luminal B": 0.02001404580797239 }, "max_abs_log2_fold_change": 5.64678428259 }, { "feature": "233103_at", "symbol": null, "f_statistic": 266.878570131, "p_value": 2.49766148106e-63, "q_value": 3.4138661538498345e-59, "log2_fold_change": { "TNBC": -2.1247270233599997, "Her2": -2.0658374484799995, "Luminal A": -2.0968617948499997, "Luminal B": -2.0950971392399995 }, "fold_change": { "TNBC": 0.22929439217403963, "Her2": 0.23884764405185138, "Luminal A": 0.23376619235066287, "Luminal B": 0.23405230216752973 }, "max_abs_log2_fold_change": 2.1247270233599997 }, { "feature": "1561754_at", "symbol": null, "f_statistic": 265.277271163, "p_value": 3.58784533144e-63, "q_value": 3.923165356116383e-59, "log2_fold_change": { "TNBC": -5.7745349289000005, "Her2": -5.92646906831, "Luminal A": -5.75632335825, "Luminal B": -5.84492264967 }, "fold_change": { "TNBC": 0.018268032492360056, "Her2": 0.016442015075305003, "Luminal A": 0.018500096953861067, "Luminal B": 0.01739814556423046 }, "max_abs_log2_fold_change": 5.92646906831 }, { "feature": "224012_at", "symbol": "ANKRD20A4///ANKRD20A2///ANKRD20A3///ANKRD20A1", "f_statistic": 245.037995616, "p_value": 4.15671862479e-61, "q_value": 3.787671289552394e-57, "log2_fold_change": { "TNBC": -4.942404290900001, "Her2": -5.0076395258, "Luminal A": -4.944756041730001, "Luminal B": -4.95570520137 }, "fold_change": { "TNBC": 0.032522809682795924, "Her2": 0.031084958740658968, "Luminal A": 0.03246983713041692, "Luminal B": 0.03222434397467185 }, "max_abs_log2_fold_change": 5.0076395258 }, { "feature": "220232_at", "symbol": "SCD5", "f_statistic": 234.894027172, "p_value": 5.12976874658e-60, "q_value": 4.0065692383109757e-56, "log2_fold_change": { "TNBC": -4.518268412179999, "Her2": -4.480718048709999, "Luminal A": -3.906904955469999, "Luminal B": -4.166671699489999 }, "fold_change": { "TNBC": 0.043638084555953055, "Her2": 0.04478880396242103, "Luminal A": 0.06666600310346917, "Luminal B": 0.05568097564105584 }, "max_abs_log2_fold_change": 4.518268412179999 }, { "feature": "213715_s_at", "symbol": "KANK3", "f_statistic": 217.642816859, "p_value": 4.61326942356e-58, "q_value": 3.152765989928699e-54, "log2_fold_change": { "TNBC": -2.9920782796199994, "Her2": -2.863983415919999, "Luminal A": -2.714238889499999, "Luminal B": -2.7549960764699994 }, "fold_change": { "TNBC": 0.12568825260844704, "Her2": 0.1373583561509497, "Luminal A": 0.15238165246555652, "Luminal B": 0.14813699923812698 }, "max_abs_log2_fold_change": 2.9920782796199994 }, { "feature": "210052_s_at", "symbol": "TPX2", "f_statistic": 198.926416208, "p_value": 8.73150221998e-56, "q_value": 5.304193565255184e-52, "log2_fold_change": { "TNBC": 6.887070978050001, "Her2": 5.7338231968, "Luminal A": 1.48094919547, "Luminal B": 5.0351848579 }, "fold_change": { "TNBC": 118.362722692384, "Her2": 53.217292083169255, "Luminal A": 2.791323230019315, "Luminal B": 32.79001957547048 }, "max_abs_log2_fold_change": 6.887070978050001 }, { "feature": "238062_at", "symbol": "GPIHBP1", "f_statistic": 190.209921504, "p_value": 1.16035050946e-54, "q_value": 6.343984340370658e-51, "log2_fold_change": { "TNBC": -4.56845248067, "Her2": -4.539332340530001, "Luminal A": -4.35510717246, "Luminal B": -4.5888628670500005 }, "fold_change": { "TNBC": 0.04214623356149854, "Her2": 0.0430055796044705, "Luminal A": 0.04886322269325187, "Luminal B": 0.04155417180485321 }, "max_abs_log2_fold_change": 4.5888628670500005 }, { "feature": "1562527_at", "symbol": "LOC441666", "f_statistic": 187.273408469, "p_value": 2.83737151216e-54, "q_value": 1.4102510244029424e-50, "log2_fold_change": { "TNBC": -5.10640139472, "Her2": -5.4901913679, "Luminal A": -5.38556109105, "Luminal B": -5.42695345113 }, "fold_change": { "TNBC": 0.029028193559602053, "Her2": 0.022247833021734175, "Luminal A": 0.023921288459309353, "Luminal B": 0.02324471502173738 }, "max_abs_log2_fold_change": 5.4901913679 }, { "feature": "209408_at", "symbol": "KIF2C", "f_statistic": 179.081248737, "p_value": 3.66469484854e-53, "q_value": 1.6696655121185618e-49, "log2_fold_change": { "TNBC": 6.49450323941, "Her2": 5.28226471137, "Luminal A": 1.4166111255399998, "Luminal B": 4.12623737668 }, "fold_change": { "TNBC": 90.16547646695226, "Her2": 38.91527673512428, "Luminal A": 2.669576932520871, "Luminal B": 17.463095121378956 }, "max_abs_log2_fold_change": 6.49450323941 }, { "feature": "223229_at", "symbol": "UBE2T", "f_statistic": 177.818099605, "p_value": 5.48455737029e-53, "q_value": 2.3065938854297324e-49, "log2_fold_change": { "TNBC": 6.7001122427499995, "Her2": 6.06224404655, "Luminal A": 2.91929410031, "Luminal B": 5.3483256925800005 }, "fold_change": { "TNBC": 103.9763958600572, "Her2": 66.82166596389997, "Luminal A": 7.564758889248669, "Luminal B": 40.7386337552487 }, "max_abs_log2_fold_change": 6.7001122427499995 }, { "feature": "229839_at", "symbol": "SCARA5", "f_statistic": 172.234337748, "p_value": 3.35635999141e-52, "q_value": 1.310730498645421e-48, "log2_fold_change": { "TNBC": -7.067162829920001, "Her2": -7.1270175164700005, "Luminal A": -6.694566225680001, "Luminal B": -7.19168640078 }, "fold_change": { "TNBC": 0.007457134975183894, "Her2": 0.007154082563379558, "Luminal A": 0.00965461051260218, "Luminal B": 0.006840481519950067 }, "max_abs_log2_fold_change": 7.19168640078 }, { "feature": "220725_x_at", "symbol": "DNAH3", "f_statistic": 167.824817817, "p_value": 1.45311383014e-51, "q_value": 5.2964061623496144e-48, "log2_fold_change": { "TNBC": -2.9993996423800002, "Her2": -3.06648569421, "Luminal A": -2.9132319107799995, "Luminal B": -2.9926445932099996 }, "fold_change": { "TNBC": 0.1250520278485384, "Her2": 0.11937017340965575, "Luminal A": 0.13274855749133516, "Luminal B": 0.12563892479132824 }, "max_abs_log2_fold_change": 3.06648569421 }, { "feature": "205225_at", "symbol": "ESR1", "f_statistic": 166.451070437, "p_value": 2.3089131737e-51, "q_value": 7.889700621606256e-48, "log2_fold_change": { "TNBC": -4.676863909270001, "Her2": -4.330043190930001, "Luminal A": 3.533782592329999, "Luminal B": 3.2787568661299993 }, "fold_change": { "TNBC": 0.039095221467257586, "Her2": 0.04971954172510115, "Luminal A": 11.581759928264427, "Luminal B": 9.705192751740892 }, "max_abs_log2_fold_change": 4.676863909270001 }, { "feature": "207828_s_at", "symbol": "CENPF", "f_statistic": 165.956401549, "p_value": 2.72998638844e-51, "q_value": 8.779796812657654e-48, "log2_fold_change": { "TNBC": 6.67008052678, "Her2": 5.34693388272, "Luminal A": 2.53789928095, "Luminal B": 4.8239444997 }, "fold_change": { "TNBC": 101.8343538410145, "Her2": 40.699350962245, "Luminal A": 5.807427670785895, "Luminal B": 28.3238308313134 }, "max_abs_log2_fold_change": 6.67008052678 }, { "feature": "202954_at", "symbol": "UBE2C", "f_statistic": 162.666167636, "p_value": 8.40775572088e-51, "q_value": 2.5537623807092906e-47, "log2_fold_change": { "TNBC": 6.645100246610001, "Her2": 6.00728980071, "Luminal A": 