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2.5763477788, "fold_change": {"Her2": 0.8839136066660013, "TNBC": 0.7371032520237105, "Luminal A": 0.7385218789889358, "Luminal B": 0.6189444119937498}, "log2_fold_change": {"Her2": -0.1780227267699992, "TNBC": -0.4400613714299997, "Luminal A": -0.4372874328799998, "Luminal B": -0.6921182494899991}, "max_abs_log2_fold_change": 0.6921182494899991}, {"symbol": "ATP6V0A4", "feature": "220197_at", "p_value": 0.0403449629908, "q_value": 0.04934410455004269, "f_statistic": 2.57607340127, "fold_change": {"Her2": 2.2063804966260676, "TNBC": 1.7203506246233284, "Luminal A": 1.090789681790972, "Luminal B": 2.042258994963885}, "log2_fold_change": {"Her2": 1.14168160927, "TNBC": 0.7827026305400002, "Luminal A": 0.1253729584100003, "Luminal B": 1.0301658373500002}, "max_abs_log2_fold_change": 1.14168160927}, {"symbol": "NUP62CL", "feature": "220520_s_at", "p_value": 0.0404818542326, "q_value": 0.049500456621464926, "f_statistic": 2.57390285301, "fold_change": {"Her2": 0.485220863040319, "TNBC": 0.6368546540649738, "Luminal A": 0.6506852444831088, "Luminal B": 0.5008588181768322}, "log2_fold_change": {"Her2": -1.04328651154, "TNBC": -0.6509639434199999, "Luminal A": -0.61996825662, "Luminal B": -0.9975241002899996}, "max_abs_log2_fold_change": 1.04328651154}, {"symbol": "SMARCE1", "feature": "211988_at", "p_value": 0.0404884923351, "q_value": 0.04950746631710961, "f_statistic": 2.5737977817, "fold_change": {"Her2": 1.2435711815985666, "TNBC": 1.1534924696506317, "Luminal A": 1.5044521093068444, "Luminal B": 1.564421766950297}, "log2_fold_change": {"Her2": 0.3144890893000003, "TNBC": 0.2060085857000011, "Luminal A": 0.5892381826000008, "Luminal B": 0.6456295146000013}, "max_abs_log2_fold_change": 0.6456295146000013}, {"symbol": "ST13", "feature": "208666_s_at", "p_value": 0.0405203066136, "q_value": 0.0495419353598263, "f_statistic": 2.57329444255, "fold_change": {"Her2": 1.5700465332827287, "TNBC": 1.4767689372859714, "Luminal A": 1.4155591773723808, "Luminal B": 1.43934611904867}, "log2_fold_change": {"Her2": 0.650807318570001, "TNBC": 0.5624441124199997, "Luminal A": 0.5013720622900006, "Luminal B": 0.5254135581600003}, "max_abs_log2_fold_change": 0.650807318570001}, {"symbol": "AQP3", "feature": "39248_at", "p_value": 0.0405325962498, "q_value": 0.049554744845933835, "f_statistic": 2.57310010954, "fold_change": {"Her2": 2.1849983767069614, "TNBC": 0.8548775419997124, "Luminal A": 0.7650300552684097, "Luminal B": 0.8114961982441182}, "log2_fold_change": {"Her2": 1.1276322079099987, "TNBC": -0.22621032073999991, "Luminal A": -0.38641166769, "Luminal B": -0.3013437589399999}, "max_abs_log2_fold_change": 1.1276322079099987}, {"symbol": "IGK///IGKC", "feature": "211644_x_at", "p_value": 0.040563433571, "q_value": 0.04959022838548519, "f_statistic": 2.57261273998, "fold_change": {"Her2": 5.309621391642399, "TNBC": 5.445184933019599, "Luminal A": 3.0296880611894212, "Luminal B": 2.2806827057998516}, "log2_fold_change": {"Her2": 2.4086089917500004, "TNBC": 2.44498104755, "Luminal A": 1.599169260450001, "Luminal B": 1.18946574932}, "max_abs_log2_fold_change": 2.44498104755}, {"symbol": null, "feature": "243271_at", "p_value": 0.0406069401128, "q_value": 0.04963675714416604, "f_statistic": 2.57192575484, "fold_change": {"Her2": 0.9348074224244048, "TNBC": 1.5877040235766344, "Luminal A": 0.8170016910884964, "Luminal B": 1.0746430273857388}, "log2_fold_change": {"Her2": -0.0972589056400004, "TNBC": 0.6669419933900009, "Luminal A": -0.29158903031999905, "Luminal B": 0.10385750804999994}, "max_abs_log2_fold_change": 0.6669419933900009}, {"symbol": "PPM1E", "feature": "236302_at", "p_value": 