metadata
license: mit
language:
- en
tags:
- genomics
- yeast
- transcription
- binding
pretty_name: Harbison, 2004 ChIP-chip
size_categories:
- 1M<n<10M
strain_information:
background: W303
base_strain: Z1256
configs:
- config_name: harbison_2004
description: ChIP-chip transcription factor binding data with environmental conditions
dataset_type: annotated_features
default: true
metadata_fields:
- regulator_locus_tag
- regulator_symbol
- condition
data_files:
- split: train
path: harbison_2004.parquet
dataset_info:
features:
- name: condition
dtype:
class_label:
names:
- YPD
- SM
- RAPA
- H2O2Hi
- H2O2Lo
- Acid
- Alpha
- BUT14
- BUT90
- Thi-
- GAL
- HEAT
- Pi-
- RAFF
description: >-
Environmental condition of the experiment. Nearly all of the 204
regulators have a YPD condition, and some have others in addition.
role: experimental_condition
definitions:
YPD:
description: Rich media baseline condition
temperature_celsius: 30
cultivation_method: unspecified
growth_phase_at_harvest:
od600: 0.8
media:
name: YPD
carbon_source:
- compound: D-glucose
concentration_percent: 2
nitrogen_source:
- compound: yeast_extract
concentration_percent: 1
- compound: peptone
concentration_percent: 2
SM:
description: Amino acid starvation stress condition
temperature_celsius: 30
cultivation_method: unspecified
growth_phase_at_harvest:
od600: 0.6
media:
name: synthetic_complete
carbon_source: unspecified
nitrogen_source: unspecified
chemical_treatment:
compound: sulfometuron_methyl
concentration_percent: 0.02
duration_hours: 2
RAPA:
description: Nutrient deprivation via TOR inhibition
temperature_celsius: 30
cultivation_method: unspecified
growth_phase_at_harvest:
od600: 0.8
media:
name: YPD
carbon_source:
- compound: D-glucose
concentration_percent: 2
nitrogen_source:
- compound: yeast_extract
concentration_percent: 1
- compound: peptone
concentration_percent: 2
chemical_treatment:
compound: rapamycin
concentration_percent: 0.000009142
duration_minutes: 20
H2O2Hi:
description: High oxidative stress condition
temperature_celsius: 30
cultivation_method: unspecified
growth_phase_at_harvest:
od600: 0.5
media:
name: YPD
carbon_source:
- compound: D-glucose
concentration_percent: 2
nitrogen_source:
- compound: yeast_extract
concentration_percent: 1
- compound: peptone
concentration_percent: 2
chemical_treatment:
compound: hydrogen_peroxide
concentration_percent: 0.0136
duration_minutes: 30
H2O2Lo:
description: Moderate oxidative stress condition
temperature_celsius: 30
cultivation_method: unspecified
growth_phase_at_harvest:
od600: 0.5
media:
name: YPD
carbon_source:
- compound: D-glucose
concentration_percent: 2
nitrogen_source:
- compound: yeast_extract
concentration_percent: 1
- compound: peptone
concentration_percent: 2
chemical_treatment:
compound: hydrogen_peroxide
concentration_percent: 0.00136
duration_minutes: 20
Acid:
description: Acidic pH stress condition
temperature_celsius: 30
cultivation_method: unspecified
growth_phase_at_harvest:
od600: 0.5
media:
name: YPD
carbon_source:
- compound: D-glucose
concentration_percent: 2
nitrogen_source:
- compound: yeast_extract
concentration_percent: 1
- compound: peptone
concentration_percent: 2
chemical_treatment:
compound: succinic_acid
concentration_percent: 0.59
target_pH: 4
duration_minutes: 30
Alpha:
description: Mating pheromone induction condition
temperature_celsius: 30
cultivation_method: unspecified
growth_phase_at_harvest:
od600: 0.8
media:
name: YPD
carbon_source:
- compound: D-glucose
concentration_percent: 2
nitrogen_source:
- compound: yeast_extract
concentration_percent: 1
- compound: peptone
concentration_percent: 2
chemical_treatment:
compound: alpha_factor_pheromone
concentration_percent: 0.5
duration_minutes: 30
BUT14:
description: Long-term filamentation induction with butanol
temperature_celsius: 30
cultivation_method: unspecified
growth_phase_at_harvest:
od600: 0.8
media:
name: YPD
carbon_source:
- compound: D-glucose
concentration_percent: 2
nitrogen_source:
- compound: yeast_extract
concentration_percent: 1
- compound: peptone
concentration_percent: 2
additives:
- compound: butanol
concentration_percent: 1
incubation_duration_hours: 14
BUT90:
description: Short-term filamentation induction with butanol