2.5104317687499997, "Luminal B": 5.582211550989999 }, "fold_change": { "TNBC": 100.08626863878567, "Her2": 64.32420430472568, "Luminal A": 5.697905792448289, "Luminal B": 47.90856018062557 }, "max_abs_log2_fold_change": 6.645100246610001 }, { "feature": "232538_at", "symbol": null, "f_statistic": 162.082192521, "p_value": 1.02857606723e-50, "q_value": 2.959754701245568e-47, "log2_fold_change": { "TNBC": -5.68539040031, "Her2": -5.5488210770799995, "Luminal A": -5.0251532463799995, "Luminal B": -5.21465246226 }, "fold_change": { "TNBC": 0.01943242286289184, "Her2": 0.02136182806447004, "Luminal A": 0.0307098814571552, "Luminal B": 0.026929803959554147 }, "max_abs_log2_fold_change": 5.68539040031 }, { "feature": "219918_s_at", "symbol": "ASPM", "f_statistic": 161.899588804, "p_value": 1.09563983012e-50, "q_value": 2.9950958216075374e-47, "log2_fold_change": { "TNBC": 7.01503319686, "Her2": 5.81508226714, "Luminal A": 1.8042414859899996, "Luminal B": 4.91855022016 }, "fold_change": { "TNBC": 129.34076128706627, "Her2": 56.30075121853428, "Luminal A": 3.4924549013392854, "Luminal B": 30.24343746230652 }, "max_abs_log2_fold_change": 7.01503319686 }, { "feature": "240988_x_at", "symbol": null, "f_statistic": 160.457941641, "p_value": 1.80774048397e-50, "q_value": 4.7064093085758e-47, "log2_fold_change": { "TNBC": -2.88966211079, "Her2": -2.8948497933199997, "Luminal A": -2.86163759947, "Luminal B": -2.8187247108299998 }, "fold_change": { "TNBC": 0.13493512860790904, "Her2": 0.13445079646842376, "Luminal A": 0.13758188197344887, "Luminal B": 0.1417357194476905 }, "max_abs_log2_fold_change": 2.8948497933199997 }, { "feature": "230353_at", "symbol": "MIR497HG///MIR497///MIR195///LOC284112", "f_statistic": 158.61804045, "p_value": 3.44369617036e-50, "q_value": 8.558054578276922e-47, "log2_fold_change": { "TNBC": -2.556479699, "Her2": -2.56401547569, "Luminal A": -2.50557729576, "Luminal B": -2.5670156624900002 }, "fold_change": { "TNBC": 0.16998982519442124, "Her2": 0.1691042149023285, "Luminal A": 0.1760946158686445, "Luminal B": 0.16875291607942045 }, "max_abs_log2_fold_change": 2.5670156624900002 }, { "feature": "224447_s_at", "symbol": "MIEN1", "f_statistic": 158.062426681, "p_value": 4.18860561436e-50, "q_value": 9.956679771908883e-47, "log2_fold_change": { "TNBC": 0.9961627544800002, "Her2": 5.13729845159, "Luminal A": 0.9191844035500001, "Luminal B": 4.2717267656899995 }, "fold_change": { "TNBC": 1.994687516313356, "Her2": 35.194996844926294, "Luminal A": 1.8910459292774033, "Luminal B": 19.31603082351579 }, "max_abs_log2_fold_change": 5.13729845159 }, { "feature": "216153_x_at", "symbol": "RECK", "f_statistic": 157.394355022, "p_value": 5.3045985996e-50, "q_value": 1.2084096634830449e-46, "log2_fold_change": { "TNBC": -2.7388293508600006, "Her2": -2.7405478212000007, "Luminal A": -2.4718154850400005, "Luminal B": -2.6120081330600007 }, "fold_change": { "TNBC": 0.1498063464587083, "Her2": 0.1496280104328435, "Luminal A": 0.18026416252797522, "Luminal B": 0.16357133681097838 }, "max_abs_log2_fold_change": 2.7405478212000007 }, { "feature": "242731_x_at", "symbol": "BMPR1A", "f_statistic": 153.825790558, "p_value": 1.89986617392e-49, "q_value": 4.154855333069126e-46, "log2_fold_change": { "TNBC": -1.3625765505799996, "Her2": -1.3206484685799995, "Luminal A": -1.2860290655299997, "Luminal B": -1.3360670529899994 }, "fold_change": { "TNBC": 0.38888714453527895, "Her2": 0.400354945136309, "Luminal A": 0.4100781937968232, "Luminal B": 0.39609899530757203 }, "max_abs_log2_fold_change": 1.3625765505799996 }, { "feature": "236359_at", "symbol": "SCN4B", "f_statistic": 150.974139653, "p_value": 5.3588680302e-49, "q_value": 1.1268668915966331e-45, "log2_fold_change": { "TNBC": -4.97596782329, "Her2": -4.96475692103, "Luminal A": -4.0940841498800005, "Luminal B": -5.02051088211 }, "fold_change": { "TNBC": 0.031774917214671426, "Her2": 0.032022795770192264, "Luminal A": 0.05855417496724154, "Luminal B": 0.03080886015794941 }, "max_abs_log2_fold_change": 5.02051088211 }, { "feature": "202779_s_at", "symbol": "UBE2S", "f_statistic": 150.40083808, "p_value": 6.61373513556e-49, "q_value": 1.3392323743202663e-45, "log2_fold_change": { "TNBC": 5.748250285020001, "Her2": 4.61719916635, "Luminal A": 2.73049291568, "Luminal B": 4.524884823880001 }, "fold_change": { "TNBC": 53.752139894958084, "Her2": 24.54231042598747, "Luminal A": 6.6368235369849105, "Luminal B": 23.021099340298814 }, "max_abs_log2_fold_change": 5.748250285020001 }, { "feature": "204962_s_at", "symbol": "SLC35F6///CENPA", "f_statistic": 150.103028269, "p_value": 7.37944902751e-49, "q_value": 1.440916488146622e-45, "log2_fold_change": { "TNBC": 6.14461328774, "Her2": 5.04988135056, "Luminal A": 1.1714541910399996, "Luminal B": 3.6578268921 }, "fold_change": { "TNBC": 70.74779542931326, "Her2": 33.125753138446576, "Luminal A": 2.2523861596665924, "Luminal B": 12.62163490223506 }, "max_abs_log2_fold_change": 6.14461328774 }, { "feature": "209773_s_at", "symbol": "RRM2", "f_statistic": 149.284763613, "p_value": 9.98028581432e-49, "q_value": 1.8815591942286808e-45, "log2_fold_change": { "TNBC": 8.035595881419999, "Her2": 7.89653149239, "Luminal A": 3.4285591768500003, "Luminal B": 6.5609212787099995 }, "fold_change": { "TNBC": 262.39490220934874, "Her2": 238.2828802012822, "Luminal A": 10.767110103721109, "Luminal B": 94.41350139848045 }, "max_abs_log2_fold_change": 8.035595881419999 }, { "feature": "241632_x_at", "symbol": null, "f_statistic": 148.078875201, "p_value": 1.56113897523e-48, "q_value": 2.845071706424993e-45, "log2_fold_change": { "TNBC": -1.7958543338200004, "Her2": -1.8204503602899997, "Luminal A": -1.7644718090699998, "Luminal B": -1.79159911155 }, "fold_change": { "TNBC": 0.2880009880324945, "Her2": 0.28313257317422214, "Luminal A": 0.2943344245502617, "Luminal B": 0.28885169956670653 }, "max_abs_log2_fold_change": 1.8204503602899997 }, { "feature": "202870_s_at", "symbol": "CDC20", "f_statistic": 147.935024908, "p_value": 1.64704297894e-48, "q_value": 2.90479938024473e-45, "log2_fold_change": { "TNBC": 7.2367399938200005, "Her2": 5.856059010640001, "Luminal A": 1.85480164811, "Luminal B": 4.56595000896 }, "fold_change": { "TNBC": 150.82585952922355, "Her2": 57.92278279503949, "Luminal A": 3.6170201826104025, "Luminal B": 23.68579201388609 }, "max_abs_log2_fold_change": 7.2367399938200005 }, { "feature": "216836_s_at", "symbol": "ERBB2", "f_statistic": 146.807664164, "p_value": 2.50990781413e-48, "q_value": 4.288255935060296e-45, "log2_fold_change": { "TNBC": -0.5291033501499989, "Her2": 4.66139927233, "Luminal A": 0.5136618543299996, "Luminal B": 3.7390143736300008 }, "fold_change": { "TNBC": 0.6929852977527408, "Her2": 25.305854271077475, "Luminal A": 1.4276693165967866, "Luminal B": 13.352281527153618 }, "max_abs_log2_fold_change": 4.66139927233 }, { "feature": "203358_s_at", "symbol": "EZH2", "f_statistic": 