--- license: mit language: - en tags: - genomics - yeast - transcription - binding pretty_name: "Harbison, 2004 ChIP-chip" size_categories: - 1M- 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 # Harbison et al 2004: grown at 30°C (from HEAT condition context) temperature_celsius: 30 growth_phase_at_harvest: # Harbison et al 2004: OD600 ~0.8 od600: 0.8 media: # Harbison et al 2004: 1% yeast extract / 2% peptone / 2% glucose 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 growth_phase_at_harvest: # Harbison et al 2004: OD600 ~0.6 od600: 0.6 media: # Harbison et al 2004: synthetic complete medium name: synthetic_complete chemical_treatment: compound: sulfometuron_methyl # Harbison et al 2004: 0.2 mg/ml concentration_percent: 0.02 duration_hours: 2 RAPA: description: Nutrient deprivation via TOR inhibition temperature_celsius: 30 growth_phase_at_harvest: # Harbison et al 2004: OD600 ~0.8 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 # Harbison et al 2004: 100 nM concentration_percent: 9.142e-6 duration_minutes: 20 H2O2Hi: description: High oxidative stress condition temperature_celsius: 30 growth_phase_at_harvest: # Harbison et al 2004: OD600 ~0.5 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 # Harbison et al 2004: 4 mM concentration_percent: 0.0136 duration_minutes: 30 H2O2Lo: description: Moderate oxidative stress condition temperature_celsius: 30 growth_phase_at_harvest: # Harbison et al 2004: OD600 ~0.5 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 # Harbison et al 2004: 0.4 mM concentration_percent: 0.00136 duration_minutes: 20 Acid: description: Acidic pH stress condition temperature_celsius: 30 growth_phase_at_harvest: # Harbison et al 2004: OD600 ~0.5 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 # Harbison et al 2004: 0.05 M to reach pH 4.0 concentration_percent: 0.59 target_pH: 4.0 duration_minutes: 30 Alpha: description: Mating pheromone induction condition temperature_celsius: 30 growth_phase_at_harvest: # Harbison et al 2004: OD600 ~0.8 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 # Harbison et al 2004: 5 mg/ml concentration_percent: 0.5 duration_minutes: 30 BUT14: description: Long-term filamentation induction with butanol temperature_celsius: 30 growth_phase_at_harvest: # Harbison et al 2004: OD600 ~0.8 od600: 0.8 media: # Harbison et al 2004: YPD containing 1% butanol 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 growth_phase_at_harvest: # Harbison et al 2004: OD600 ~0.8 od600: 0.8 media: # Harbison et al 2004: YPD containing 1% butanol 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 growth_phase_at_harvest: # Harbison et al 2004: OD600 ~0.8 od600: 0.8 media: # Harbison et al 2004: synthetic complete medium lacking thiamin name: synthetic_complete_minus_thiamine GAL: description: Galactose-based growth medium condition temperature_celsius: 30 growth_phase_at_harvest: # Harbison et al 2004: OD600 ~0.8 od600: 0.8 media: # Harbison et al 2004: YEP medium supplemented with galactose (2%) name: yeast_extract_peptone carbon_source: - compound: D-galactose concentration_percent: 2 nitrogen_source: - compound: yeast_extract - compound: peptone HEAT: description: Heat shock stress condition # Harbison et al 2004: grown at 30°C, shifted to 37°C for 45 min initial_temperature_celsius: 30 temperature_shift_celsius: 37 temperature_shift_duration_minutes: 45 growth_phase_at_harvest: # Harbison et al 2004: OD600 ~0.5 od600: 0.5 media: # Harbison et al 2004: YPD 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 growth_phase_at_harvest: # Harbison et al 2004: OD600 ~0.8 od600: 0.8 media: # Harbison et al 2004: synthetic complete medium lacking phosphate name: synthetic_complete_minus_phosphate RAFF: description: Raffinose-based growth medium condition temperature_celsius: 30 growth_phase_at_harvest: # Harbison et al 2004: OD600 ~0.8 od600: 0.8 media: # Harbison et al 2004: YEP medium supplemented with raffinose (2%) name: yeast_extract_peptone carbon_source: - compound: D-raffinose concentration_percent: 2 nitrogen_source: - compound: yeast_extract - compound: peptone - 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 at [their website](http://younglab.wi.mit.edu/regulatory_code/GWLD.html). To cite this data, please use: [Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, et al. 2004. Transcriptional regulatory code of a eukaryotic genome. Nature 431: 99–104.doi:10.1038/nature02800](https://www.nature.com/articles/nature02800) This repo provides 1 dataset: - **harbison_2004**: ChIP-chip transcription factor binding data with environmental conditions. ### `tfbpapi` After [installing tfbpapi](https://github.com/BrentLab/tfbpapi/?tab=readme-ov-file#installation), you can adapt this [tutorial](https://brentlab.github.io/tfbpapi/tutorials/hfqueryapi_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. ```python 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](https://huggingface.co/docs/hub/en/security-tokens). 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: ```python 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}")