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--- |
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license: mit |
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language: |
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- en |
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tags: |
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- genomics |
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- transcription-factors |
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- yeast |
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- saccharomyces-cerevisiae |
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pretty_name: "Yeast Direct Target Overlap Analysis" |
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size_categories: |
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- 1K<n<10K |
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configs: |
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- config_name: dto |
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description: >- |
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Direct target overlap analysis results comparing transcription factor |
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binding experiments with gene expression perturbation experiments. The |
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dataset is partitioned by binding dataset and perturbation dataset, |
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allowing efficient queries for specific binding-perturbation comparisons. |
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dataset_type: comparative |
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data_files: |
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- split: train |
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path: dto/*/*/*.parquet |
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dataset_info: |
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features: |
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- name: binding_id |
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dtype: string |
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description: >- |
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Composite sample identifier for the binding experiment in format |
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'repo_id;config_name;sample_id' (e.g., |
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'BrentLab/callingcards;annotated_features;1') |
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role: source_sample |
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- name: perturbation_id |
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dtype: string |
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description: >- |
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Composite sample identifier for the perturbation experiment in format |
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'repo_id;config_name;sample_id' (e.g., |
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'BrentLab/Hackett_2020;hackett_2020;200') |
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role: source_sample |
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- name: binding_rank_threshold |
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dtype: float64 |
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description: >- |
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Rank threshold used for the binding dataset in the DTO analysis. This |
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represents the rank cutoff that maximizes overlap significance between |
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binding and perturbation datasets. |
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role: quantitative_measure |
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- name: perturbation_rank_threshold |
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dtype: float64 |
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description: >- |
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Rank threshold used for the perturbation dataset in the DTO analysis. |
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This represents the rank cutoff that maximizes overlap significance |
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between binding and perturbation datasets. |
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role: quantitative_measure |
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- name: binding_set_size |
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dtype: int64 |
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description: >- |
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Number of targets in the binding dataset at the optimal rank threshold. |
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This is the size of the set used to calculate overlap with the |
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perturbation dataset. |
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role: quantitative_measure |
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- name: perturbation_set_size |
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dtype: int64 |
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description: >- |
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Number of targets in the perturbation dataset at the optimal rank |
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threshold. This is the size of the set used to calculate overlap with |
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the binding dataset. |
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role: quantitative_measure |
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- name: dto_fdr |
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dtype: float64 |
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description: >- |
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False discovery rate (FDR) for the direct target overlap test. Lower |
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values indicate more significant overlap between binding and |
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perturbation target sets. Missing values (NA) indicate insufficient |
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data for DTO analysis. |
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role: quantitative_measure |
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- name: dto_empirical_pvalue |
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dtype: float64 |
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description: >- |
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Empirical p-value from permutation testing for the direct target |
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overlap. This represents the probability of observing the observed |
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overlap by chance. Missing values (NA) indicate insufficient data for |
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DTO analysis. |
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role: quantitative_measure |
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partitioning: |
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enabled: true |
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partition_by: ["binding_repo_dataset", "perturbation_repo_dataset"] |
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path_template: "dto/binding_repo_dataset={binding_repo_dataset}/perturbation_repo_dataset={perturbation_repo_dataset}/*.parquet" |
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--- |
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# Yeast Comparative Analysis |
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