146.476140774, "p_value": 2.84233313622e-48, "q_value": 4.7090569562592744e-45, "log2_fold_change": { "TNBC": 5.58482259952, "Her2": 5.00854641899, "Luminal A": 2.4189489999599996, "Luminal B": 4.24006417882 }, "fold_change": { "TNBC": 47.99534556376828, "Her2": 32.19012823606742, "Luminal A": 5.347812930236556, "Luminal B": 18.896723191862677 }, "max_abs_log2_fold_change": 5.58482259952 }, { "feature": "209464_at", "symbol": "AURKB", "f_statistic": 146.335295848, "p_value": 2.99677163629e-48, "q_value": 4.818896931496564e-45, "log2_fold_change": { "TNBC": 4.570662126049999, "Her2": 3.3246351502300002, "Luminal A": 0.4312381793000002, "Luminal B": 2.61098647278 }, "fold_change": { "TNBC": 23.763280804596643, "Her2": 10.018781492955073, "Luminal A": 1.3483903235843855, "Luminal B": 6.109212709430762 }, "max_abs_log2_fold_change": 4.570662126049999 }, { "feature": "206209_s_at", "symbol": "CA4", "f_statistic": 145.510013572, "p_value": 4.08938155341e-48, "q_value": 6.387964504845284e-45, "log2_fold_change": { "TNBC": -4.52777457782, "Her2": -4.50933491281, "Luminal A": -4.51963856179, "Luminal B": -4.52852194583 }, "fold_change": { "TNBC": 0.043351490959096343, "Her2": 0.04390913996054146, "Luminal A": 0.04359666047133843, "Luminal B": 0.043329039140797374 }, "max_abs_log2_fold_change": 4.52852194583 }, { "feature": "203362_s_at", "symbol": "MAD2L1", "f_statistic": 145.12225089, "p_value": 4.7348197721e-48, "q_value": 7.19074448333398e-45, "log2_fold_change": { "TNBC": 5.9828173732500005, "Her2": 4.9103635935100005, "Luminal A": 2.24475939281, "Luminal B": 4.40159003582 }, "fold_change": { "TNBC": 63.242275525671666, "Her2": 30.07230595720533, "Luminal A": 4.739580568633716, "Luminal B": 21.13540768308938 }, "max_abs_log2_fold_change": 5.9828173732500005 }, { "feature": "225687_at", "symbol": "FAM83D", "f_statistic": 144.521107068, "p_value": 5.94626882562e-48, "q_value": 8.786496094678981e-45, "log2_fold_change": { "TNBC": 6.22838439283, "Her2": 5.353680150599999, "Luminal A": 0.8414580421600002, "Luminal B": 3.9692111879299996 }, "fold_change": { "TNBC": 74.97742598272634, "Her2": 40.89011316861198, "Luminal A": 1.7918601486919066, "Luminal B": 15.662158933017597 }, "max_abs_log2_fold_change": 6.22838439283 }, { "feature": "206364_at", "symbol": "KIF14", "f_statistic": 144.380734692, "p_value": 6.27185390663e-48, "q_value": 9.02371233255742e-45, "log2_fold_change": { "TNBC": 5.114896441670001, "Her2": 3.8533371884200003, "Luminal A": 0.3707955484100003, "Luminal B": 3.0184366646700003 }, "fold_change": { "TNBC": 34.65271395539329, "Her2": 14.45340183415596, "Luminal A": 1.2930656720449207, "Luminal B": 8.102890612962474 }, "max_abs_log2_fold_change": 5.114896441670001 }, { "feature": "219787_s_at", "symbol": "ECT2", "f_statistic": 144.196072955, "p_value": 6.72790032141e-48, "q_value": 9.431653699293564e-45, "log2_fold_change": { "TNBC": 5.28681777383, "Her2": 4.94964623479, "Luminal A": 2.9508128753799996, "Luminal B": 4.3525155384800005 }, "fold_change": { "TNBC": 39.03828510883008, "Her2": 30.90238398092237, "Luminal A": 7.731845853164562, "Luminal B": 20.428559020999824 }, "max_abs_log2_fold_change": 5.28681777383 }, { "feature": "202705_at", "symbol": "CCNB2", "f_statistic": 143.871739857, "p_value": 7.61195257625e-48, "q_value": 1.0404207080032907e-44, "log2_fold_change": { "TNBC": 6.164903756839999, "Her2": 5.16902698993, "Luminal A": 1.9858917871999995, "Luminal B": 4.47572775257 }, "fold_change": { "TNBC": 71.74984235375159, "Her2": 35.97759862331489, "Luminal A": 3.9610743667106556, "Luminal B": 22.249912424963263 }, "max_abs_log2_fold_change": 6.164903756839999 }, { "feature": "231031_at", "symbol": "FGF7P3", "f_statistic": 142.158068374, "p_value": 1.4669472714e-47, "q_value": 1.9561562968110294e-44, "log2_fold_change": { "TNBC": -2.71483251327, "Her2": -2.6861466976900004, "Luminal A": -2.6781329513000003, "Luminal B": -2.8423058674000004 }, "fold_change": { "TNBC": 0.15231896509170495, "Her2": 0.15537790850381575, "Luminal A": 0.15624338857852657, "Luminal B": 0.13943784978109267 }, "max_abs_log2_fold_change": 2.8423058674000004 }, { "feature": "218542_at", "symbol": "CEP55", "f_statistic": 141.570332587, "p_value": 1.83979145947e-47, "q_value": 2.394926630085793e-44, "log2_fold_change": { "TNBC": 5.316710330199999, "Her2": 4.235901234709999, "Luminal A": 0.8176348206699999, "Luminal B": 3.12635087161 }, "fold_change": { "TNBC": 39.855594136949584, "Her2": 18.842274668301613, "Luminal A": 1.7625141264425763, "Luminal B": 8.732234487123637 }, "max_abs_log2_fold_change": 5.316710330199999 }, { "feature": "224159_x_at", "symbol": "TRIM4", "f_statistic": 140.798926155, "p_value": 2.47946268937e-47, "q_value": 3.1525503166494417e-44, "log2_fold_change": { "TNBC": -3.6786189287699997, "Her2": -3.7134852892700003, "Luminal A": -3.28170881278, "Luminal B": -3.4894062370600007 }, "fold_change": { "TNBC": 0.07809538312259888, "Her2": 0.07623063535481786, "Luminal A": 0.102827010646183, "Luminal B": 0.08903977534955151 }, "max_abs_log2_fold_change": 3.7134852892700003 }, { "feature": "239963_at", "symbol": null, "f_statistic": 140.227417457, "p_value": 3.09551818285e-47, "q_value": 3.8463924002490467e-44, "log2_fold_change": { "TNBC": -3.0228481744100004, "Her2": -3.1508499002400003, "Luminal A": -2.9249960720400003, "Luminal B": -3.1329243461200003 }, "fold_change": { "TNBC": 0.12303595006623254, "Her2": 0.11258996086914476, "Luminal A": 0.13167048798709982, "Luminal B": 0.11399762348580414 }, "max_abs_log2_fold_change": 3.1508499002400003 }, { "feature": "229150_at", "symbol": null, "f_statistic": 140.018398263, "p_value": 3.3578378995e-47, "q_value": 4.0796238106525224e-44, "log2_fold_change": { "TNBC": -3.941172539980001, "Her2": 1.3691747841799984, "Luminal A": 2.869078933739999, "Luminal B": 2.45006407054 }, "fold_change": { "TNBC": 0.06510117803292942, "Her2": 2.5832276426771554, "Luminal A": 7.305985719360956, "Luminal B": 5.464403697513898 }, "max_abs_log2_fold_change": 3.941172539980001 }, { "feature": "204825_at", "symbol": "MELK", "f_statistic": 139.518102562, "p_value": 4.08118848352e-47, "q_value": 4.850669955641064e-44, "log2_fold_change": { "TNBC": 6.02990693043, "Her2": 4.839187912, "Luminal A": 2.00284514221, "Luminal B": 4.29103779405 }, "fold_change": { "TNBC": 65.34056073025961, "Her2": 28.624684998726934, "Luminal A": 4.007896192695359, "Luminal B": 19.576321489138724 }, "max_abs_log2_fold_change": 6.02990693043 }, { "feature": "222608_s_at", "symbol": "ANLN", "f_statistic": 139.448685078, "p_value": 4.19335828846e-47, "q_value": 4.877946334148374e-44, "log2_fold_change": { "TNBC": 5.7505059608, "Her2": 5.435028305100001, "Luminal A": 1.3069299966700005, "Luminal B": 4.10658749549 }, "fold_change": { "TNBC": 53.836247923437575, "Her2": 43.26199543163057, "Luminal A": 2.4741449024914672, "Luminal B": 17.22685570307287 }, "max_abs_log2_fold_change": 5.7505059608 }, { "feature": "1570255_s_at", "symbol": "ANKRD20A12P///ANKRD20A8P///ANKRD20A4///ANKRD20A2///ANKRD20A3///ANKRD20A5P///ANKRD20A1", "f_statistic": 137.374919787, "p_value": 9.47363491049e-47, "q_value": 1.0790667530442078e-43, "log2_fold_change": { "TNBC": -4.25590761537, "Her2": -4.39148124758, "Luminal A": -4.24808217304, "Luminal B": -4.24521714627 }, "fold_change": { "TNBC": 0.052341257094334195, "Her2": 0.04764665526084058, "Luminal A": 0.05262593704645858, "Luminal B": 0.05273054995767815 }, "max_abs_log2_fold_change": 4.39148124758 }, { "feature": "214710_s_at", "symbol": "CCNB1", "f_statistic": 137.085107502, "p_value": 1.06248233606e-46, "q_value": 1.1854917706001712e-43, "log2_fold_change": { "TNBC": 6.06742691631, "Her2": 5.701653691640001, "Luminal A": 2.86001660343, "Luminal B": 5.05280101618 }, "fold_change": { "TNBC": 67.06215395187986, "Her2": 52.04377445471217, "Luminal A": 7.260236797367922, "Luminal B": 33.19285952676556 }, "max_abs_log2_fold_change": 6.06742691631 }, { "feature": "235849_at", "symbol": "SCARA5", "f_statistic": 134.860789627, "p_value": 2.57867606509e-46, "q_value": 2.8196791301333113e-43, "log2_fold_change": { "TNBC": -6.33656862976, "Her2": -6.44704166425, "Luminal A": -5.85860886815, "Luminal B": -6.40012634953 }, "fold_change": { "TNBC": 0.012373790902581139, "Her2": 0.011461648240345235, "Luminal A": 0.017233877349555168, "Luminal B": 0.011840498653546527 }, "max_abs_log2_fold_change": 6.44704166425 } ], "differential_bound": { "state": "bounded", "shown": 50, "total": 22426, "omitted": 22376, "complete_result_hash": "9dd46f386a0e57d0d15cb2c6ecea5f48be988ebee6bdb03185e9373809493ac6", "complete_result_run": "2d090760-f2ae-423e-849f-dc58da829431", "note": "This record carries the first 50 of these. The complete result is the run's own result, named by its hash." }, "sample_count": 141, "group_count": 5, "analysis_scope": { "groups_compared": [ "TNBC", "Her2", "Luminal A", "Luminal B", "Healthy" ], "groups_present": [ "TNBC", "Her2", "Luminal A", "Luminal B", "CellLine", "Healthy" ], "groups_not_compared": [ "CellLine" ], "samples_compared": 141, "samples_present": 155, "samples_not_compared": 14, "detail": "The comparison used 141 samples in 5 groups, out of 155 samples in 6 groups. Not part of the comparison: CellLine." }, "published_target": { "record_id": "pmid:28529692", "source": { "authority": "Corpus Engine", "record_id": "pmid:28529692", "content_hash": "sha256:116bf117cc3112c78abf15a5c35878e88e5fab508f979460005284568439dbe5", "document_sha256": "0c8dece4a24a9764724f10dd654d240fe1e33dc9058ffa47724ceb5e64e53b97", "sci_version": "1.5", "revision": 6, "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." }, "software_access": { "asset_id": "data:geo:GSE65194", "repository": "GEO", "statement_verbatim": "Expression Console 1.4 software and Transcriptome Analysis Console 3.0 software (Affymetrix, Inc. USA) are available after free customer registration at:\nhttp://www.affymetrix.com/support/technical/software_downloads.affx.", "statement_kind": "software_availability_statement", "uri": "http://www.affymetrix.com/support/technical/software_downloads.affx", "condition": "The statement is published verbatim, with its condition in it. The software is not part of this platform: obtaining it is a step a recreator takes outside the run, and a run that reads a deposited matrix without it is a re-analysis of declared data rather than a reproduction of the paper's pipeline.", "source": "corpus.data.assets.structure.software_access_statement_verbatim" }, "built_by": "App\\Support\\Science\\CorpusReplicationTarget", "built_at": "2026-11-03T15:44:29+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": { "Her2": 30, "Luminal A": 29, "Luminal B": 30, "TNBC": 41, "Healthy": 11 }, "expected_group_sizes_source": "corpus.data.paper_group_sizes", "cohort": { "paper": { "sizes": { "Her2": 30, "Lum A": 29, "Lum B": 30, "TNBC": 41, "normal breast tissue": 11 }, "total": 141, "source": "Array data for 41 triple negative samples (TNBC group), 30 Her2-positive (Her2 group), 30 Luminal B (Lum B group), 29 Luminal A (Lum A group) breast cancer samples and 11 normal breast tissue samples were investigated.", "reference_group": "normal breast tissue" }, "repository": { "CellLine": 14, "Healthy": 11, "Her2": 39, "Luminal A": 29, "Luminal B": 30, "TNBC": 55 }, "paper_group_sizes_mapped": { "Her2": 30, "Luminal A": 29, "Luminal B": 30, "TNBC": 41, "Healthy": 11 }, "note": "The paper's cohort and the repository's arrays are different things. The paper counted samples; the repository holds arrays, some of which are technical replicates of one another. The run is compared against the paper's cohort, never against the repository's own counts." } }, "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.", "method": { "verdict": "unresolved", "steps": [ { "id": "method-1", "label": "Microarray preprocessing", "family": "microarray_preprocessing", "specific": "robust multiarray average normalisation", "quote": "Preanalytical procedures consisted of a robust multichip analysis (RMA) algorithm 21, including background correction, probe set signal integration, and quantile normalization. For this purpose, we used Expression Console 1.4 software (Affymetrix, Inc. USA).", "software": "Expression Console 1.4", "operations_required": [], "operations_missing_here": [ "microarray_rma_normalise" ], "implemented_here": [], "state": "not_implemented_here" }, { "id": "method-2", "label": "One-way analysis of variance", "family": "group_comparison", "specific": "one-way between subjects ANOVA", "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.", "software": "Transcriptome Analysis Console 3.0", "operations_required": [ "group_comparison_anova" ], "operations_missing_here": [], "implemented_here": [ "group_comparison_anova" ], "state": "implemented_here" }, { "id": "method-3", "label": "Group comparison against a reference group", "family": "group_comparison", "specific": "expression relative to a reference group", "quote": "NKA genes expression in breast cancer samples relative to normal breast tissue.", "software": null, "operations_required": [], "operations_missing_here": [ "group_relative_expression" ], "implemented_here": [], "state": "not_implemented_here" } ], "steps_published": 3, "steps_implemented_here": 1, "published_multiplicity_procedure": null, "platform_multiplicity_procedure": { "across_pairs": "holm", "across_features": "benjamini_hochberg", "note": "These are the platform's declared corrections. The paper states no multiplicity procedure, so neither of them is a reproduction of the paper's." }, "reasons": [ "The paper's step \"Microarray preprocessing\" is not implemented on this platform (missing: microarray_rma_normalise).", "The paper's step \"Group comparison against a reference group\" is not implemented on this platform (missing: group_relative_expression).", "The