0.0407287356101, "q_value": 0.04977228284072056, "f_statistic": 2.5700063761, "fold_change": {"Her2": 0.955222769501533, "TNBC": 1.2890473393094355, "Luminal A": 0.9833181979754786, "Luminal B": 1.6852899189586776}, "log2_fold_change": {"Her2": -0.0660908685699999, "TNBC": 0.3663052465800005, "Luminal A": -0.02426975221999994, "Luminal B": 0.7529967983299999}, "max_abs_log2_fold_change": 0.7529967983299999}, {"symbol": null, "feature": "230818_at", "p_value": 0.0407716618993, "q_value": 0.049821399826123755, "f_statistic": 2.56933123629, "fold_change": {"Her2": 0.6218551823598597, "TNBC": 0.8159227426435182, "Luminal A": 0.6837020846641032, "Luminal B": 0.9106390435065368}, "log2_fold_change": {"Her2": -0.6853494502499999, "TNBC": -0.29349554082999996, "Luminal A": -0.5485602706599999, "Luminal B": -0.1350487788799999}, "max_abs_log2_fold_change": 0.6853494502499999}, {"symbol": "UBALD1", "feature": "225874_at", "p_value": 0.0407847882603, "q_value": 0.04983632587344126, "f_statistic": 2.56912492508, "fold_change": {"Her2": 1.1949728286174324, "TNBC": 1.1025528755119285, "Luminal A": 1.0854515511581933, "Luminal B": 1.5417939695966705}, "log2_fold_change": {"Her2": 0.2569778144700008, "TNBC": 0.1408478452700006, "Luminal A": 0.11829533308000072, "Luminal B": 0.6246099903500006}, "max_abs_log2_fold_change": 0.6246099903500006}, {"symbol": "CAPN9", "feature": "210641_at", "p_value": 0.0407910593697, "q_value": 0.04984287477470964, "f_statistic": 2.56902638295, "fold_change": {"Her2": 1.390155584320642, "TNBC": 1.0121667220376231, "Luminal A": 0.9855799470756248, "Luminal B": 1.5120658622313117}, "log2_fold_change": {"Her2": 0.47524635645000024, "TNBC": 0.017446947390000078, "Luminal A": -0.020955192089999963, "Luminal B": 0.5965209815200001}, "max_abs_log2_fold_change": 0.5965209815200001}, {"symbol": "LOC102723721", "feature": "235921_at", "p_value": 0.0408531048585, "q_value": 0.04991645738007353, "f_statistic": 2.56805221796, "fold_change": {"Her2": 1.1615811142888006, "TNBC": 1.6576840382385252, "Luminal A": 0.9753515223962008, "Luminal B": 0.9763957352499338}, "log2_fold_change": {"Her2": 0.2160899023999998, "TNBC": 0.7291690491100002, "Luminal A": -0.036005826569999844, "Luminal B": -0.03446210122999993}, "max_abs_log2_fold_change": 0.7291690491100002}, {"symbol": "SSR1", "feature": "225435_at", "p_value": 0.0409165715869, "q_value": 0.04998841854641424, "f_statistic": 2.56705723327, "fold_change": {"Her2": 1.6446918734531322, "TNBC": 1.158325100163193, "Luminal A": 1.4577913133835718, "Luminal B": 1.5666853042358593}, "log2_fold_change": {"Her2": 0.7178173260399987, "TNBC": 0.21204022272999976, "Luminal A": 0.5437842089, "Luminal B": 0.6477154187299998}, "max_abs_log2_fold_change": 0.7178173260399987}], "sample_count": 141, "feature_count": 54673, "analysis_scope": {"detail": "The comparison used 141 samples in 5 groups, out of 155 samples in 6 groups. Not part of the comparison: CellLine.", "groups_present": ["TNBC", "Her2", "Luminal A", "Luminal B", "CellLine", "Healthy"], "groups_compared": ["TNBC", "Her2", "Luminal A", "Luminal B", "Healthy"], "samples_present": 155, "samples_compared": 141, "groups_not_compared": ["CellLine"], "samples_not_compared": 14}, "method_inference": {"gaps": [{"kind": "no_candidate_within_tolerance", "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.", "symbol": "ATP1A2"}], "genes": [{"state": "resolved", "reason": "Probe 220948_s_at reproduces the published value in every group (4 of 4), and no other candidate does.", "symbol": "ATP1A1", "evidence": [{"note": null, "source_cell": "1.53 (0.009016)", "contrast_group": "Luminal A", "observed_ratio": 