Automated Assays Automated Assays

Run

group_comparison_anova 0.1.0

Run against the fork of Abnormal expression of ATP1A1 and ATP1A2 in breast cancer . Run identifier b1a80714-f07f-4e92-8712-5875211bd4a5.

What the run did

54,673 features were tested across 164 samples in 5 groups, and 22,628 of them came out differential.

The comparison used 164 samples in 5 groups, out of 178 samples in 6 groups. Not part of the comparison: CellLine..

The evidence manifest

The cohort the run used

This run was recorded before the platform compared a run against the cohort the paper states, so its sample-set comparison is a superseded record and not a current claim about the paper.

What the paper published, and what the run found

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).

  • ATP1A1 partly reproduced 4 contrasts · 0 reproduced · 0 direction only · 3 partly · 1 contradicted
    Luminal A against Healthy partly reproduced
    244606_at contradicted paper 1.53 , p 0.009016 run 0.967619 , p 1.9e-6 36.8% from the published value , tolerance 25.0%
    220948_s_at reproduced paper 1.53 , p 0.009016 run 1.477288 , p 0.002024 3.4% from the published value , tolerance 25.0%
    Luminal B against Healthy contradicted
    244606_at contradicted paper 1.38 , p 0.04454 run 0.973736 , p 1.9e-6 29.4% from the published value , tolerance 25.0%
    220948_s_at significance only paper 1.38 , p 0.04454 run 1.365716 , p 0.002024 1.0% from the published value , tolerance 25.0%
    Her2 against Healthy partly reproduced
    244606_at contradicted paper 1.66 , p 0.005926 run 0.977778 , p 1.9e-6 41.1% from the published value , tolerance 25.0%
    220948_s_at reproduced paper 1.66 , p 0.005926 run 1.708785 , p 0.002024 2.9% from the published value , tolerance 25.0%
    TNBC against Healthy partly reproduced
    244606_at contradicted paper 1.44 , p 0.015725 run 0.975762 , p 1.9e-6 32.2% from the published value , tolerance 25.0%
    220948_s_at reproduced paper 1.44 , p 0.015725 run 1.607839 , p 0.002024 11.7% from the published value , tolerance 25.0%

    Luminal A: the observed change is not an increase; the run goes the other way (published ratio 1.5300, run ratio 0.9676); Luminal B: the observed change is not an increase; the run goes the other way (published ratio 1.3800, run ratio 0.9737); the run agrees with the published ratio 1.3800 but reaches a significance the paper did not (published p 0.044540, run p 0.096332 against the same two groups); Her2: the observed change is not an increase; the run goes the other way (published ratio 1.6600, run ratio 0.9778); TNBC: the observed change is not an increase; the run goes the other way (published ratio 1.4400, run ratio 0.9758)

  • ATP1A2 direction only 4 contrasts · 0 reproduced · 4 direction only · 0 partly · 0 contradicted
    Luminal A against Healthy direction only
    203296_s_at direction only paper 0.401606 , p 1.85e-7 run 0.036208 , p 1.71e-44 91.0% from the published value , tolerance 25.0%
    203295_s_at direction only paper 0.401606 , p 1.85e-7 run 0.224409 , p 3.02e-19 44.1% from the published value , tolerance 25.0%
    Luminal B against Healthy direction only
    203296_s_at direction only paper 0.396825 , p 8.5e-9 run 0.028244 , p 1.71e-44 92.9% from the published value , tolerance 25.0%
    203295_s_at direction only paper 0.396825 , p 8.5e-9 run 0.222551 , p 3.02e-19 43.9% from the published value , tolerance 25.0%
    Her2 against Healthy direction only
    203296_s_at direction only paper 0.359712 , p 5.48e-8 run 0.029026 , p 1.71e-44 91.9% from the published value , tolerance 25.0%
    203295_s_at direction only paper 0.359712 , p 5.48e-8 run 0.224655 , p 3.02e-19 37.5% from the published value , tolerance 25.0%
    TNBC against Healthy direction only
    203296_s_at direction only paper 0.348432 , p 2.08e-11 run 0.030499 , p 1.71e-44 91.2% from the published value , tolerance 25.0%
    203295_s_at direction only paper 0.348432 , p 2.08e-11 run 0.230763 , p 3.02e-19 33.8% from the published value , tolerance 25.0%

    Luminal A: the run gets the direction right but its ratio 0.0362 is 91.0% from the published ratio 0.4016, outside the declared tolerance of 25%; the run gets the direction right but its ratio 0.2244 is 44.1% from the published ratio 0.4016, outside the declared tolerance of 25%; Luminal B: the run gets the direction right but its ratio 0.0282 is 92.9% from the published ratio 0.3968, outside the declared tolerance of 25%; the run gets the direction right but its ratio 0.2226 is 43.9% from the published ratio 0.3968, outside the declared tolerance of 25%; Her2: the run gets the direction right but its ratio 0.0290 is 91.9% from the published ratio 0.3597, outside the declared tolerance of 25%; the run gets the direction right but its ratio 0.2247 is 37.5% from the published ratio 0.3597, outside the declared tolerance of 25%; TNBC: the run gets the direction right but its ratio 0.0305 is 91.2% from the published ratio 0.3484, outside the declared tolerance of 25%; the run gets the direction right but its ratio 0.2308 is 33.8% from the published ratio 0.3484, outside the declared tolerance of 25%

  • ATP1A3 reproduced 4 contrasts · 4 reproduced · 0 direction only · 0 partly · 0 contradicted
    Luminal A against Healthy reproduced
    214432_at reproduced paper 0.952381 , p 0.429089 run 0.987372 , p 0.004335 3.7% from the published value , tolerance 25.0%
    Luminal B against Healthy reproduced
    214432_at reproduced paper 1.03 , p 0.308298 run 0.991701 , p 0.004335 3.7% from the published value , tolerance 25.0%
    Her2 against Healthy reproduced
    214432_at reproduced paper 0.961538 , p 0.768041 run 0.995987 , p 0.004335 3.6% from the published value , tolerance 25.0%
    TNBC against Healthy reproduced
    214432_at reproduced paper 0.961538 , p 0.527878 run 0.99376 , p 0.004335 3.4% from the published value , tolerance 25.0%

3 published claims were checked.

Which probe the platform placed each gene on

The paper's method text names the analysis but not the probe set, so the platform infers which probe carries each gene and records the inference here.

  • ATP1A1 · 220948_s_at · sequence_tagged

    Probe 220948_s_at reproduces the published value in every group (4 of 4), and no other candidate does.

  • ATP1A2 · sequence_tagged

    No candidate probe reproduces the published value within the declared tolerance. The closest is 203295_s_at, whose ratios sit 39.8% from the published values on average.

  • ATP1A3 · 214432_at · legacy_clone

    The platform carries one probe for ATP1A3, so the published value is placed without a choice to make.