paper states no multiplicity procedure, so the corrections this platform applies across pairs (Holm) and across features (Benjamini-Hochberg) are the platform's own and are not a reproduction of a correction the paper made." ] } }, "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." }, { "target_id": "target-atp1a3-lum-a", "kind": "cell", "symbol": "ATP1A3", "paper_group": "Lum A", "unit": "relative expression fold change", "published_value": -1.05, "table_value": -1.05, "status": "agreed", "detail": "The machine-readable target and the published table cell state the same value." }, { "target_id": "target-atp1a3-lum-a-p", "kind": "cell", "symbol": "ATP1A3", "paper_group": "Lum A", "unit": "ANOVA p-value", "published_value": 0.429089, "table_value": 0.429089, "status": "agreed", "detail": "The machine-readable target and the published table cell state the same value." }, { "target_id": "target-atp1a3-lum-b", "kind": "cell", "symbol": "ATP1A3", "paper_group": "Lum B", "unit": "relative expression fold change", "published_value": 1.03, "table_value": 1.03, "status": "agreed", "detail": "The machine-readable target and the published table cell state the same value." }, { "target_id": "target-atp1a3-lum-b-p", "kind": "cell", "symbol": "ATP1A3", "paper_group": "Lum B", "unit": "ANOVA p-value", "published_value": 0.308298, "table_value": 0.308298, "status": "agreed", "detail": "The machine-readable target and the published table cell state the same value." }, { "target_id": "target-atp1a3-her2", "kind": "cell", "symbol": "ATP1A3", "paper_group": "Her2", "unit": "relative expression fold change", "published_value": -1.04, "table_value": -1.04, "status": "agreed", "detail": "The machine-readable target and the published table cell state the same value." }, { "target_id": "target-atp1a3-her2-p", "kind": "cell", "symbol": "ATP1A3", "paper_group": "Her2", "unit": "ANOVA p-value", "published_value": 0.768041, "table_value": 0.768041, "status": "agreed", "detail": "The machine-readable target and the published table cell state the same value." }, { "target_id": "target-atp1a3-tnbc", "kind": "cell", "symbol": "ATP1A3", "paper_group": "TNBC", "unit": "relative expression fold change", "published_value": -1.04, "table_value": -1.04, "status": "agreed", "detail": "The machine-readable target and the published table cell state the same value." }, { "target_id": "target-atp1a3-tnbc-p", "kind": "cell", "symbol": "ATP1A3", "paper_group": "TNBC", "unit": "ANOVA p-value", "published_value": 0.527878, "table_value": 0.527878, "status": "agreed", "detail": "The machine-readable target and the published table cell state the same value." } ], "gaps": [ "The paper's step \"Microarray preprocessing\" is not implemented on this platform (missing: microarray_rma_normalise).", "The paper's step \"Group comparison against a reference group\" is not implemented on this platform (missing: group_relative_expression).", "The paper states no multiplicity procedure, so the corrections this platform applies across pairs (Holm) and across features (Benjamini-Hochberg) are the platform's own and are not a reproduction of a correction the paper made.", "The paper's own pipeline needs software the platform does not run: Expression Console 1.4 software and Transcriptome Analysis Console 3.0 software (Affymetrix, Inc. USA) are available after free customer registration at:\nhttp://www.affymetrix.com/support/technical/software_downloads.affx. The route is published with the record, and the condition it carries is part of the route." ] }, "replication": { "target": { "record_id": "pmid:28529692", "source": { "authority": "Corpus Engine", "record_id": "pmid:28529692", "content_hash": "sha256:116bf117cc3112c78abf15a5c35878e88e5fab508f979460005284568439dbe5", "document_sha256": "0c8dece4a24a9764724f10dd654d240fe1e33dc9058ffa47724ceb5e64e53b97", "sci_version": "1.5", "revision": 6, "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." }, "software_access": { "asset_id": "data:geo:GSE65194", "repository": "GEO", "statement_verbatim": "Expression Console 1.4 software and Transcriptome Analysis Console 3.0 software (Affymetrix, Inc. USA) are available after free customer registration at:\nhttp://www.affymetrix.com/support/technical/software_downloads.affx.", "statement_kind": "software_availability_statement", "uri": "http://www.affymetrix.com/support/technical/software_downloads.affx", "condition": "The statement is published verbatim, with its condition in it. The software is not part of this platform: obtaining it is a step a recreator takes outside the run, and a run that reads a deposited matrix without it is a re-analysis of declared data rather than a reproduction of the paper's pipeline.", "source": "corpus.data.assets.structure.software_access_statement_verbatim" }, "built_by": "App\\Support\\Science\\CorpusReplicationTarget", "built_at": "2026-11-03T15:44:29+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 0.9761)", "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": 2.37894763535e-6, "q_value": 5.030329674639949e-6, "f_statistic": 8.80237975121, "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": 0.00255323706094, "q_value": 0.003631360522170927, "f_statistic": 4.31762695905, "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": 2.37894763535e-6, "q_value": 5.030329674639949e-6, "f_statistic": 8.80237975121, "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": 0.00255323706094, "q_value": 0.003631360522170927, "f_statistic": 4.31762695905, "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": -0.03239801492000005, "observed_ratio": 0.9777936796581725, "p_value": 2.37894763535e-6, "q_value": 5.030329674639949e-6, "f_statistic": 8.80237975121, "contrast_p_value": 0.0152286505361, "contrast_p_value_holm": 0.106600553753, "contrast_t_statistic": -2.8567757748, "contrast_degrees_of_freedom": 11.3019760152, "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": 0.9777936796581725, "observed_p_value": 0.0152286505361, "relative_difference": 0.41096766285652253, "tolerance": 0.25, "source_cell": "1.66 (0.005926)", "asset_id": "asset:table:pmid:28529692:1" } }, { "feature": "220948_s_at", "log2_fold_change": 0.7723494348699997, "observed_ratio": 1.7080490849032697, "p_value": 0.00255323706094, "q_value": 0.003631360522170927, "f_statistic": 4.31762695905, "contrast_p_value": 0.00952851004931, "contrast_p_value_holm": 0.0952851004931, "contrast_t_statistic": 2.96163763427, "contrast_degrees_of_freedom": 15.317918165, "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": 1.7080490849032697, "observed_p_value": 0.00952851004931, "relative_difference": 0.028945231869439612, "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 0.9761)", "probes_tested": 2, "probes_reproduced": 1, "probes_direction_only": 0, "probes_significance_only": 0, "probes_contradicted": 1, "observed": [ { "feature": "244606_at", "log2_fold_change": -0.03483483350999972, "observed_ratio": 0.9761435078632721, "p_value": 2.37894763535e-6, "q_value": 5.030329674639949e-6, "f_statistic": 8.80237975121, "contrast_p_value": 0.010333191536, "contrast_p_value_holm": 0.082665532288, "contrast_t_statistic": -3.06836966974, "contrast_degrees_of_freedom": 11.3539054847, "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 0.9761)", "fold_verdict": "contradicted", "significance_verdict": "reproduced", "published_fold_factor": 1.44, "published_ratio": 1.44, "published_p_value": 0.015725, "observed_ratio": 0.9761435078632721, "observed_p_value": 0.010333191536, "relative_difference": 0.3221225639838388, "tolerance": 0.25, "source_cell": "1.44 (0.015725)", "asset_id": "asset:table:pmid:28529692:1" } }, { "feature": "220948_s_at", "log2_fold_change": 0.6971557130699999, "observed_ratio": 1.6213052211648489, "p_value": 0.00255323706094, "q_value": 0.003631360522170927, "f_statistic": 4.31762695905, "contrast_p_value": 0.0154645181658, "contrast_p_value_holm": 0.139180663492, "contrast_t_statistic": 2.77071778779, "contrast_degrees_of_freedom": 13.4718185916, "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": 1.6213052211648489, "observed_p_value": 0.0154645181658, "relative_difference": 0.12590640358670066, "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 0.0291 is 91.9% from the published ratio 0.3597, outside the declared tolerance of 25%; the run gets the direction right but its ratio 0.2252 is 37.4% from the published ratio 0.3597, outside the declared tolerance of 25%; TNBC: the run gets the direction right but its ratio 0.0313 is 91.0% from the published ratio 0.3484, outside the declared tolerance of 25%; the run gets the direction right but its ratio 0.2335 is 33.0% 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": 1.21739348978e-37, "q_value": 3.657063421249557e-35, "f_statistic": 91.7194597599, "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, "p_value": 3.08987381003e-16, "q_value": 2.7220862200414147e-15, "f_statistic": 26.4574475114, "contrast_p_value": 0.0115406150428, "contrast_p_value_holm": 0.112038683302, "contrast_t_statistic": -3.08364127382, "contrast_degrees_of_freedom": 10.021446574, "verdict": "direction_only", "problems": [], "against_published": { "verdict": "direction_only", "detail": "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%", "fold_verdict": "direction_only", "significance_verdict": "reproduced", "published_fold_factor": -2.49, "published_ratio": 0.4016064257028112, "published_p_value": 1.85e-7, "observed_ratio": 0.22440864888078413, "observed_p_value": 0.0115406150428, "relative_difference": 0.4412224642868474, "tolerance": 0.25, "source_cell": "-2.49 (1.85·10 -07)", "asset_id": "asset:table:pmid:28529692:1" } } ] }, { "contrast_group": "Luminal B", "reference_group": "Healthy", "verdict": "direction_only", "reason": "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%", "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": -5.145934605580001, "observed_ratio": 0.028243552904532433, "p_value": 1.21739348978e-37, "q_value": 3.657063421249557e-35, "f_statistic": 91.7194597599, "contrast_p_value": 1.34200371803e-5, "contrast_p_value_holm": 0.000134200371803, "contrast_t_statistic": -7.86908981764, "contrast_degrees_of_freedom": 10.0225492971, "verdict": "direction_only", "problems": [], "against_published": { "verdict": "direction_only", "detail": "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%", "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": 3.08987381003e-16, "q_value": 2.7220862200414147e-15, "f_statistic": 26.4574475114, "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 0.0291 is 91.9% from the published ratio 0.3597, outside the declared tolerance of 25%; the run gets the direction right but its ratio 0.2252 is 37.4% 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": -5.10458672023, "observed_ratio": 0.02906472925432372, "p_value": 1.21739348978e-37, "q_value": 3.657063421249557e-35, "f_statistic": 91.7194597599, "contrast_p_value": 1.45010594113e-5, "contrast_p_value_holm": 0.000134200371803, "contrast_t_statistic": -7.80954107825, "contrast_degrees_of_freedom": 10.0036764013, "verdict": "direction_only", "problems": [], "against_published": { "verdict": "direction_only", "detail": "the run gets the direction right but its ratio 0.0291 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": 0.02906472925432372, "observed_p_value": 1.45010594113e-5, "relative_difference": 0.91920005267298, "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": -2.15090577271, "observed_ratio": 0.22517120117403724, "p_value": 3.08987381003e-16, "q_value": 2.7220862200414147e-15, "f_statistic": 26.4574475114, "contrast_p_value": 0.0116748628484, "contrast_p_value_holm": 0.112038683302, "contrast_t_statistic": -3.07821635032, "contrast_degrees_of_freedom": 10.0009498555, "verdict": "direction_only", "problems": [], "against_published": { "verdict": "direction_only", "detail": "the run gets the direction right but its ratio 0.2252 is 37.4% 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": 0.22517120117403724, "observed_p_value": 0.0116748628484, "relative_difference": 0.37402406073617656, "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 0.0313 is 91.0% from the published ratio 0.3484, outside the declared tolerance of 25%; the run gets the direction right but its ratio 0.2335 is 33.0% 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": -4.999793002940001, "observed_ratio": 0.031254484053818386, "p_value": 1.21739348978e-37, "q_value": 3.657063421249557e-35, "f_statistic": 91.7194597599, "contrast_p_value": 1.39607429764e-5, "contrast_p_value_holm": 0.000134200371803, "contrast_t_statistic": -7.53116278133, "contrast_degrees_of_freedom": 10.6431363058, "verdict": "direction_only", "problems": [], "against_published": { "verdict": "direction_only", "detail": "the run gets the direction right but its ratio 0.0313 is 91.0% 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": 0.031254484053818386, "observed_p_value": 1.39607429764e-5, "relative_difference": 0.9102996307655413, "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": -2.0985130789299995, "observed_ratio": 0.23349878062991802, "p_value": 3.08987381003e-16, "q_value": 2.7220862200414147e-15, "f_statistic": 26.4574475114, "contrast_p_value": 0.0133106462792, "contrast_p_value_holm": 0.112038683302, "contrast_t_statistic": -2.99284959125, "contrast_degrees_of_freedom": 10.1403771142, "verdict": "direction_only", "problems": [], "against_published": { "verdict": "direction_only", "detail": "the run gets the direction right but its ratio 0.2335 is 33.0% 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": 0.23349878062991802, "observed_p_value": 0.0133106462792, "relative_difference": 0.3298584995921352, "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": 