1.4772881509433262, "published_ratio": 1.53, "direction_agrees": true, "within_tolerance": true, "relative_difference": 0.03445218892593059}, {"note": null, "source_cell": "1.38 (0.04454)", "contrast_group": "Luminal B", "observed_ratio": 1.365715774423173, "published_ratio": 1.38, "direction_agrees": true, "within_tolerance": true, "relative_difference": 0.01035088809914997}, {"note": null, "source_cell": "1.66 (0.005926)", "contrast_group": "Her2", "observed_ratio": 1.7080490849032697, "published_ratio": 1.66, "direction_agrees": true, "within_tolerance": true, "relative_difference": 0.028945231869439612}, {"note": null, "source_cell": "1.44 (0.015725)", "contrast_group": "TNBC", "observed_ratio": 1.6213052211648489, "published_ratio": 1.44, "direction_agrees": true, "within_tolerance": true, "relative_difference": 0.12590640358670066}], "candidates": [{"symbol": "ATP1A1", "feature": "220948_s_at", "evidence": [{"note": null, "source_cell": "1.53 (0.009016)", "contrast_group": "Luminal A", "observed_ratio": 1.4772881509433262, "published_ratio": 1.53, "direction_agrees": true, "within_tolerance": true, "relative_difference": 0.03445218892593059}, {"note": null, "source_cell": "1.38 (0.04454)", "contrast_group": "Luminal B", "observed_ratio": 1.365715774423173, "published_ratio": 1.38, "direction_agrees": true, "within_tolerance": true, "relative_difference": 0.01035088809914997}, {"note": null, "source_cell": "1.66 (0.005926)", "contrast_group": "Her2", "observed_ratio": 1.7080490849032697, "published_ratio": 1.66, "direction_agrees": true, "within_tolerance": true, "relative_difference": 0.028945231869439612}, {"note": null, "source_cell": "1.44 (0.015725)", "contrast_group": "TNBC", "observed_ratio": 1.6213052211648489, "published_ratio": 1.44, "direction_agrees": true, "within_tolerance": true, "relative_difference": 0.12590640358670066}], "probe_class": "sequence_tagged", "groups_tested": 4, "groups_direction_agrees": 4, "groups_within_tolerance": 4, "max_relative_difference": 0.12590640358670066, "mean_relative_difference": 0.049913678120305206}, {"symbol": "ATP1A1", "feature": "244606_at", "evidence": [{"note": null, "source_cell": "1.53 (0.009016)", "contrast_group": "Luminal A", "observed_ratio": 0.9676194627982302, "published_ratio": 1.53, "direction_agrees": false, "within_tolerance": false, "relative_difference": 0.3675689785632482}, {"note": null, "source_cell": "1.38 (0.04454)", "contrast_group": "Luminal B", "observed_ratio": 0.9737355211122102, "published_ratio": 1.38, "direction_agrees": false, "within_tolerance": false, "relative_difference": 0.29439454991868824}, {"note": null, "source_cell": "1.66 (0.005926)", "contrast_group": "Her2", "observed_ratio": 0.9777936796581724, "published_ratio": 1.66, "direction_agrees": false, "within_tolerance": false, "relative_difference": 0.4109676628565226}, {"note": null, "source_cell": "1.44 (0.015725)", "contrast_group": "TNBC", "observed_ratio": 0.976143507863272, "published_ratio": 1.44, "direction_agrees": false, "within_tolerance": false, "relative_difference": 0.3221225639838388}], "probe_class": "legacy_clone", "groups_tested": 4, "groups_direction_agrees": 0, "groups_within_tolerance": 0, "max_relative_difference": 0.4109676628565226, "mean_relative_difference": 0.3487634388305744}], "probe_class": "sequence_tagged", "closest_feature": "220948_s_at", "selected_feature": "220948_s_at"}, {"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.", "symbol": "ATP1A2", "evidence": [{"note": null, "source_cell": "-2.49 (1.85·10 -07)", "contrast_group": "Luminal A", "observed_ratio": 0.22440864888078413, "published_ratio": 