---
license: mit
language:
- en
tags:
- biology
- genomics
- yeast
- transcription-factors
- gene-expression
- perturbation-screen
- overexpression
- knockout
- microarray
- functional-genomics
pretty_name: "Hughes 2006 Yeast Transcription Factor Perturbation Dataset"
size_categories:
- 100K<n<1M
task_categories:
- other
source_datasets:
- original
configs:
- config_name: metadata
  description: Transcription factor metadata including essentiality and QC status
  default: true
  data_files:
  - split: train
    path: metadata.parquet
  dataset_info:
    features:
      - name: regulator_locus_tag
        dtype: string
        description: Systematic gene name (ORF identifier) of the transcription factor
      - name: regulator_symbol
        dtype: string
        description: Standard gene symbol of the transcription factor
      - name: found_domain
        dtype: string
        description: Identified DNA-binding domain(s) or protein family classification
      - name: sgd_description
        dtype: string
        description: Functional description from Saccharomyces Genome Database (SGD)
      - name: essential
        dtype: bool
        description: Boolean indicating whether the gene is essential for viability
      - name: oe_passed_qc
        dtype: bool
        description: Boolean indicating whether overexpression experiments passed quality control
      - name: del_passed_qc
        dtype: bool
        description: Boolean indicating whether deletion experiments passed quality control

- config_name: overexpression
  description: Overexpression perturbation normalized log2 fold changes
  data_files:
  - split: train  
    path: overexpression.parquet
  dataset_info:
    features:
      - name: regulator_locus_tag
        dtype: string
        description: Systematic gene name (ORF identifier) of the perturbed transcription factor
      - name: regulator_symbol
        dtype: string
        description: Standard gene symbol of the perturbed transcription factor
      - name: target_locus_tag
        dtype: string
        description: Systematic gene name (ORF identifier) of the target gene measured
      - name: target_symbol
        dtype: string
        description: Standard gene symbol of the target gene measured
      - name: dye_plus
        dtype: float64
        description: Normalized log2 fold change for positive (+) dye orientation
      - name: dye_minus
        dtype: float64
        description: Normalized log2 fold change for negative (-) dye orientation
      - name: mean_norm_log2fc
        dtype: float64
        description: Average log2 fold change across dye orientations

- config_name: knockout
  description: Deletion/knockout perturbation normalized log2 fold changes
  data_files:
  - split: train
    path: knockout.parquet
  dataset_info:
    features:
      - name: regulator_locus_tag
        dtype: string
        description: Systematic gene name (ORF identifier) of the perturbed transcription factor
      - name: regulator_symbol
        dtype: string
        description: Standard gene symbol of the perturbed transcription factor
      - name: target_locus_tag
        dtype: string
        description: Systematic gene name (ORF identifier) of the target gene measured
      - name: target_symbol
        dtype: string
        description: Standard gene symbol of the target gene measured
      - name: dye_plus
        dtype: float64
        description: Normalized log2 fold change for positive (+) dye orientation
      - name: dye_minus
        dtype: float64
        description: Normalized log2 fold change for negative (-) dye orientation
      - name: mean_norm_log2fc
        dtype: float64
        description: Average log2 fold change across dye orientations
---
# Hughes 2006

This data is parsed from data presented in

[G. Chua, Q.D. Morris, R. Sopko, M.D. Robinson, O. Ryan, E.T. Chan, B.J. Frey, B.J. Andrews, C. Boone, & T.R. Hughes, Identifying transcription factor functions and targets by phenotypic activation, Proc. Natl. Acad. Sci. U.S.A. 103 (32) 12045-12050, https://doi.org/10.1073/pnas.0605140103 (2006).](https://doi.org/10.1073/pnas.0605140103)

The data is made [available by the author](https://hugheslab.ccbr.utoronto.ca/supplementary-data/yeastTF/) and on
NCBI with accession [GSE5499](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5499).
I used the data provided by the author.    

Details on my parsing can be found in `scripts/`. The gene features are from
BrentLab/yeast_genome_resources

## Data

`overexpression.parquet` and `knockout.parquet` have the same structure

| Field                 | Description                                                                                                                                 |
|-----------------------|---------------------------------------------------------------------------------------------------------------------------------------------|
| `regulator_locus_tag` | Systematic gene name (ORF identifier) of the perturbed transcription factor                                                                 |
| `regulator_symbol`    | Standard gene symbol of the perturbed transcription factor                                                                                  |
| `target_locus_tag`    | Systematic gene name (ORF identifier) of the target gene measured                                                                           |
| `target_symbol`       | Standard gene symbol of the target gene measured                                                                                            |
| `dye_plus`            | Normalized log2 fold change for positive (+) dye orientation                                                                                |
| `dye_minus`           | Normalized log2 fold change for negative (-) dye orientation                                                                                |
| `mean_norm_log2fc`    | Average log2 fold change across dye orientations; 0 when orientations have opposite signs, single value when only one orientation available |

`metadata.parquet` contains transcription factor information

| Field                 | Description                                                                                                             |
|-----------------------|-------------------------------------------------------------------------------------------------------------------------|
| `regulator_locus_tag` | Systematic gene name (ORF identifier) of the transcription factor                                                      |
| `regulator_symbol`    | Standard gene symbol of the transcription factor                                                                       |
| `found_domain`        | Identified DNA-binding domain(s) or protein family classification                                                      |
| `sgd_description`     | Functional description from Saccharomyces Genome Database (SGD)                                                       |
| `essential`           | Boolean indicating whether the gene is essential for viability                                                         |
| `oe_passed_qc`        | Boolean indicating whether overexpression experiments passed quality control                                           |
| `del_passed_qc`       | Boolean indicating whether deletion experiments passed quality control                                                 |


## Usage

There are three parquet files in this repo. This is a way of getting that information programmatically

```python
from huggingface_hub import ModelCard
from pprint import pprint

card = ModelCard.load("BrentLab/hughes_2006", repo_type="dataset")

# cast to dict
card_dict = card.data.to_dict()

# Get partition information
dataset_paths_dict = {d.get("config_name"): d.get("data_files")[0].get("path") for d in card_dict.get("configs")}

pprint(dataset_paths_dict)
```

With the result

```raw
{'knockout': 'knockout.parquet',
 'metadata': 'metadata.parquet',
 'overexpression': 'overexpression.parquet'}
```

I recommend using `huggingface_hub.snapshot_download` to pull the repository. After that, use your favorite
method of interacting with `parquet` files (eg duckDB, but you could use dplyr in R or pandas, too).

```python
from huggingface_hub import snapshot_download
import duckdb
import os

repo_id = "BrentLab/hughes_2006"

# Download entire repo to local directory
repo_path = snapshot_download(
    repo_id=repo_id,
    repo_type="dataset"
)

print(f"Repository downloaded to: {repo_path}")

# Construct path to the knockout parquet file
parquet_path = os.path.join(repo_path, "knockout.parquet")
print(f"Parquet file at: {parquet_path}")

# Connect to DuckDB and query the parquet file
conn = duckdb.connect()

query = """
SELECT * 
FROM read_parquet(?)
WHERE regulator_symbol = 'CST6'
"""

result = conn.execute(query, [parquet_path]).fetchall()
print(f"Found {len(result)} rows for CST6")
```

**Dataset Author and Contact**: Chase Mateusiak [@cmatKhan](https://github.com/cmatkhan/)