0.00298548225137, "q_value": 0.004211504273528705, "f_statistic": 4.21944873794, "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": 0.00298548225137, "q_value": 0.004211504273528705, "f_statistic": 4.21944873794, "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": -0.006151742090000134, "observed_ratio": 0.995745015522144, "p_value": 0.00298548225137, "q_value": 0.004211504273528705, "f_statistic": 4.21944873794, "contrast_p_value": 0.476221803942, "contrast_p_value_holm": 1, "contrast_t_statistic": -0.737668356577, "contrast_degrees_of_freedom": 10.953758894, "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": 0.995745015522144, "observed_p_value": 0.476221803942, "relative_difference": 0.03557481614302986, "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": -0.008654018700000154, "observed_ratio": 0.9940194464713875, "p_value": 0.00298548225137, "q_value": 0.004211504273528705, "f_statistic": 4.21944873794, "contrast_p_value": 0.324843155982, "contrast_p_value_holm": 1, "contrast_t_statistic": -1.02929688242, "contrast_degrees_of_freedom": 11.3137684955, "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": 0.9940194464713875, "observed_p_value": 0.324843155982, "relative_difference": 0.03378022433024311, "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_cohort", "statement": "This run counted 141 experimental units in the paper's 5 groups (30 Her2, 29 Luminal A, 30 Luminal B, 41 TNBC, 11 Healthy), which is the same group count as the paper states. This is an agreement of counts: the paper publishes no sample identifiers, so it is not an identity of specimens, and the paper does not say how it handled its own technical replicates. The repository holds 178 arrays; 46 of them carry the repository's own replicate marker, and averaging them removed 23 arrays and left the experimental units this run counted. CellLine 14 is outside the paper's cohort.", "basis": { "paper_cohort_source": "Array data for 41 triple negative samples (TNBC group), 30 Her2-positive (Her2 group), 30 Luminal B (Lum B group), 29 Luminal A (Lum A group) breast cancer samples and 11 normal breast tissue samples were investigated.", "paper_cohort_total": 141, "paper_group_sizes": { "Her2": 30, "Luminal A": 29, "Luminal B": 30, "TNBC": 41, "Healthy": 11 }, "observed_group_sizes": { "CellLine": 14, "Healthy": 11, "Her2": 30, "Luminal A": 29, "Luminal B": 30, "TNBC": 41 }, "observed_unit": "experimental units", "sample_selection_rule": { "mode": "average_technical_replicates", "pattern": "/_rep[A-Z0-9]+$/", "combination": "mean of the member arrays" }, "arrays_in_repository": 178, "arrays_merged": 23, "arrays_carrying_the_replicate_marker": 46, "repository_group_sizes": { "CellLine": 14, "Healthy": 11, "Her2": 39, "Luminal A": 29, "Luminal B": 30, "TNBC": 55 }, "group_name_mapping": { "Lum A": "Luminal A", "Lum B": "Luminal B", "Her2": "Her2", "TNBC": "TNBC" } }, "expected_group_sizes": { "Her2": 30, "Luminal A": 29, "Luminal B": 30, "TNBC": 41, "Healthy": 11 }, "observed_group_sizes": { "CellLine": 14, "Healthy": 11, "Her2": 30, "Luminal A": 29, "Luminal B": 30, "TNBC": 41 }, "differences": [], "groups_outside_the_paper_cohort": { "CellLine": 14 }, "limits": [ "The paper publishes no sample identifiers, so what is compared here is the number of experimental units in each group and not the identity of each specimen.", "The paper does not publish how it handled its own technical replicates, so the rule that produced these units is the repository's structure as the platform read it and not the paper's own rule.", "The experimental units are the repository's arrays averaged after the depositor's own replicate marker was removed." ], "detail": "every group the paper names has the number of experimental units the paper states. The comparison used 141 samples in 5 groups, out of 155 samples in 6 groups. Not part of the comparison: CellLine", "analysis_scope": { "groups_compared": [ "TNBC", "Her2", "Luminal A", "Luminal B", "Healthy" ], "groups_present": [ "TNBC", "Her2", "Luminal A", "Luminal B", "CellLine", "Healthy" ], "groups_not_compared": [ "CellLine" ], "samples_compared": 141, "samples_present": 155, "samples_not_compared": 14, "detail": "The comparison used 141 samples in 5 groups, out of 155 samples in 6 groups. Not part of the comparison: CellLine." } }, "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": "sha256:116bf117cc3112c78abf15a5c35878e88e5fab508f979460005284568439dbe5", "document_sha256": "0c8dece4a24a9764724f10dd654d240fe1e33dc9058ffa47724ceb5e64e53b97", "sci_version": "1.5", "revision": 6, "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." }, "software_access": { "asset_id": "data:geo:GSE65194", "repository": "GEO", "statement_verbatim": "Expression Console 1.4 software and Transcriptome Analysis Console 3.0 software (Affymetrix, Inc. USA) are available after free customer registration at:\nhttp://www.affymetrix.com/support/technical/software_downloads.affx.", "statement_kind": "software_availability_statement", "uri": "http://www.affymetrix.com/support/technical/software_downloads.affx", "condition": "The statement is published verbatim, with its condition in it. The software is not part of this platform: obtaining it is a step a recreator takes outside the run, and a run that reads a deposited matrix without it is a re-analysis of declared data rather than a reproduction of the paper's pipeline.", "source": "corpus.data.assets.structure.software_access_statement_verbatim" }, "built_by": "App\\Support\\Science\\CorpusReplicationTarget", "built_at": "2026-11-03T15:44:29+00:00" }, "reference_group": "Healthy", "tolerance": 0.25, "tolerance_basis": { "state": "platform_convention", "value": 0.25, "note": "This band is the platform's declared comparison tolerance. The paper states no tolerance for the values it published, so the band is the platform's and not the paper's." }, "interpretation": { "state": "hypothesis_generation", "note": "A probe that reproduces the published ratio within the band is a hypothesis about which probe the paper used. It is not independent confirmation that the paper measured the gene on that probe, because the published values are the thing the band was applied to." }, "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": 0.049913678120305206, "max_relative_difference": 0.12590640358670066, "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": 1.7080490849032697, "relative_difference": 0.028945231869439612, "within_tolerance": true, "direction_agrees": true, "source_cell": "1.66 (0.005926)", "note": null }, { "contrast_group": "TNBC", "published_ratio": 1.44, "observed_ratio": 1.6213052211648489, "relative_difference": 0.12590640358670066, "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": 0.3487634388305744, "max_relative_difference": 0.41096766285652253, "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": 