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README.md

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+---
+license: mit
+language:
+  - en
+tags:
+  - genomics
+  - transcription-factors
+  - yeast
+  - saccharomyces-cerevisiae
+pretty_name: "Yeast Direct Target Overlap Analysis"
+size_categories:
+  - 1K<n<10K
+
+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
+        - 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
+      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"
+---
+
+# Yeast DTO
+