0.4016064257028112, "direction_agrees": true, "within_tolerance": false, "relative_difference": 0.4412224642868474}, {"note": null, "source_cell": "-2.52 (8.50·10 -09)", "contrast_group": "Luminal B", "observed_ratio": 0.2225505114504105, "published_ratio": 0.3968253968253968, "direction_agrees": true, "within_tolerance": false, "relative_difference": 0.4391727111449656}, {"note": null, "source_cell": "-2.78 (5.48·10 -08)", "contrast_group": "Her2", "observed_ratio": 0.22517120117403724, "published_ratio": 0.3597122302158274, "direction_agrees": true, "within_tolerance": false, "relative_difference": 0.37402406073617656}, {"note": null, "source_cell": "-2.87 (2.08·10-11)", "contrast_group": "TNBC", "observed_ratio": 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"within_tolerance": false, "relative_difference": 0.9288262466805782}, {"note": null, "source_cell": "-2.78 (5.48·10 -08)", "contrast_group": "Her2", "observed_ratio": 0.02906472925432372, "published_ratio": 0.3597122302158274, "direction_agrees": true, "within_tolerance": false, "relative_difference": 0.91920005267298}, {"note": null, "source_cell": "-2.87 (2.08·10-11)", "contrast_group": "TNBC", "observed_ratio": 0.031254484053818386, "published_ratio": 0.3484320557491289, "direction_agrees": true, "within_tolerance": false, "relative_difference": 0.9102996307655412}], "probe_class": "sequence_tagged", "groups_tested": 4, "groups_direction_agrees": 4, "groups_within_tolerance": 0, "max_relative_difference": 0.9288262466805782, "mean_relative_difference": 0.917042045305098}], "probe_class": "sequence_tagged", "closest_feature": "203295_s_at", "selected_feature": null}, {"state": "resolved", "reason": "The platform carries one probe for ATP1A3, so the published value is placed without 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"ATP1A2", "target_id": "target-atp1a2-lum-b-p", "paper_group": "Lum B", "table_value": 0.0000000085, "published_value": 0.0000000085}, {"kind": "cell", "unit": "relative expression fold change", "detail": "The machine-readable target and the published table cell state the same value.", "status": "agreed", "symbol": "ATP1A2", "target_id": "target-atp1a2-her2", "paper_group": "Her2", "table_value": -2.78, "published_value": -2.78}, {"kind": "cell", "unit": "ANOVA p-value", "detail": "The machine-readable target and the published table cell state the same value.", "status": "agreed", "symbol": "ATP1A2", "target_id": "target-atp1a2-her2-p", "paper_group": "Her2", "table_value": 0.000000054800000000000014, "published_value": 0.0000000548}, {"kind": "cell", "unit": "relative expression fold change", "detail": "The machine-readable target and the published table cell state the same value.", "status": "agreed", "symbol": "ATP1A2", "target_id": "target-atp1a2-tnbc", "paper_group": "TNBC", "table_value": -2.87, "published_value": -2.87}, {"kind": "cell", "unit": "ANOVA p-value", "detail": "The machine-readable target and the published table cell state the same value.", "status": "agreed", "symbol": "ATP1A2", "target_id": "target-atp1a2-tnbc-p", "paper_group": "TNBC", "table_value": 0.0000000000208, "published_value": 0.0000000000208}, {"kind": "cell", "unit": "relative expression fold change", "detail": "The machine-readable target and the published table cell state the same value.", "status": "agreed", "symbol": "ATP1A3", "target_id": "target-atp1a3-lum-a", "paper_group": "Lum A", "table_value": -1.05, "published_value": -1.05}, {"kind": "cell", "unit": "ANOVA p-value", "detail": "The machine-readable target and the published table cell state the same value.", "status": "agreed", "symbol": "ATP1A3", "target_id": "target-atp1a3-lum-a-p", "paper_group": "Lum A", "table_value": 