0.9777936796581725, "relative_difference": 0.41096766285652253, "within_tolerance": false, "direction_agrees": false, "source_cell": "1.66 (0.005926)", "note": null }, { "contrast_group": "TNBC", "published_ratio": 1.44, "observed_ratio": 0.9761435078632721, "relative_difference": 0.3221225639838388, "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": 1.7080490849032697, "relative_difference": 0.028945231869439612, "within_tolerance": true, "direction_agrees": true, "source_cell": "1.66 (0.005926)", "note": null }, { "contrast_group": "TNBC", "published_ratio": 1.44, "observed_ratio": 1.6213052211648489, "relative_difference": 0.12590640358670066, "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 39.6% 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": 0.3960694339400312, "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": 0.22517120117403724, "relative_difference": 0.37402406073617656, "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": 0.23349878062991802, "relative_difference": 0.3298584995921352, "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": 0.917042045305098, "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": 0.02906472925432372, "relative_difference": 0.91920005267298, "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": 0.031254484053818386, "relative_difference": 0.9102996307655413, "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": 0.22517120117403724, "relative_difference": 0.37402406073617656, "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": 0.23349878062991802, "relative_difference": 0.3298584995921352, "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": 0.035819840523192426, "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": 0.995745015522144, "relative_difference": 0.03557481614302986, "within_tolerance": true, "direction_agrees": true, "source_cell": "-1.04 (0.768041)", "note": null }, { "contrast_group": "TNBC", "published_ratio": 0.9615384615384615, "observed_ratio": 0.9940194464713875, "relative_difference": 0.03378022433024311, "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": 0.995745015522144, "relative_difference": 0.03557481614302986, "within_tolerance": true, "direction_agrees": true, "source_cell": "-1.04 (0.768041)", "note": null }, { "contrast_group": "TNBC", "published_ratio": 0.9615384615384615, "observed_ratio": 0.9940194464713875, "relative_difference": 0.03378022433024311, "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 39.6% from the published values on average." } ] }, "probe_stats": [ { "feature": "203295_s_at", "symbol": "ATP1A2", "p_value": 3.08987381003e-16, "q_value": 2.7220862200414147e-15, "log2_fold_change": { "TNBC": -2.0985130789299995, "Her2": -2.15090577271, "Luminal A": -2.1557998152999995, "Luminal B": -2.16779527859 }, "fold_change": { "TNBC": 0.23349878062991802, "Her2": 0.22517120117403724, "Luminal A": 0.22440864888078413, "Luminal B": 0.22255051145041047 } }, { "feature": "203296_s_at", "symbol": "ATP1A2", "p_value": 1.21739348978e-37, "q_value": 3.657063421249557e-35, "log2_fold_change": { "TNBC": -4.999793002940001, "Her2": -5.10458672023, "Luminal A": -4.787550438, "Luminal B": -5.145934605580001 }, "fold_change": { "TNBC": 0.031254484053818386, "Her2": 0.02906472925432372, "Luminal A": 0.036207931284621436, "Luminal B": 0.028243552904532433 } }, { "feature": "214432_at", "symbol": "LOC101927137///ATP1A3", "p_value": 0.00298548225137, "q_value": 0.004211504273528705, "log2_fold_change": { "TNBC": -0.008654018700000154, "Her2": -0.006151742090000134, "Luminal A": -0.018334374230000172, "Luminal B": -0.01202323764000024 }, "fold_change": { "TNBC": 0.9940194464713875, "Her2": 0.995745015522144, "Luminal A": 0.9873719911695374, "Luminal B": 0.9917007571817732 } }, { "feature": "220948_s_at", "symbol": "ATP1A1", "p_value": 0.00255323706094, "q_value": 0.003631360522170927, "log2_fold_change": { "TNBC": 0.6971557130699999, "Her2": 0.7723494348699997, "Luminal A": 0.562951256969999, "Luminal B": 0.44965726877000023 }, "fold_change": { "TNBC": 1.6213052211648489, "Her2": 1.7080490849032697, "Luminal A": 1.4772881509433262, "Luminal B": 1.365715774423173 } }, { "feature": "244606_at", "symbol": "ATP1A1", "p_value": 2.37894763535e-6, "q_value": 5.030329674639949e-6, "log2_fold_change": { "TNBC": -0.03483483350999972, "Her2": -0.03239801492000005, "Luminal A": -0.04748830676000004, "Luminal B": -0.038398123599999945 }, "fold_change": { "TNBC": 0.9761435078632721, "Her2": 0.9777936796581725, "Luminal A": 0.9676194627982302, "Luminal B": 0.9737355211122102 } } ], "provenance": { "execution_id": "2d090760-f2ae-423e-849f-dc58da829431", "operation": "group_comparison_anova", "operation_version": "0.1.0", "parameters": { "reference_group": "Healthy", "contrast_groups": [ "TNBC", "Her2", "Luminal A", "Luminal B" ], "alpha": 0.05, "fold_change_threshold": 1.5, "multiple_testing": "benjamini_hochberg" }, "target": { "authority": "Corpus Engine", "record_id": "pmid:28529692", "content_hash": "sha256:116bf117cc3112c78abf15a5c35878e88e5fab508f979460005284568439dbe5", "document_sha256": "0c8dece4a24a9764724f10dd654d240fe1e33dc9058ffa47724ceb5e64e53b97", "sci_version": "1.5", "revision": 6, "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_at": "2026-11-03T15:44:29+00:00" }, "dataset": { "asset_id": "geo:GSE65194", "sha256": "f92d2109fe0d64ed056d9673e8733b2af25173230f3632e370201b6a4054caba", "group_characteristic": "sample_group", "sample_selection": { "rule": { "mode": "average_technical_replicates", "pattern": "/_rep[A-Z0-9]+$/", "combination": "mean of the member arrays" }, "arrays_in_repository": 178, "samples_after_rule": 155, "arrays_merged": 23, "groups_before": { "CellLine": 14, "Healthy": 11, "Her2": 39, "Luminal A": 29, "Luminal B": 30, "TNBC": 55 }, "groups_after": { "CellLine": 14, "Healthy": 11, "Her2": 30, "Luminal A": 29, "Luminal B": 30, "TNBC": 41 }, "titles_matching_pattern": 46, "reconciliation": { "rule": { "mode": "average_technical_replicates", "pattern": "/_rep[A-Z0-9]+$/", "combination": "mean of the member arrays" }, "mode": "average_technical_replicates", "paper_group_sizes": { "Her2": 30, "Luminal A": 29, "Luminal B": 30, "TNBC": 41, "Healthy": 11 }, "observed_group_sizes": { "CellLine": 14, "Healthy": 11, "Her2": 30, "Luminal A": 29, "Luminal B": 30, "TNBC": 41 }, "arrays_in_repository": 178, "arrays_merged": 23, "observed_unit": "experimental units", "differences": [], "verdict": "confirmed", "detail": "The rule turns the repository's arrays into the cohort the paper states." } }, "value_scale": { "scale": "log2", "state": "resolved", "origin": "declared", "basis": "caller", "statement": null, "evidence": { "declared_scale": "log2" }, "reason": "The caller declared the scale of the values." }, "platform": null }, "recorded_at": "2026-11-03T15:44:30+00:00" } }, "operation": "group_comparison_anova" } } ] }