BrentLab/hughes_2006

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