temperature_celsius: 30
cultivation_method: unspecified
growth_phase_at_harvest:
od600: 0.8
media:
name: YPD
carbon_source:
- compound: D-glucose
concentration_percent: 2
nitrogen_source:
- compound: yeast_extract
concentration_percent: 1
- compound: peptone
concentration_percent: 2
additives:
- compound: butanol
concentration_percent: 1
incubation_duration_minutes: 90
Thi-:
description: Vitamin B1 deprivation stress condition
temperature_celsius: 30
cultivation_method: unspecified
growth_phase_at_harvest:
od600: 0.8
media:
name: synthetic_complete_minus_thiamine
carbon_source: unspecified
nitrogen_source: unspecified
GAL:
description: Galactose-based growth medium condition
temperature_celsius: 30
cultivation_method: unspecified
growth_phase_at_harvest:
od600: 0.8
media:
name: yeast_extract_peptone
carbon_source:
- compound: D-galactose
concentration_percent: 2
nitrogen_source:
- compound: yeast_extract
concentration_percent: unspecified
- compound: peptone
concentration_percent: unspecified
HEAT:
description: Heat shock stress condition
initial_temperature_celsius: 30
temperature_shift_celsius: 37
temperature_shift_duration_minutes: 45
cultivation_method: unspecified
growth_phase_at_harvest:
od600: 0.5
media:
name: YPD
carbon_source:
- compound: D-glucose
concentration_percent: 2
nitrogen_source:
- compound: yeast_extract
concentration_percent: 1
- compound: peptone
concentration_percent: 2
Pi-:
description: Phosphate deprivation stress condition
temperature_celsius: 30
cultivation_method: unspecified
growth_phase_at_harvest:
od600: 0.8
media:
name: synthetic_complete_minus_phosphate
carbon_source: unspecified
nitrogen_source: unspecified
RAFF:
description: Raffinose-based growth medium condition
temperature_celsius: 30
cultivation_method: unspecified
growth_phase_at_harvest:
od600: 0.8
media:
name: yeast_extract_peptone
carbon_source:
- compound: D-raffinose
concentration_percent: 2
nitrogen_source:
- compound: yeast_extract
concentration_percent: unspecified
- compound: peptone
concentration_percent: unspecified
- name: regulator_locus_tag
dtype: string
description: >-
Systematic gene name (ORF identifier) of the ChIPd transcription
factor
role: regulator_identifier
- name: regulator_symbol
dtype: string
description: Standard gene symbol of the ChIPd transcription factor
role: regulator_identifier
- name: target_locus_tag
dtype: string
description: Systematic gene name (ORF identifier) of the target gene measured
role: target_identifier
- name: target_symbol
dtype: string
description: Standard gene symbol of the target gene measured
role: target_identifier
- name: effect
dtype: float64
description: The chip channel ratio (effect size)
role: quantitative_measure
- name: pvalue
dtype: float64
description: pvalue of the chip channel ratio (effect)
role: quantitative_measure
Harbison 2004
This Dataset is a parsed version of the data provided by Richard A. Young's lab. To cite this data, please use:
This repo provides 1 dataset:
- harbison_2004: ChIP-chip transcription factor binding data with environmental conditions.
tfbpapi
After installing tfbpapi, you can adapt this tutorial in order to explore the contents of this repository.
huggingface_cli/duckdb
You can retrieves and displays the file paths for each configuration of the "BrentLab/harbison_2004" dataset from Hugging Face Hub.
from huggingface_hub import ModelCard
from pprint import pprint
card = ModelCard.load("BrentLab/harbison_2004", 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)
If you wish to pull the entire repo, due to its size you may need to use an authentication token. If you do not have one, try omitting the token related code below and see if it works. Else, create a token and provide it like so:
from huggingface_hub import snapshot_download
import os
repo_id = "BrentLab/harbison_2004"
hf_token = os.getenv("HF_TOKEN")
# Download entire repo to local directory
repo_path = snapshot_download(
repo_id=repo_id,
repo_type="dataset",
token=hf_token
)
print(f"\n✓ Repository downloaded to: {repo_path}")
# Construct path to the rossi_annotated_features parquet file
parquet_path = os.path.join(repo_path, "harbison_2004.parquet")
print(f"✓ Parquet file at: {parquet_path}")