File size: 3,660 Bytes
1bf0af7 ac03d06 1bf0af7 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 |
---
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
|