README.md

metadata

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).

The data is made available by the author and on NCBI with accession 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

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

{'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).

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