---
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 Comparative Analysis