| --- |
| license: mit |
| language: |
| - en |
| tags: |
| - genomics |
| - transcription-factors |
| - yeast |
| - saccharomyces-cerevisiae |
| pretty_name: "Yeast Direct Target Overlap Analysis" |
| size_categories: |
| - 1K<n<10K |
|
|
| features: |
| - applies_to: |
| - dto |
| - dto_rossi_cc_mahendrawada_mindel |
| fields: |
| - name: pr_ranking_column |
| dtype: |
| class_label: ["log2fc", "pvalue"] |
| description: >- |
| Describes which column, effect (log2fc) or pvalue was used |
| in ranking the perturbation response data. see scripts/dto_preparation.R |
| for more info on each dataset |
| - name: binding_rank_threshold |
| dtype: float64 |
| description: >- |
| Rank threshold used for the binding dataset in the DTO analysis. This |
| represents the rank cutoff that maximizes overlap significance between |
| binding and perturbation datasets. |
| role: quantitative_measure |
| - name: perturbation_rank_threshold |
| dtype: float64 |
| description: >- |
| Rank threshold used for the perturbation dataset in the DTO analysis. |
| This represents the rank cutoff that maximizes overlap significance |
| between binding and perturbation datasets. |
| role: quantitative_measure |
| - name: binding_set_size |
| dtype: int64 |
| description: >- |
| Number of targets in the binding dataset at the optimal rank threshold. |
| This is the size of the set used to calculate overlap with the |
| perturbation dataset. |
| role: quantitative_measure |
| - name: perturbation_set_size |
| dtype: int64 |
| description: >- |
| Number of targets in the perturbation dataset at the optimal rank |
| threshold. This is the size of the set used to calculate overlap with |
| the binding dataset. |
| role: quantitative_measure |
| - name: dto_fdr |
| dtype: float64 |
| description: >- |
| False discovery rate (FDR) for the direct target overlap test. Lower |
| values indicate more significant overlap between binding and |
| perturbation target sets. Missing values (NA) indicate insufficient |
| data for DTO analysis. |
| role: quantitative_measure |
| - name: dto_empirical_pvalue |
| dtype: float64 |
| description: >- |
| Empirical p-value from permutation testing for the direct target |
| overlap. This represents the probability of observing the observed |
| overlap by chance. Missing values (NA) indicate insufficient data for |
| DTO analysis. |
| role: quantitative_measure |
|
|
| configs: |
| - config_name: dto |
| description: >- |
| Direct target overlap analysis results comparing transcription factor |
| binding experiments with gene expression perturbation experiments. The |
| dataset is partitioned by binding dataset and perturbation dataset, |
| allowing efficient queries for specific binding-perturbation comparisons. |
| dataset_type: comparative |
| data_files: |
| - split: train |
| path: dto/*/*/*.parquet |
| dataset_info: |
| features: |
| - name: binding_id |
| dtype: string |
| description: >- |
| Composite sample identifier for the binding experiment in format |
| 'repo_id;config_name;sample_id' (e.g., |
| 'BrentLab/callingcards;annotated_features;1') |
| role: source_sample |
| - name: perturbation_id |
| dtype: string |
| description: >- |
| Composite sample identifier for the perturbation experiment in format |
| 'repo_id;config_name;sample_id' (e.g., |
| 'BrentLab/Hackett_2020;hackett_2020;200') |
| role: source_sample |
| partitioning: |
| enabled: true |
| partition_by: ["binding_repo_dataset", "perturbation_repo_dataset"] |
| path_template: "dto/binding_repo_dataset={binding_repo_dataset}/perturbation_repo_dataset={perturbation_repo_dataset}/*.parquet" |
| - config_name: dto_rossi_cc_mahendrawada_mindel |
| description: >- |
| Only the rossi, mahendrawada and cc datasets, which are called over the Barkai |
| Mindel promoter regions. |
| dataset_type: comparative |
| data_files: |
| - split: train |
| path: dto_rossi_cc_mahendrawada_mindel/*/*/*.parquet |
| dataset_info: |
| features: |
| - name: binding_id |
| dtype: string |
| description: >- |
| Composite sample identifier for the binding experiment in format |
| 'repo_id;config_name;sample_id' (e.g., |
| 'BrentLab/callingcards;annotated_features;1') |
| role: source_sample |
| - name: perturbation_id |
| dtype: string |
| description: >- |
| Composite sample identifier for the perturbation experiment in format |
| 'repo_id;config_name;sample_id' (e.g., |
| 'BrentLab/Hackett_2020;hackett_2020;200') |
| role: source_sample |
| partitioning: |
| enabled: true |
| partition_by: ["binding_repo_dataset", "perturbation_repo_dataset"] |
| path_template: "dto_rossi_cc_mahendrawada_mindel/binding_repo_dataset={binding_repo_dataset}/perturbation_repo_dataset={perturbation_repo_dataset}/*.parquet" |
| --- |
| |
| # Yeast Comparative Analysis |
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