0.429089, "published_value": 0.429089}, {"kind": "cell", "unit": "relative expression fold 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"symbol": "ATP1A3", "target_id": "target-atp1a3-her2-p", "paper_group": "Her2", "table_value": 0.768041, "published_value": 0.768041}, {"kind": "cell", "unit": "relative expression fold change", "detail": "The machine-readable target and the published table cell state the same value.", "status": "agreed", "symbol": "ATP1A3", "target_id": "target-atp1a3-tnbc", "paper_group": "TNBC", "table_value": -1.04, "published_value": -1.04}, {"kind": "cell", "unit": "ANOVA p-value", "detail": "The machine-readable target and the published table cell state the same value.", "status": "agreed", "symbol": "ATP1A3", "target_id": "target-atp1a3-tnbc-p", "paper_group": "TNBC", "table_value": 0.527878, "published_value": 0.527878}], "equivalence": {"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.", "method": {"steps": [{"id": "method-1", "label": "Microarray preprocessing", "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. 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The paper states no multiplicity procedure, so neither of them is a reproduction of the paper's.", "across_pairs": "holm", "across_features": "benjamini_hochberg"}, "published_multiplicity_procedure": null}, "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.", "fold_change_relative_tolerance": 0.25}}, "differential_count": 22426, "sample_set_fidelity": {"basis": {"arrays_merged": 23, "observed_unit": "experimental units", "paper_group_sizes": {"Her2": 30, "TNBC": 41, "Healthy": 11, "Luminal A": 29, "Luminal B": 30}, "group_name_mapping": {"Her2": "Her2", "TNBC": "TNBC", "Lum A": "Luminal A", "Lum B": "Luminal B"}, "paper_cohort_total": 141, "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.", "arrays_in_repository": 178, "observed_group_sizes": {"Her2": 30, "TNBC": 41, "Healthy": 11, "CellLine": 14, "Luminal A": 29, "Luminal B": 30}, "sample_selection_rule": {"mode": "average_technical_replicates", "pattern": "/_rep[A-Z0-9]+$/", "combination": "mean of the member arrays"}, "repository_group_sizes": {"Her2": 39, "TNBC": 55, "Healthy": 11, "CellLine": 14, "Luminal A": 29, "Luminal B": 30}, "arrays_carrying_the_replicate_marker": 46}, "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", "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."], "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.", "differences": [], "analysis_scope": {"detail": "The comparison used 141 samples in 5 groups, out of 155 samples in 6 groups. Not part of the comparison: CellLine.", "groups_present": ["TNBC", "Her2", "Luminal A", "Luminal B", "CellLine", "Healthy"], "groups_compared": ["TNBC", "Her2", "Luminal A", "Luminal B", "Healthy"], "samples_present": 155, "samples_compared": 141, "groups_not_compared": ["CellLine"], "samples_not_compared": 14}, "expected_group_sizes": {"Her2": 30, "TNBC": 41, "Healthy": 11, "Luminal A": 29, "Luminal B": 30}, "observed_group_sizes": {"Her2": 30, "TNBC": 41, "Healthy": 11, "CellLine": 14, "Luminal A": 29, "Luminal B": 30}, "groups_outside_the_paper_cohort": {"CellLine": 14}}}, "schema": "https://automatedassays.local/schemas/real-data-evidence-bundle/1.0.0", "dataset": {"bytes": 76464351, "groups": ["CellLine", "Healthy", "Her2", "Luminal A", "Luminal B", "TNBC"], "sha256": "f92d2109fe0d64ed056d9673e8733b2af25173230f3632e370201b6a4054caba", "licence": {"state": "public_data", "reason": "The NCBI GEO data-use statement is rendered client-side and could not be retrieved as text, so no verbatim licence statement was read. 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